PDB_ID PUBMED_CID STRUCTURE TITLE DEPOSITION DATE RELEASE DATE AUTHORS CITATION TITLE JOURNAL YEAR VOLUME FIRST PAGE LAST PAGE 1WOR 15355973 Crystal Structure of T-protein of the Glycine Cleavage System 2004-08-24 2004-09-07 Lee, H.H.,Kim, D.J.,Ahn, H.J.,Ha, J.Y.,Suh, S.W. Crystal Structure of T-protein of the Glycine Cleavage System: Cofactor binding, insights into H-protein recognition, and molecular basis for understanding nonketotic hyperglycinemia J.Biol.Chem. 2004 279 50514 50523 1WU4 15718242 Crystal structure of reducing-end-xylose releasing exo-oligoxylanase 2004-12-01 2005-02-22 Fushinobu, S.,Hidaka, M.,Honda, Y.,Wakagi, T.,Shoun, H.,Kitaoka, M. Structural Basis for the Specificity of the Reducing End Xylose-releasing Exo-oligoxylanase from Bacillus halodurans C-125 J.Biol.Chem. 2005 280 17180 17186 1WU5 15718242 Crystal structure of reducing-end-xylose releasing exo-oligoxylanase complexed with xylose 2004-12-01 2005-02-22 Fushinobu, S.,Hidaka, M.,Honda, Y.,Wakagi, T.,Shoun, H.,Kitaoka, M. Structural Basis for the Specificity of the Reducing End Xylose-releasing Exo-oligoxylanase from Bacillus halodurans C-125 J.Biol.Chem. 2005 280 17180 17186 1WXR 15728184 Crystal structure of Heme Binding protein, an autotransporter hemoglobine protease from pathogenic Escherichia coli 2005-01-31 2005-03-01 Otto, B.R.,Sijbrandi, R.,Luirink, J.,Oudega, B.,Heddle, J.G.,Mizutani, K.,Park, S.-Y.,Tame, J.R.H. Crystal structure of heme binding protein, an autotransporter hemoglobin protease from pathogenic escherichia coli J.Biol.Chem. 2005 280 17339 17345 1WZU 15937336 Crystal structure of quinolinate synthase (nadA) 2005-03-09 2005-06-07 Sakuraba, H.,Tsuge, H.,Yoneda, K.,Katunuma, N.,Ohshima, T. Crystal Structure of the NAD Biosynthetic Enzyme Quinolinate Synthase J.Biol.Chem. 2005 280 26645 26648 1X3W 15964983 Structure of a peptide:N-glycanase-Rad23 complex 2005-05-11 2005-06-14 Lee, J.H.,Choi, J.M.,Lee, C.,Yi, K.J.,Cho, Y. Structure of a peptide:N-glycanase-Rad23 complex: insight into the deglycosylation for denatured glycoproteins. Proc.Natl.Acad.Sci.Usa 2005 102 9144 9149 1VRQ 15946648 Crystal Structure of Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 in complex with Folinic Acid 2005-04-27 2005-07-05 Ida, K.,Moriguchi, T.,Suzuki, H. Crystal structure of heterotetrameric sarcosine oxidase from Corynebacterium sp. 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Crystal structure of a flavoenzyme TTHA0420 from Thermus thermophilus HB8 To be published 0 0 0 0 2A6R 16109374 Crystal structure of YoeB under PEG condition 2005-07-04 2005-08-23 Kamada, K.,Hanaoka, F. Conformational Change in the Catalytic Site of the Ribonuclease YoeB Toxin by YefM Antitoxin Mol.Cell 2005 19 497 509 2A6S 16109374 Crystal structure of YoeB under isopropanol condition 2005-07-04 2005-08-23 Kamada, K.,Hanaoka, F. Conformational Change in the Catalytic Site of the Ribonuclease YoeB Toxin by YefM Antitoxin Mol.Cell 2005 19 497 509 2AFM 16135565 Crystal structure of human glutaminyl cyclase at pH 6.5 2005-07-26 2005-08-23 Huang, K.F.,Liu, Y.L.,Cheng, W.J.,Ko, T.P.,Wang, A.H. 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Crystal structures of human glutaminyl cyclase, an enzyme responsible for protein N-terminal pyroglutamate formation Proc.Natl.Acad.Sci.Usa 2005 102 13117 13122 2AFW 16135565 Crystal structure of human glutaminyl cyclase in complex with N-acetylhistamine 2005-07-26 2005-08-23 Huang, K.F.,Liu, Y.L.,Cheng, W.J.,Ko, T.P.,Wang, A.H. Crystal structures of human glutaminyl cyclase, an enzyme responsible for protein N-terminal pyroglutamate formation Proc.Natl.Acad.Sci.Usa 2005 102 13117 13122 2AFX 16135565 Crystal structure of human glutaminyl cyclase in complex with 1-benzylimidazole 2005-07-26 2005-08-23 Huang, K.F.,Liu, Y.L.,Cheng, W.J.,Ko, T.P.,Wang, A.H. Crystal structures of human glutaminyl cyclase, an enzyme responsible for protein N-terminal pyroglutamate formation Proc.Natl.Acad.Sci.Usa 2005 102 13117 13122 2AFZ 16135565 Crystal structure of human glutaminyl cyclase in complex with 1-vinylimidazole 2005-07-26 2005-08-23 Huang, K.F.,Liu, Y.L.,Cheng, W.J.,Ko, T.P.,Wang, A.H. Crystal structures of human glutaminyl cyclase, an enzyme responsible for protein N-terminal pyroglutamate formation Proc.Natl.Acad.Sci.Usa 2005 102 13117 13122 2A68 16096056 Crystal structure of the T. thermophilus RNA polymerase holoenzyme in complex with antibiotic rifabutin 2005-07-01 2005-09-20 Artsimovitch, I.,Vassylyeva, M.N.,Svetlov, D.,Svetlov, V.,Perederina, A.,Igarashi, N.,Matsugaki, N.,Wakatsuki, S.,Tahirov, T.H.,Vassylyev, D.G. Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins. Cell(Cambridge,Mass.) 2005 122 351 363 2A69 16096056 Crystal structure of the T. Thermophilus RNA polymerase holoenzyme in complex with antibiotic rifapentin 2005-07-02 2005-09-20 Artsimovitch, I.,Vassylyeva, M.N.,Svetlov, D.,Svetlov, V.,Perederina, A.,Igarashi, N.,Matsugaki, N.,Wakatsuki, S.,Tahirov, T.H.,Vassylyev, D.G. Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins. Cell(Cambridge,Mass.) 2005 122 351 363 2A6E 16096056 Crystal structure of the T. Thermophilus RNA polymerase holoenzyme 2005-07-02 2005-09-20 Artsimovitch, I.,Vassylyeva, M.N.,Svetlov, D.,Svetlov, V.,Perederina, A.,Igarashi, N.,Matsugaki, N.,Wakatsuki, S.,Tahirov, T.H.,Vassylyev, D.G. Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins. Cell(Cambridge,Mass.) 2005 122 351 363 2A6H 16167380 Crystal structure of the T. thermophilus RNA polymerase holoenzyme in complex with antibiotic sterptolydigin 2005-07-02 2005-09-20 Temiakov, D.,Zenkin, N.,Vassylyeva, M.N.,Perederina, A.,Tahirov, T.H.,Kashkina, E.,Savkina, M.,Zorov, S.,Nikiforov, V.,Igarashi, N.,Matsugaki, N.,Wakatsuki, S.,Severinov, K.,Vassylyev, D.G. Structural basis of transcription inhibition by antibiotic streptolydigin. 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Biochemistry 2005 44 16529 16539 2A6X 16439369 Crystal structure of Emp46p carbohydrate recognition domain (CRD), Y131F mutant 2005-07-04 2006-01-31 Satoh, T.,Sato, K.,Kanoh, A.,Yamashita, K.,Yamada, Y.,Igarashi, N.,Kato, R.,Nakano, A.,Wakatsuki, S. Structures of the carbohydrate recognition domain of Ca2+-independent cargo receptors Emp46p and Emp47p. J.Biol.Chem. 2006 281 10410 10419 1WZD 16769893 Crystal Structure Of An Artificial Metalloprotein: Fe(10-CH2CH2COOH-Salophen)/Wild Type Heme oxygenase 2005-03-04 2006-02-21 Ueno, T.,Yokoi, N.,Unno, M.,Matsui, T.,Tokita, Y.,Yamada, M.,Ikeda-Saito, M.,Nakajima, H.,Watanabe, Y. Design of metal cofactors activated by a protein-protein electron transfer system. Proc.Natl.Acad.Sci.Usa 2006 103 9416 9421 1WZF 16769893 Crystal Structure Of An Artificial Metalloprotein: Fe(10-COOH-Salophen)/Wild Type Heme oxygenase 2005-03-04 2006-02-21 Ueno, T.,Yokoi, N.,Unno, M.,Matsui, T.,Tokita, Y.,Yamada, M.,Ikeda-Saito, M.,Nakajima, H.,Watanabe, Y. 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Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, both in the native form and covalently linked to various antibiotics Biochemistry 2006 45 783 792 2EXB 16411754 Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, complexed with FLOMOX 2005-11-08 2006-06-13 Kishida, H.,Unzai, S.,Roper, D.I.,Lloyd, A.,Park, S.-Y.,Tame, J.R.H. Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, both in the native form and covalently linked to various antibiotics Biochemistry 2006 45 783 792 2DGE 16777100 Crystal structure of oxidized cytochrome C6A from Arabidopsis thaliana 2006-03-11 2006-07-04 Chida, H.,Yokoyama, T.,Kawai, F.,Nakazawa, A.,Akazaki, H.,Takayama, Y.,Hirano, T.,Suruga, K.,Satoh, T.,Yamada, S.,Kawachi, R.,Unzai, S.,Nishio, T.,Park, S.-Y.,Oku, T. 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Crystal structure of Probable phosphoribosylglycinamide formyl transferase from Pyrococcus horikoshii OT3 complexed with ADP To be Published 0 0 0 0 2DDX Crystal structure of beta-1,3-xylanase from Vibrio sp. AX-4 2006-02-06 2007-02-13 Sakaguchi, K.,Kawamura, T.,Watanabe, N.,Kiyohara, M.,Yamaguchi, K.,Ito, M.,Tanaka, I. Atomic resolution analysis of beta-1,3-xylanase catalytic module from Vibrio sp. AX-4 To be Published 0 0 0 0 2E50 17360516 Crystal structure of SET/TAF-1beta/INHAT 2006-12-18 2007-02-20 Muto, S.,Senda, M.,Akai, Y.,Sato, L.,Suzuki, T.,Nagai, R.,Senda, T.,Horikoshi, M. Relationship between the structure of SET/TAF-Ibeta/INHAT and its histone chaperone activity Proc.Natl.Acad.Sci.Usa 2007 104 4285 4290 2E7S 17292842 Crystal structure of the yeast Sec2p GEF domain 2007-01-12 2007-02-27 Sato, Y.,Shirakawa, R.,Horiuchi, H.,Dohmae, N.,Fukai, S.,Nureki, O. Asymmetric Coiled-Coil Structure with Guanine Nucleotide Exchange Activity Structure 2007 15 245 252 2DG7 Crystal structure of the putative transcriptional regulator SCO0337 from Streptomyces coelicolor A3(2) 2006-03-08 2007-03-13 Hayashi, T.,Tanaka, Y.,Sakai, N.,Yao, M.,Tamura, T.,Tanaka, I. Crystal structure of the putative transcriptional regulator SCO0337 from Streptomyces coelicolor A3(2) To be Published 0 0 0 0 2DYJ 17996707 Crystal structure of ribosome-binding factor A from Thermus thermophilus HB8 2006-09-14 2007-03-14 Datta, P.P.,Wilson, D.N.,Kawazoe, M.,Swami, N.K.,Kaminishi, T.,Sharma, M.R.,Booth, T.M.,Takemoto, C.,Fucini, P.,Yokoyama, S.,Agrawal, R.K. Structural aspects of RbfA action during small ribosomal subunit assembly. Mol.Cell 2007 28 434 445 2GXG Crystal structure of EmrR homolog from hyperthermophilic archaea Sulfolobus tokodaii strain7 2006-05-08 2007-03-20 Miyazono, K.,Tsujimura, M.,Kawarabayasi, Y.,Tanokura, M. Crystal structure of archaeal homolog of multi drug resistance repressor protein, EmrR, from hyperthermophilic archaea Sulfolobus tokodaii strain7 To be Published 0 0 0 0 2DTD 17300803 Structure of Thermoplasma acidophilum aldohexose dehydrogenase (AldT) in ligand-free form 2006-07-12 2007-03-27 Yasutake, Y.,Nishiya, Y.,Tamura, N.,Tamura, T. Structural Insights into Unique Substrate Selectivity of Thermoplasma acidophilumd-Aldohexose Dehydrogenase J.Mol.Biol. 2007 367 1034 1046 2DTE 17300803 Structure of Thermoplasma acidophilum aldohexose dehydrogenase (AldT) in complex with NADH 2006-07-12 2007-03-27 Yasutake, Y.,Nishiya, Y.,Tamura, N.,Tamura, T. 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Crystal structure of the Sec4p{middle dot}Sec2p complex in the nucleotide exchanging intermediate state Proc.Natl.Acad.Sci.Usa 2007 104 8305 8310 2GR0 17850818 Crystal structure of Ferredoxin reductase, BphA4 (oxidized form, NAD+ complex) 2006-04-22 2007-05-22 Senda, M.,Kishigami, S.,Kimura, S.,Fukuda, M.,Ishida, T.,Senda, T. Molecular Mechanism of the Redox-dependent Interaction between NADH-dependent Ferredoxin Reductase and Rieske-type [2Fe-2S] Ferredoxin J.Mol.Biol. 2007 373 382 400 2GR2 Crystal structure of Ferredoxin reductase, BphA4 (oxidized form) 2006-04-22 2007-05-22 Senda, M.,Kishigami, S.,Kimura, S.,Ishida, T.,Fukuda, M.,Senda, T. A ferredoxin reductase BphA4 uses a butterfly motion of FAD to regulate affinity for ferredoxin To be Published 0 0 0 0 2Z0D 19322194 The crystal structure of human Atg4B- LC3(1-120) complex 2007-05-07 2007-05-22 Satoo, K.,Noda, N.N.,Kumeta, H.,Fujioka, Y.,Mizushima, N.,Ohsumi, Y.,Inagaki, F. The structure of Atg4B-LC3 complex reveals the mechanism of LC3 processing and delipidation during autophagy. Embo J. 2009 28 1341 1350 2CKX 18367475 Crystal structure of NgTRF1, double-stranded telomeric repeat binding factor from Nicotiana tabacum. 2006-04-24 2007-05-29 Ko, S.,Jun, S.,Bae, H.,Byun, J.-S.,Han, W.,Park, H.,Yang, S.W.,Park, S.,Jeon, Y.H.,Cheong, C.,Kim, W.T.,Lee, W.,Cho, H.-S. Structure of the DNA-Binding Domain of Ngtrf1 Reveals Unique Features of Plant Telomere-Binding Proteins. Nucleic Acids Res. 2008 36 2739 0 2E8T 17535895 S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with magnesium, FsPP and IPP 2007-01-23 2007-06-12 Guo, R.T.,Cao, R.,Liang, P.H.,Ko, T.P.,Chang, T.H.,Hudock, M.P.,Jeng, W.Y.,Chen, C.K.-M.,Zhang, Y.,Song, Y.,Kuo, C.J.,Yin, F.,Oldfield, E.,Wang, A.H.-J. 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Crystal structure of UDP-galactose 4-epimerase-like L-threonine dehydrogenase belonging to the intermediate short-chain dehydrogenase-reductase superfamily Febs J. 2010 277 5124 5132 2YYR Structural analysis of PHD domain of Pygopus complexed with trimethylated histone H3 peptide 2007-05-01 2008-05-06 Nakamura, Y.,Umehara, T.,Padmanabhan, B.,Yokoyama, S. Structural analysis of PHD domain of Pygopus complexed with trimethylated histone H3 peptide To be Published 0 0 0 0 2YZB Crystal structure of uricase from Arthrobacter globiformis in complex with uric acid (substrate) 2007-05-05 2008-05-06 Juan, E.C.M.,Hossain, M.T.,Hoque, M.M.,Yamamoto, T.,Imamura, S.,Suzuki, K.,Sekiguchi, T.,Takenaka, A. 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Cloning, expression and purification of cytochrome c(6) from the brown alga Hizikia fusiformis and complete X-ray diffraction analysis of the structure ACTA CRYSTALLOGR.,SECT.F 2008 64 674 680 3BWE 18922803 Crystal structure of aggregated form of DJ1 2008-01-09 2008-10-14 Cha, S.S.,Jung, H.I.,Jeon, H.,An, Y.J.,Kim, I.K.,Yun, S.,Ahn, H.J.,Chung, K.C.,Lee, S.H.,Suh, P.G.,Kang, S.O. Crystal structure of filamentous aggregates of human DJ-1 formed in an inorganic phosphate-dependent manner. J.Biol.Chem. 2008 283 34069 34075 2ZJX 18829434 Bovine pancreatic trypsin inhibitor (BPTI) containing only the [5,55] disulfide bond 2008-03-11 2008-10-21 Islam, M.M.,Sohya, S.,Noguchi, K.,Yohda, M.,Kuroda, Y. 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Catalytic mechanism of nitrile hydratase proposed by time-resolved X-ray crystallography using a novel substrate, tert-butylisonitrile J.Biol.Chem. 2008 283 36617 36623 2ZPH 18948265 Complex of Fe-type nitrile hydratase with tert-butylisonitrile, photo-activated for 340min at 293K 2008-07-11 2008-10-21 Hashimoto, K.,Suzuki, H.,Taniguchi, K.,Noguchi, T.,Yohda, M.,Odaka, M. Catalytic mechanism of nitrile hydratase proposed by time-resolved X-ray crystallography using a novel substrate, tert-butylisonitrile J.Biol.Chem. 2008 283 36617 36623 2ZPI 18948265 Complex of Fe-type nitrile hydratase with tert-butylisonitrile, photo-activated for 440min at 293K 2008-07-11 2008-10-21 Hashimoto, K.,Suzuki, H.,Taniguchi, K.,Noguchi, T.,Yohda, M.,Odaka, M. 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Febs Lett. 2010 584 1205 1211 3H3S 20036255 Crystal structure of the CERT START domain in complex with HPA-15 2009-04-17 2010-03-02 Kudo, N.,Kumagai, K.,Matsubara, R.,Kobayashi, S.,Hanada, K.,Wakatsuki, S.,Kato, R. Crystal structures of the CERT START domain with inhibitors provide insights into the mechanism of ceramide transfer. J.Mol.Biol. 2010 396 245 251 3HVN 21204001 Crystal structure of cytotoxin protein suilysin from Streptococcus suis 2009-06-16 2010-03-02 Xu, L.,Huang, B.,Du, H.,Zhang, X.C.,Xu, J.,Li, X.,Rao, Z. Crystal structure of cytotoxin protein suilysin from Streptococcus suis. Protein Cell 2010 1 96 105 3A04 Crystal structure of tryptophanyl-tRNA synthetase from hyperthermophilic archaeon, Aeropyrum pernix K1 2009-03-02 2010-03-09 Tsuchiya, W.,Fujimoto, Z.,Hasegawa, T. 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Crystallographic and functional analyses of J-domain of JAC1 essential for chloroplast photorelocation movement in Arabidopsis thaliana Plant Cell.Physiol. 2010 51 1372 1376 3A5L 20946985 Crystal Structure of a Dictyostelium P109A Mg2+-Actin in Complex with Human Gelsolin Segment 1 2009-08-09 2010-10-27 Murakami, K.,Yasunaga, T.,Noguchi, T.Q.P.,Gomibuchi, Y.,Ngo, K.X.,Uyeda, T.Q.P.,Wakabayashi, T. Structural basis for actin assembly, activation of ATP hydrolysis, and delayed phosphate release Cell(Cambridge,Mass.) 2010 143 275 287 3A5M 20946985 Crystal Structure of a Dictyostelium P109I Mg2+-Actin in Complex with Human Gelsolin Segment 1 2009-08-09 2010-10-27 Murakami, K.,Yasunaga, T.,Noguchi, T.Q.P.,Gomibuchi, Y.,Ngo, K.X.,Uyeda, T.Q.P.,Wakabayashi, T. 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Structural basis for actin assembly, activation of ATP hydrolysis, and delayed phosphate release Cell(Cambridge,Mass.) 2010 143 275 287 3A9C 22511789 Crystal structure of ribose-1,5-bisphosphate isomerase from Thermococcus kodakaraensis KOD1 in complex with ribulose-1,5-bisphosphate 2009-10-22 2010-11-03 Nakamura, A.,Fujihashi, M.,Aono, R.,Sato, T.,Nishiba, Y.,Yoshida, S.,Yano, A.,Atomi, H.,Imanaka, T.,Miki, K. Dynamic, ligand-dependent conformational change triggers reaction of ribose-1,5-bisphosphate isomerase from Thermococcus kodakarensis KOD1 J.Biol.Chem. 2012 287 20784 20796 3AQB 21068379 M. luteus B-P 26 heterodimeric hexaprenyl diphosphate synthase in complex with magnesium 2010-10-28 2010-11-10 Sasaki, D.,Fujihashi, M.,Okuyama, N.,Kobayashi, Y.,Noike, M.,Koyama, T.,Miki, K. Crystal structure of heterodimeric hexaprenyl diphosphate synthase from Micrococcus luteus B-P 26 reveals that the small subunit is directly involved in the product chain length regulation. 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Crystal structure of UDP-galactose 4-epimerase from the hyperthermophilic archaeon Pyrobaculum calidifontis Arch.Biochem.Biophys. 2011 512 126 134 3AE0 21098670 Crystal structure of the C(30) carotenoid dehydrosqualene synthase from Staphylococcus aureus complexed with geranylgeranyl thiopyrophosphate 2010-01-31 2010-11-24 Lin, F.Y.,Liu, C.I.,Liu, Y.L.,Zhang, Y.,Wang, K.,Jeng, W.Y.,Ko, T.P.,Cao, R.,Wang, A.H.,Oldfield, E. Mechanism of action and inhibition of dehydrosqualene synthase. Proc.Natl.Acad.Sci.USA 2010 107 21337 21342 3LFH Crystal structure of manxA from Thermoanaerobacter tengcongensis 2010-01-17 2010-12-08 Fu, T.M.,Su, X.-D. Crystal structure of manxA and manxB from Thermoanaerobacter tengcongensis To be Published 0 0 0 0 3ACS Crystal Structure of Cellvibrio gilvus Cellobiose Phosphorylase W488F mutant 2010-01-08 2010-12-22 Arai, T.,Hayashi, M.A.,Hidaka, M.,Kitaoka, M.,Wakagi, T.,Shoun, H.,Fushinobu, S. Engineering of cellobiose phosphorylase To be Published 0 0 0 0 3LJ8 21206059 Crystal Structure of MKP-4 2010-01-26 2010-12-29 Jeong, D.G.,Yoon, T.S.,Jung, S.-K.,Park, B.C.,Park, H.S.,Ryu, S.E.,Kim, S.J. Exploring binding sites other than the catalytic core in the crystal structure of the catalytic domain of MKP-4 Acta Crystallogr.,Sect.D 2011 67 25 31 3OIC 21185310 Crystal Structure of Enoyl-ACP Reductases III (FabL) from B. subtilis (apo form) 2010-08-19 2011-01-05 Kim, K.-H.,Ha, B.H.,Kim, S.J.,Hong, S.K.,Hwang, K.Y.,Kim, E.E. Crystal Structures of Enoyl-ACP Reductases I (FabI) and III (FabL) from B. subtilis J.Mol.Biol. 2011 406 403 415 3AK8 21206015 Crystal structure of the SEp22 dodecamer, a Dps-like protein from Salmonella enterica subsp. enterica serovar Enteritidis 2010-07-08 2011-01-12 Miyamoto, T.,Asahina, Y.,Miyazaki, S.,Shimizu, H.,Ohto, U.,Noguchi, S.,Satow, Y. Structures of the SEp22 dodecamer, a Dps-like protein from Salmonella enterica subsp. enterica serovar Enteritidis Acta Crystallogr.,Sect.F 2011 67 17 22 3AK9 21206015 Crystal structure of the SEp22 dodecamer, a Dps-like protein from Salmonella enterica subsp. enterica serovar Enteritidis, FE-soaked form 2010-07-08 2011-01-12 Miyamoto, T.,Asahina, Y.,Miyazaki, S.,Shimizu, H.,Ohto, U.,Noguchi, S.,Satow, Y. Structures of the SEp22 dodecamer, a Dps-like protein from Salmonella enterica subsp. enterica serovar Enteritidis Acta Crystallogr.,Sect.F 2011 67 17 22 3ALX 21217702 Crystal structure of the measles virus hemagglutinin bound to its cellular receptor SLAM (MV-H(L482R)-SLAM(N102H/R108Y) fusion) 2010-08-09 2011-01-12 Hashiguchi, T.,Ose, T.,Kubota, M.,Maita, N.,Kamishikiryo, J.,Maenaka, K.,Yanagi, Y. Structure of the measles virus hemagglutinin bound to its cellular receptor SLAM Nat.Struct.Mol.Biol. 2011 18 135 141 3AFI 20645368 Crystal structure of DBJA (HIS-DBJA) 2010-03-02 2011-01-19 Prokop, Z.,Sato, Y.,Brezovsky, J.,Mozga, T.,Chaloupkova, R.,Koudelakova, T.,Jerabek, P.,Stepankova, V.,Natsume, R.,van Leeuwen, J.G.,Janssen, D.B.,Florian, J.,Nagata, Y.,Senda, T.,Damborsky, J. Enantioselectivity of haloalkane dehalogenases and its modulation by surface loop engineering Angew.Chem.Int.Ed.Engl. 2010 49 6111 6115 3AQ0 21220764 Ligand-bound form of Arabidopsis medium/long-chain length prenyl pyrophosphate synthase (surface polar residue mutant) 2010-10-24 2011-01-19 Hsieh, F.-L.,Chang, T.-H.,Ko, T.-P.,Wang, A.H.-J. Structure and mechanism of an Arabidopsis medium/long-chain-length prenyl pyrophosphate synthase Plant Physiol. 2011 155 1079 1090 3LBM D-sialic acid aldolase 2010-01-08 2011-01-19 Chou, C.-Y.,Ko, T.-P.,Wu, K.-J.,Huang, K.-F.,Lin, C.-H.,Wong, C.-H.,Wang, A.H.-J. Modulation of substrate specificities of D-sialic acid aldolase through single mutations of Val251 To be Published 0 0 0 0 3AP7 21288902 Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain in complex with lactose sialic acid 2010-10-12 2011-01-26 Ideo, H.,Matsuzaka, T.,Nonaka, T.,Seko, A.,Yamashita, K. Galectin-8-N-domain recognition mechanism for sialylated and sulfated glycans J.Biol.Chem. 2011 286 11346 11355 3ALR 20948543 Crystal structure of Nanos 2010-08-06 2011-02-02 Hashimoto, H.,Hara, K.,Hishiki, A.,Kawaguchi, S.,Shichijo, N.,Nakamura, K.,Unzai, S.,Tamaru, Y.,Shimizu, T.,Sato, M. Crystal structure of zinc-finger domain of Nanos and its functional implications Embo Rep. 2010 11 848 853 3AEL Reaction intermediate structure of Entamoeba histolytica methionine gamma-lyase 1 containing methionine imine-pyridoxamine-5'-phosphate and alpha-amino-alpha, beta-butenoic acid-pyridoxal-5'-phosphate 2010-02-10 2011-02-09 Karaki, T.,Sato, D.,Shimizu, A.,Nozaki, T.,Harada, S. Crystal structure of Entamoeba histolytica methionine gamma-lyase 1 To be Published 0 0 0 0 3AI2 21277857 The crystal structure of L-sorbose reductase from Gluconobacter frateurii complexed with NADPH 2010-05-07 2011-02-09 Kubota, K.,Nagata, K.,Okai, M.,Miyazono, K.,Soemphol, W.,Ohtsuka, J.,Yamamura, A.,Saichana, N.,Toyama, H.,Matsushita, K.,Tanokura, M. The Crystal Structure of l-Sorbose Reductase from Gluconobacter frateurii Complexed with NADPH and l-Sorbose J.Mol.Biol. 2011 407 543 555 3ORY 21301087 Crystal structure of Flap endonuclease 1 from hyperthermophilic archaeon Desulfurococcus amylolyticus 2010-09-08 2011-02-09 Mase, T.,Kubota, K.,Miyazono, K.,Kawarabayasi, Y.,Tanokura, M. Structure of flap endonuclease 1 from the hyperthermophilic archaeon Desulfurococcus amylolyticus Acta Crystallogr.,Sect.F 2011 67 209 213 3AGY 20809635 Crystal structure of human Hsp40 Hdj1 peptide-binding domain complexed with a C-terminal peptide of Hsp70 2010-04-12 2011-02-23 Suzuki, H.,Noguchi, S.,Arakawa, H.,Tokida, T.,Hashimoto, M.,Satow, Y. 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Structural insights into differences in drug-binding selectivity between two forms of human alpha1-acid glycoprotein genetic variants, the A and F1*S forms. J. Biol. Chem. 2011 286 14427 14434 3M4V 21110374 Crystal structure of the A330P mutant of cytochrome P450 BM3 2010-03-12 2011-03-23 Whitehouse, C.J.C.,Yang, W.,Yorke, J.A.,Rowlatt, B.C.,Strong, A.J.,Blanford, C.F.,Bell, S.G.,Bartlam, M.,Wong, L.L.,Rao, Z. Structural basis for the properties of two single-site proline mutants of CYP102A1 (P450BM3) Chembiochem 2010 11 2549 2556 3PYC Crystal structure of human SMURF1 C2 domain 2010-12-13 2011-04-06 Li, X.,Li, P. Crystal structure of human SMURF1 C2 domain To be Published 0 0 0 0 3AQ5 21298303 Crystal structure of truncated hemoglobin from Tetrahymena pyriformis, Fe(II)-O2 form 2010-10-25 2011-04-20 Igarashi, J.,Kobayashi, K.,Matsuoka, A. 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Crystal structure of basic 7S globulin, a xyloglucan-specific endo-beta-1,4-glucanase inhibitor protein-like protein from soybean lacking inhibitory activity against endo-beta-glucanase Febs J. 2011 278 1944 1954 3ATQ 21515284 Geranylgeranyl Reductase (GGR) from Sulfolobus acidocaldarius 2011-01-12 2011-05-04 Sasaki, D.,Fujihashi, M.,Iwata, Y.,Murakami, M.,Yoshimura, T.,Hemmi, H.,Miki, K. Structure and mutation analysis of archaeal geranylgeranyl reductase J.Mol.Biol. 2011 409 543 557 3ATR 21515284 Geranylgeranyl Reductase (GGR) from Sulfolobus acidocaldarius co-crystallized with its ligand 2011-01-12 2011-05-04 Sasaki, D.,Fujihashi, M.,Iwata, Y.,Murakami, M.,Yoshimura, T.,Hemmi, H.,Miki, K. Structure and mutation analysis of archaeal geranylgeranyl reductase J.Mol.Biol. 2011 409 543 557 3LD1 Crystal Structure of IBV Nsp2a 2010-01-12 2011-05-25 Xu, Y.,Ye, Z.,Wei, L.,Cong, L.,Fu, J.,Chen, C.,Yang, A.,Wu, W.,Tang, H.,Bartlam, M.,Rao, Z. 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High-resolution X-ray study of the effects of deuteration on crystal growth and the crystal structure of proteinase K Acta Crystallogr.,Sect.F 2011 67 1334 1338 3AJ9 22102227 X-ray analysis of Crystal of Proteinase K Obtained from D2O Solution Using PEG 8000 2010-05-27 2011-06-22 Chatake, T.,Ishikawa, T.,Yanagisawa, Y.,Yamada, T.,Tanaka, I.,Fujiwara, S.,Morimoro, Y. High-resolution X-ray study of the effects of deuteration on crystal growth and the crystal structure of proteinase K Acta Crystallogr.,Sect.F 2011 67 1334 1338 3ANZ 21280135 Crystal Structure of alpha-hemolysin 2010-09-16 2011-06-22 Tanaka, Y.,Hirano, N.,Kaneko, J.,Kamio, Y.,Yao, M.,Tanaka, I. 2-Methyl-2,4-pentanediol induces spontaneous assembly of staphylococcal alpha-hemolysin into heptameric pore structure Protein Sci. 2011 20 448 456 3AQY 21697086 Crystal structure of Plodia interpunctella beta-GRP/GNBP3 N-terminal domain 2010-11-22 2011-06-22 Kanagawa, M.,Satoh, T.,Ikeda, A.,Adachi, Y.,Ohno, N.,Yamaguchi, Y. Structural insights into recognition of triple-helical beta-glucans by an insect fungal receptor J.Biol.Chem. 2011 286 29158 29165 3NCO Crystal structure of FnCel5A from F. nodosum Rt17-B1 2010-06-05 2011-06-22 Zheng, B.S.,Rao, Z.H. Crystal structure of FnCel5A from F. nodosum Rt17-B1 To be Published 0 0 0 0 3B0F 21715324 Crystal structure of the UBA domain of p62 and its interaction with ubiquitin 2011-06-09 2011-06-29 Isogai, S.,Morimoto, D.,Arita, K.,Unzai, S.,Tenno, T.,Hasegawa, J.,Sou, Y.S.,Komatsu, M.,Tanaka, K.,Shirakawa, M.,Tochio, H. Crystal structure of the ubiquitin-associated (UBA) domain of p62 and its interaction with ubiquitin. J.Biol.Chem. 2011 286 31864 31874 3B0F 21715324 Crystal structure of the UBA domain of p62 and its interaction with ubiquitin 2011-06-09 2011-06-29 Isogai, S.,Morimoto, D.,Arita, K.,Unzai, S.,Tenno, T.,Hasegawa, J.,Sou, Y.S.,Komatsu, M.,Tanaka, K.,Shirakawa, M.,Tochio, H. 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J.Struct.Biol. 2013 183 76 85 3W0S 23747390 Crystal structure of aminoglycoside phosphotransferase APH(4)-Ia, ternary complex with AMP-PNP and hygromycin B 2012-11-02 2013-08-07 Iino, D.,Takakura, Y.,Fukano, K.,Sasaki, Y.,Hoshino, T.,Ohsawa, K.,Nakamura, A.,Yajima, S. Crystal structures of the ternary complex of APH(4)-Ia/Hph with hygromycin B and an ATP analog using a thermostable mutant. J.Struct.Biol. 2013 183 76 85 4H5S 23871486 Complex structure of Necl-2 and CRTAM 2012-09-18 2013-08-07 Zhang, S.,Lu, G.,Qi, J.,Li, Y.,Zhang, Z.,Zhang, B.,Fan, Z.,Yan, J.,Gao, G.F. Competition of cell adhesion and immune recognition: insights into the interaction between CRTAM and nectin-like 2. Structure 2013 21 1430 1439 4GOH Structure of the substrate-free HmuO, HO from Corynebacterium diphtheriae 2012-08-20 2013-08-21 Unno, M.,Ardevol, A.,Rovira, C.,Ikeda-Saito, M. Crystal Structure of the Substrate-Free and the Product-Bound forms of HmuO, a Heme Oxygenase from Corynebacterium diphtheriae To be Published 0 0 0 0 4GPF Structure of the Fe3+-biliverdin-HmuO, heme oxygenase from Corynebacterium diphtheriae (data set III) 2012-08-20 2013-08-21 Unno, M.,Ardevol, A.,Rovira, C.,Ikeda-Saito, M. Crystal Structure of the Substrate-Free and the Product-Bound forms of HmuO, a Heme Oxygenase from Corynebacterium diphtheriae To be Published 0 0 0 0 3VVH X-ray structure of the human mitogen-activated protein kinase kinase 1 (MEK1) in complex with an inhibitor and MgATP 2012-07-24 2013-08-28 Kudo, N.,Kato, R.,Wakatsuki, S. X-ray structure of the human mitogen-activated protein kinase kinase 1 (MEK1) in complex with an inhibitor and MgATP To be Published 0 0 0 0 3VZS 23913421 Crystal structure of PhaB from Ralstonia eutropha in complex with Acetoacetyl-CoA and NADP 2012-10-15 2013-08-28 Matsumoto, K.,Tanaka, Y.,Watanabe, T.,Motohashi, R.,Ikeda, K.,Tobitani, K.,Yao, M.,Tanaka, I.,Taguchi, S. Directed evolution and structural analysis of NADPH-dependent Acetoacetyl Coenzyme A (Acetoacetyl-CoA) reductase from Ralstonia eutropha reveals two mutations responsible for enhanced kinetics Appl.Environ.Microbiol. 2013 79 6134 6139 4G5H 24157361 Crystal structure of capsular polysaccharide synthesizing enzyme CapE from Staphylococcus aureus in complex with by-product 2012-07-18 2013-08-28 Miyafusa, T.,Caaveiro, J.M.,Tanaka, Y.,Tsumoto, K. Dynamic elements govern the catalytic activity of CapE, a capsular polysaccharide-synthesizing enzyme from Staphylococcus aureus. Febs Lett. 2013 587 3824 3830 3VXE 23712263 Human alpha-thrombin-Bivalirudin complex at PD5.0 2012-09-12 2013-09-04 Yamada, T.,Kurihara, K.,Ohnishi, Y.,Tamada, T.,Tomoyori, K.,Masumi, K.,Tanaka, I.,Kuroki, R.,Niimura, N. Neutron and X-ray crystallographic analysis of the human alpha-thrombin-bivalirudin complex at pD 5.0: protonation states and hydration structure of the enzyme-product complex Biochim.Biophys.Acta 2013 1834 1532 1538 3W8J 23949117 Crystal structure of P5 a0 in a complex with Prx4 c-term 2013-03-13 2013-09-04 Sato, Y.,Kojima, R.,Okumura, M.,Hagiwara, M.,Masui, S.,Maegawa, K.,Saiki, M.,Horibe, T.,Suzuki, M.,Inaba, K. Synergistic cooperation of PDI family members in peroxiredoxin 4-driven oxidative protein folding Sci Rep 2013 3 2456 2456 4B18 25999477 The crystal structure of human Importin alpha 5 with TERT NLS peptide 2012-07-08 2013-09-04 Jeong, S.A.,Kim, K.,Lee, J.H.,Cha, J.S.,Khadka, P.,Cho, H.,Chung, I.K. Akt-Mediated Phosphorylation Increases the Binding Affinity of Htert for Importin Alpha to Promote Nuclear Translocation. J.Cell.Sci. 2015 128 2287 0 4H4L 23748184 Crystal Structure of ternary complex of HutP(HutP-L-His-Zn) 2012-09-17 2013-09-04 Dhakshnamoorthy, B.,Mizuno, H.,Kumar, P.K.R. Alternative binding modes of l-histidine guided by metal ions for the activation of the antiterminator protein HutP of Bacillus subtilis. J.Struct.Biol. 2013 183 512 518 3WD3 24043811 Serratia marcescens Chitinase B complexed with azide inhibitor 2013-06-06 2013-09-18 Hirose, T.,Maita, N.,Gouda, H.,Koseki, J.,Yamamoto, T.,Sugawara, A.,Nakano, H.,Hirono, S.,Shiomi, K.,Watanabe, T.,Taniguchi, H.,Sharpless, K.B.,Omura, S.,Sunazuka, T. Observation of the controlled assembly of preclick components in the in situ click chemistry generation of a chitinase inhibitor Proc.Natl.Acad.Sci.USA 2013 110 15892 15897 4JEK 23722833 Structure of dibenzothiophene monooxygenase (DszC) from Rhodococcus erythropolis 2013-02-27 2013-09-18 Duan, X.,Zhang, L.,Zhou, D.,Ji, K.,Ma, T.,Shui, W.,Li, G.,Li, X. Crystallization and preliminary structural analysis of dibenzothiophene monooxygenase (DszC) from Rhodococcus erythropolis Acta Crystallogr.,Sect.F 2013 69 597 601 3VY2 N33D mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F) 2012-09-21 2013-09-25 Takagi, R.,Nakanishi, T.,Kitamura, M. Crystal structure of N33D mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F) To be Published 0 0 0 0 3VY7 24790092 Crystal structure of human pancreatic secretory protein ZG16p with O-(alpha-D-mannosyl)-L-serine 2012-09-21 2013-09-25 Kanagawa, M.,Liu, Y.,Hanashima, S.,Ikeda, A.,Chai, W.,Nakano, Y.,Kojima-Aikawa, K.,Feizi, T.,Yamaguchi, Y. Structural Basis for Multiple Sugar Recognition of Jacalin-related Human ZG16p Lectin J.Biol.Chem. 2014 289 16954 16965 3VYL 24311575 Structure of L-ribulose 3-epimerase 2012-09-27 2013-10-02 Uechi, K.,Sakuraba, H.,Yoshihara, A.,Morimoto, K.,Takata, G. Structural insight into L-ribulose 3-epimerase from Mesorhizobium loti. Acta Crystallogr.,Sect.D 2013 69 2330 2339 4H4P Crystal Structure of Ferredoxin reductase, BphA4 E175Q/Q177K mutant (oxidized form) 2012-09-18 2013-10-09 Nishizawa, A.,Harada, A.,Senda, M.,Tachihara, Y.,Muramatsu, D.,Kishigami, S.,Mori, S.,Sugiyama, K.,Senda, T.,Kimura, S. Random Mutagenesis with the Project Assessment for Complete Conversion of Co-Factor Specificity of a Ferredoxin Reductase BphA4 To be Published 0 0 0 0 3VZF 24790092 Crystal structure of human pancreatic secretory protein ZG16p with methyl alpha-D-mannopyranoside 2012-10-11 2013-10-16 Kanagawa, M.,Liu, Y.,Hanashima, S.,Ikeda, A.,Chai, W.,Nakano, Y.,Kojima-Aikawa, K.,Feizi, T.,Yamaguchi, Y. Structural Basis for Multiple Sugar Recognition of Jacalin-related Human ZG16p Lectin J.Biol.Chem. 2014 289 16954 16965 3VZG 24790092 Crystal structure of human pancreatic secretory protein ZG16p with O-(alpha-D-mannosyl)-L-threonine 2012-10-11 2013-10-16 Kanagawa, M.,Liu, Y.,Hanashima, S.,Ikeda, A.,Chai, W.,Nakano, Y.,Kojima-Aikawa, K.,Feizi, T.,Yamaguchi, Y. Structural Basis for Multiple Sugar Recognition of Jacalin-related Human ZG16p Lectin J.Biol.Chem. 2014 289 16954 16965 3WH2 24101491 Human Mincle in complex with citrate 2013-08-21 2013-10-23 Furukawa, A.,Kamishikiryo, J.,Mori, D.,Toyonaga, K.,Okabe, Y.,Toji, A.,Kanda, R.,Miyake, Y.,Ose, T.,Yamasaki, S.,Maenaka, K. Structural analysis for glycolipid recognition by the C-type lectins Mincle and MCL Proc.Natl.Acad.Sci.USA 2013 110 17438 17443 3WH3 24101491 human Mincle, ligand free form 2013-08-21 2013-10-23 Furukawa, A.,Kamishikiryo, J.,Mori, D.,Toyonaga, K.,Okabe, Y.,Toji, A.,Kanda, R.,Miyake, Y.,Ose, T.,Yamasaki, S.,Maenaka, K. Structural analysis for glycolipid recognition by the C-type lectins Mincle and MCL Proc.Natl.Acad.Sci.USA 2013 110 17438 17443 3VYH Crystal structure of aW116R mutant of nitrile hydratase from Pseudonocardia thermophilla 2012-09-25 2013-11-13 Yamanaka, Y.,Sato, M.,Arakawa, T.,Namima, S.,Hori, S.,Ohtaki, A.,Noguchi, K.,Katayama, Y.,Yohda, M.,Odaka, M. Effects of argnine residue around the substrate pocket on the substrate specificity of thiocyanate hydrolase To be published 0 0 0 0 3W1M Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with 5-bromoorotate 2012-11-16 2013-11-20 Inaoka, D.K.,Iida, M.,Tabuchi, T.,Lee, N.,Matsuoka, S.,Shiba, T.,Sakamoto, K.,Suzuki, S.,Balogun, E.O.,Nara, T.,Aoki, T.,Inoue, M.,Honma, T.,Tanaka, A. Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with 5-bromoorotate To be Published 0 0 0 0 3W1N Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with 5-iodoorotate 2012-11-19 2013-11-20 Inaoka, D.K.,Iida, M.,Tabuchi, T.,Lee, N.,Matsuoka, S.,Shiba, T.,Sakamoto, K.,Suzuki, S.,Balogun, E.O.,Nara, T.,Aoki, T.,Inoue, M.,Honma, T.,Tanaka, A.,Harada, S.,Kita, K. Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with 5-iodoorotate To be Published 0 0 0 0 3W1U Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-3-111 2012-11-21 2013-11-27 Inaoka, D.K.,Iida, M.,Tabuchi, T.,Lee, N.,Matsuoka, S.,Shiba, T.,Sakamoto, K.,Suzuki, S.,Balogun, E.O.,Nara, T.,Aoki, T.,Inoue, M.,Honma, T.,Tanaka, A.,Harada, S.,Kita, K. Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-3-111 To be Published 0 0 0 0 4N2X 24071515 Crystal Structure of DL-2-haloacid dehalogenase 2013-10-06 2013-11-27 Siwek, A.,Omi, R.,Hirotsu, K.,Jitsumori, K.,Esaki, N.,Kurihara, T.,Paneth, P. Binding modes of DL-2-haloacid dehalogenase revealed by crystallography, modeling and isotope effects studies. Arch.Biochem.Biophys. 2013 540 26 32 3WJW 24151964 Wild-type orotidine 5'-monophosphate decarboxylase from M. thermoautotrophicus complexed with 6-methyl-UMP 2013-10-17 2013-12-04 Fujihashi, M.,Ishida, T.,Kuroda, S.,Kotra, L.P.,Pai, E.F.,Miki, K. Substrate distortion contributes to the catalysis of orotidine 5'-monophosphate decarboxylase. J.Am.Chem.Soc. 2013 135 17432 17443 3WJW 24151964 Wild-type orotidine 5'-monophosphate decarboxylase from M. thermoautotrophicus complexed with 6-methyl-UMP 2013-10-17 2013-12-04 Fujihashi, M.,Ishida, T.,Kuroda, S.,Kotra, L.P.,Pai, E.F.,Miki, K. Substrate distortion contributes to the catalysis of orotidine 5'-monophosphate decarboxylase. J.Am.Chem.Soc. 2013 135 17432 17443 3W2Y Crystal structure of DNA uridine endonuclease Mth212 mutant W205S 2012-12-06 2013-12-11 Tabata, N.,Shida, T.,Arai, R. Crystal structure of DNA uridine endonuclease Mth212 To be Published 0 0 0 0 3W2D 24423621 Crystal Structure of Staphylococcal Eenterotoxin B in complex with a novel neutralization monoclonal antibody Fab fragment 2012-11-28 2013-12-25 Xia, T.,Liang, S.,Wang, H.,Hu, S.,Sun, Y.,Yu, X.,Han, J.,Li, J.,Guo, S.,Dai, J.,Lou, Z.,Guo, Y. Structural basis for the neutralization and specificity of Staphylococcal enterotoxin B against its MHC Class II binding site. MAbs 2014 6 119 129 3WAM 24290141 Crystal structure of human LC3C_8-125 2013-05-06 2013-12-25 Suzuki, H.,Tabata, K.,Morita, E.,Kawasaki, M.,Kato, R.,Dobson, R.C.,Yoshimori, T.,Wakatsuki, S. Structural basis of the autophagy-related LC3/Atg13 LIR complex: recognition and interaction mechanism. Structure 2014 22 47 58 3WNX 24498414 Crystal structure of ERGIC-53/MCFD2, Calcium/Man3-bound form 2013-12-18 2014-01-15 Satoh, T.,Suzuki, K.,Yamaguchi, T.,Kato, K. Structural Basis for Disparate Sugar-Binding Specificities in the Homologous Cargo Receptors ERGIC-53 and VIP36 Plos One 2014 9 0 0 3WEB 24567405 Crystal structure of a Niemann-Pick type C2 protein from Japanese carpenter ant in complex with oleic acid 2013-07-02 2014-02-05 Ishida, Y.,Tsuchiya, W.,Fujii, T.,Fujimoto, Z.,Miyazawa, M.,Ishibashi, J.,Matsuyama, S.,Ishikawa, Y.,Yamazaki, T. Niemann-Pick type C2 protein mediating chemical communication in the worker ant Proc.Natl.Acad.Sci.USA 2014 111 3847 3852 3WIQ 24255995 Crystal structure of kojibiose phosphorylase complexed with kojibiose 2013-09-24 2014-02-05 Okada, S.,Yamamoto, T.,Watanabe, H.,Nishimoto, T.,Chaen, H.,Fukuda, S.,Wakagi, T.,Fushinobu, S. Structural and mutational analysis of substrate recognition in kojibiose phosphorylase Febs J. 2014 281 778 786 3WMR 24530530 Crystal structure of VinJ 2013-11-22 2014-02-05 Shinohara, Y.,Miyanaga, A.,Kudo, F.,Eguchi, T. The crystal structure of the amidohydrolase VinJ shows a unique hydrophobic tunnel for its interaction with polyketide substrates Febs Lett. 2014 588 995 1000 3WN0 24482228 Crystal Structure of Streptomyces coelicolor alpha-L-arabinofuranosidase in complex with L-arabinose 2013-11-29 2014-02-05 Maehara, T.,Fujimoto, Z.,Ichinose, H.,Michikawa, M.,Harazono, K.,Kaneko, S. Crystal structure and characterization of the glycoside hydrolase family 62 alpha-L-arabinofuranosidase from Streptomyces coelicolor J.Biol.Chem. 2014 289 7962 7972 3WN1 24482228 Crystal Structure of Streptomyces coelicolor alpha-L-arabinofuranosidase in complex with xylotriose 2013-11-29 2014-02-05 Maehara, T.,Fujimoto, Z.,Ichinose, H.,Michikawa, M.,Harazono, K.,Kaneko, S. Crystal structure and characterization of the glycoside hydrolase family 62 alpha-L-arabinofuranosidase from Streptomyces coelicolor J.Biol.Chem. 2014 289 7962 7972 3WNL 24616103 D308A mutant of Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase complexed with isomaltohexaose 2013-12-10 2014-02-05 Suzuki, N.,Fujimoto, Z.,Kim, Y.M.,Momma, M.,Kishine, N.,Suzuki, R.,Suzuki, S.,Kitamura, S.,Kobayashi, M.,Kimura, A.,Funane, K. Structural elucidation of the cyclization mechanism of alpha-1,6-glucan by Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase. J.Biol.Chem. 2014 289 12040 12051 3WNM 24616103 D308A mutant of Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase complexed with isomaltoheptaose 2013-12-10 2014-02-05 Suzuki, N.,Fujimoto, Z.,Kim, Y.M.,Momma, M.,Kishine, N.,Suzuki, R.,Suzuki, S.,Kitamura, S.,Kobayashi, M.,Kimura, A.,Funane, K. Structural elucidation of the cyclization mechanism of alpha-1,6-glucan by Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase. J.Biol.Chem. 2014 289 12040 12051 4N85 24422526 Crystal structure of human transthyretin 2013-10-17 2014-02-19 Yokoyama, T.,Kosaka, Y.,Mizuguchi, M. Crystal structures of human transthyretin complexed with glabridin J.Med.Chem. 2014 57 1090 1096 4JDB Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-5-005 2013-02-24 2014-02-26 Inaoka, D.K.,Iida, M.,Tabuchi, T.,Lee, N.,Hashimoto, S.,Matsuoka, S.,Kuranaga, T.,Shiba, T.,Sakamoto, K.,Suzuki, S.,Balogun, E.O.,Nara, T.,Aoki, T.,Inoue, M.,Honma, T.,Tanaka, A.,Harada, S.,Kita, K. Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-5-005 To be Published 0 0 0 0 3W76 Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-4-189 2013-02-27 2014-03-05 Inaoka, D.K.,Iida, M.,Tabuchi, T.,Lee, N.,Hashimoto, S.,Matsuoka, S.,Kuranaga, T.,Shiba, T.,Sakamoto, K.,Suzuki, S.,Balogun, E.O.,Nara, T.,Aoki, T.,Inoue, M.,Honma, T.,Tanaka, A.,Harada, S.,Kita, K. Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-4-189 To be Published 0 0 0 0 3W7G Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-5-013 2013-02-28 2014-03-05 Inaoka, D.K.,Iida, M.,Tabuchi, T.,Lee, N.,Hashimoto, S.,Matsuoka, S.,Kuranaga, T.,Shiba, T.,Sakamoto, K.,Suzuki, S.,Balogun, E.O.,Nara, T.,Aoki, T.,Inoue, M.,Honma, T.,Tanaka, A.,Harada, S.,Kita, K. Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-5-013 To be Published 0 0 0 0 3W7H Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-5-015 2013-02-28 2014-03-05 Inaoka, D.K.,Iida, M.,Tabuchi, T.,Lee, N.,Hashimoto, S.,Matsuoka, S.,Kuranaga, T.,Shiba, T.,Sakamoto, K.,Suzuki, S.,Balogun, E.O.,Nara, T.,Aoki, T.,Inoue, M.,Honma, T.,Tanaka, A.,Harada, S.,Kita, K. Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-5-015 To be Published 0 0 0 0 3W7I Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-5-055 2013-02-28 2014-03-05 Inaoka, D.K.,Iida, M.,Tabuchi, T.,Lee, N.,Hashimoto, S.,Matsuoka, S.,Kuranaga, T.,Shiba, T.,Sakamoto, K.,Suzuki, S.,Balogun, E.O.,Nara, T.,Aoki, T.,Inoue, M.,Honma, T.,Tanaka, A.,Harada, S.,Kita, K. Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-5-055 To be Published 0 0 0 0 3W8D Crystal structure of D-3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis complexed with NAD+ and an inhibitor methylmalonate 2013-03-12 2014-03-12 Kanazawa, H.,Tsunoda, M.,Hoque, M.M.,Suzuki, K.,Yamamoto, T.,Takenaka, A. X-ray diffraction of D-3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis complexed with NAD+ and methylmalonate To be Published 0 0 0 0 3W8E Crystal structure of D-3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis complexed with NAD+ and a substrate D-3-hydroxybutyrate 2013-03-12 2014-03-12 Kanazawa, H.,Tsunoda, M.,Hoque, M.M.,Suzuki, K.,Yamamoto, T.,Takenaka, A. High resolution X-ray diffraction of D-3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis complexed with NAD+ and D-3-hydroxybutyrate To be Published 0 0 0 0 3W8F Crystal structure of D-3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis complexed with NAD+ and an inhibitor malonate 2013-03-12 2014-03-12 Kanazawa, H.,Tsunoda, M.,Hoque, M.M.,Suzuki, K.,Yamamoto, T.,Takenaka, A. X-ray diffraction of D-3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis complexed with NAD+ and malonate To be Published 0 0 0 0 3WHC 24356978 Crystal structure of a transcriptional regulator FadR from Bacillus subtilis in complex with stearoyl-CoA 2013-08-23 2014-03-19 Fujihashi, M.,Nakatani, T.,Hirooka, K.,Matsuoka, H.,Fujita, Y.,Miki, K. Structural characterization of a ligand-bound form of Bacillus subtilis FadR involved in the regulation of fatty acid degradation. Proteins 2014 82 1301 1310 4J0E 23695566 Crystal structure of 3-hydroxyacyl-CoA dehydrogenase from Caenorhadbitis elegans in P1 space group 2013-01-30 2014-03-19 Xu, Y.,Sun, F. Purification, crystallization and preliminary crystallographic analysis of 3-hydroxyacyl-CoA dehydrogenase from Caenorhabditis elegans. Acta Crystallogr.,Sect.F 2013 69 515 519 4J0F 23695566 Crystal structure of 3-hydroxyacyl-CoA dehydrogenase from Caenorhadbitis elegans in P212121 space group 2013-01-30 2014-03-19 Xu, Y.,Sun, F. Purification, crystallization and preliminary crystallographic analysis of 3-hydroxyacyl-CoA dehydrogenase from Caenorhabditis elegans. Acta Crystallogr.,Sect.F 2013 69 515 519 4NBD 24584240 Carbazole-bound oxygenase with Phe275 replaced by Trp and ferredoxin complex of carbazole 1,9a-dioxygenase (form2) 2013-10-23 2014-03-26 Inoue, K.,Usami, Y.,Ashikawa, Y.,Noguchi, H.,Umeda, T.,Yamagami-Ashikawa, A.,Horisaki, T.,Uchimura, H.,Terada, T.,Nakamura, S.,Shimizu, K.,Habe, H.,Yamane, H.,Fujimoto, Z.,Nojiri, H. Structural basis of the divergent oxygenation reactions catalyzed by the rieske nonheme iron oxygenase carbazole 1,9a-dioxygenase. Appl.Environ.Microbiol. 2014 80 2821 2832 3WDK 24638914 Crystal structure of 4-phosphopantoate-beta-alanine ligase complexed with reaction intermediate 2013-06-19 2014-04-02 Kishimoto, A.,Kita, A.,Ishibashi, T.,Tomita, H.,Yokooji, Y.,Imanaka, T.,Atomi, H.,Miki, K. Crystal structure of phosphopantothenate synthetase from Thermococcus kodakarensis Proteins 2014 82 1924 1936 3WDL 24638914 Crystal structure of 4-phosphopantoate-beta-alanine ligase complexed with ATP 2013-06-19 2014-04-02 Kishimoto, A.,Kita, A.,Ishibashi, T.,Tomita, H.,Yokooji, Y.,Imanaka, T.,Atomi, H.,Miki, K. Crystal structure of phosphopantothenate synthetase from Thermococcus kodakarensis Proteins 2014 82 1924 1936 3W9P 25716479 Crystal structure of monomeric FraC (second crystal form) 2013-04-09 2014-04-09 Tanaka, K.,Caaveiro, J.M.M.,Morante, K.,Gonzalez-Manas, J.M.,Tsumoto, K. Structural basis for self-assembly of a cytolytic pore lined by protein and lipid Nat Commun 2015 6 6337 6337 4P2G 24697266 Crystal structure of DJ-1 in sulfinic acid form (aged crystal) 2014-03-04 2014-04-09 Tashiro, S.,Caaveiro, J.M.,Wu, C.X.,Hoang, Q.Q.,Tsumoto, K. Thermodynamic and Structural Characterization of the Specific Binding of Zn(II) to Human Protein DJ-1. Biochemistry 2014 53 2218 2220 4P34 24697266 Crystal structure of DJ-1 in sulfenic acid form (fresh crystal) 2014-03-05 2014-04-09 Tashiro, S.,Caaveiro, J.M.,Wu, C.X.,Hoang, Q.Q.,Tsumoto, K. Thermodynamic and Structural Characterization of the Specific Binding of Zn(II) to Human Protein DJ-1. Biochemistry 2014 53 2218 2220 4P35 24697266 Crystal structure of DJ-1 with Zinc(II) bound (crystal I) 2014-03-05 2014-04-09 Tashiro, S.,Caaveiro, J.M.,Wu, C.X.,Hoang, Q.Q.,Tsumoto, K. Thermodynamic and Structural Characterization of the Specific Binding of Zn(II) to Human Protein DJ-1. Biochemistry 2014 53 2218 2220 4P36 24697266 Crystal structure of DJ-1 With Zn(II) bound (crystal 2) 2014-03-05 2014-04-09 Tashiro, S.,Caaveiro, J.M.,Wu, C.X.,Hoang, Q.Q.,Tsumoto, K. Thermodynamic and Structural Characterization of the Specific Binding of Zn(II) to Human Protein DJ-1. Biochemistry 2014 53 2218 2220 3WK8 24656800 Crystal structure of soluble epoxide hydrolase in complex with fragment inhibitor 2013-10-17 2014-04-16 Amano, Y.,Yamaguchi, T.,Tanabe, E. Structural insights into binding of inhibitors to soluble epoxide hydrolase gained by fragment screening and X-ray crystallography. Bioorg.Med.Chem. 2014 22 2427 2434 3WST 24726727 Crystal structure of C.elegans PRMT7 in complex with SAH(P31) 2014-03-21 2014-04-23 Hasegawa, M.,Toma-fukai, S.,Kim, J.D.,Fukamizu, A.,Shimizu, T. Protein arginine methyltransferase 7 has a novel homodimer-like structure formed by tandem repeats Febs Lett. 2014 588 1942 1948 3WKU 24657997 Crystal structure of the anaerobic DesB-gallate complex 2013-10-31 2014-04-30 Sugimoto, K.,Senda, M.,Kasai, D.,Fukuda, M.,Masai, E.,Senda, T. Molecular Mechanism of Strict Substrate Specificity of an Extradiol Dioxygenase, DesB, Derived from Sphingobium sp. 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Nat.Chem.Biol. 2020 16 415 422 6L96 31935812 Structure of PPARalpha-LBD/pemafibrate/SRC1 peptide 2019-11-08 2020-01-15 Kawasaki, M.,Kambe, A.,Yamamoto, Y.,Arulmozhiraja, S.,Ito, S.,Nakagawa, Y.,Tokiwa, H.,Nakano, S.,Shimano, H. Elucidation of Molecular Mechanism of a Selective PPAR alpha Modulator, Pemafibrate, through Combinational Approaches of X-ray Crystallography, Thermodynamic Analysis, and First-Principle Calculations. Int J Mol Sci 2020 21 0 0 6KOS 31951376 Crystal structure of SUWA (Super WA20), a hyper-stable de novo protein with a dimeric bisecting topology 2019-08-13 2020-01-29 Kimura, N.,Mochizuki, K.,Umezawa, K.,Hecht, M.H.,Arai, R. HyperstableDe NovoProtein with a Dimeric Bisecting Topology. Acs Synth Biol 2020 9 254 259 6JHC 32679618 Hydroxynitrile lyase from the millipede, Chamberlinius hualienensis (ligand free) 2019-02-18 2020-02-19 Motojima, F.,Izumi, A.,Nuylert, A.,Zhai, Z.,Dadashipour, M.,Shichida, S.,Yamaguchi, T.,Nakano, S.,Asano, Y. 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Mbio 2020 11 0 0 6JKT Crystal structure of aspartate transcarbamoylase from Trypanosoma cruzi in complex with N-(PHOSPHONACETYL)-L-ASPARTIC ACID (PALA). 2019-03-01 2020-03-04 Matoba, K.,Shiba, T.,Nara, T.,Aoki, T.,Nagasaki, S.,Hayamizu, R.,Honma, T.,Tanaka, A.,Inoue, M.,Matsuoka, S.,Balogun, E.O.,Inaoka, D.K.,Kita, K.,Harada, S. Crystallographic snapshots of Trypanosoma cruzi aspartate transcarbamoylase revealed an ordered Bi-Bi reaction mechanism To Be Published 0 0 0 0 6JNR RXRa structure complexed with CU-6PMN and SRC1 peptide. 2019-03-18 2020-03-25 Kawasaki, M.,Nakano, S.,Motoyama, T.,Yamada, S.,Watanabe, M.,Takamura, Y.,Fujihara, M.,Tokiwa, H.,Kakuta, H.,Ito, S. RXRa structure complexed with CU-6PMN and SRC1 peptide. To Be Published 0 0 0 0 6K2G 31295915 Structure of FraE in the monomer state 2019-05-14 2020-03-25 Morante, K.,Bellomio, A.,Viguera, A.R.,Gonzalez-Manas, J.M.,Tsumoto, K.,Caaveiro, J.M.M. 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Biochem.Biophys.Res.Commun. 2020 525 720 725 6JYG 32912687 Crystal Structure of L-threonine dehydrogenase from Phytophthora infestans 2019-04-26 2020-04-01 Yoneda, K.,Nagano, R.,Mikami, T.,Sakuraba, H.,Fukui, K.,Araki, T.,Ohshima, T. Catalytic properties and crystal structure of UDP-galactose 4-epimerase-like l-threonine 3-dehydrogenase from Phytophthora infestans. Enzyme.Microb.Technol. 2020 140 109627 109627 6L27 31880458 X-ray crystal structure of the mutant green fluorescent protein 2019-10-02 2020-04-01 Shibazaki, C.,Shimizu, R.,Kagotani, Y.,Ostermann, A.,Schrader, T.E.,Adachi, M. Direct Observation of the Protonation States in the Mutant Green Fluorescent Protein. J Phys Chem Lett 2020 11 492 496 6JW7 32237736 The crystal structure of KanD2 in complex with NADH and 3""-deamino-3""-hydroxykanamycin A 2019-04-18 2020-04-15 Kudo, F.,Kitayama, Y.,Miyanaga, A.,Hirayama, A.,Eguchi, T. Biochemical and structural analysis of a dehydrogenase, KanD2, and an aminotransferase, KanS2, that are responsible for the construction of the kanosamine moiety in kanamycin biosynthesis. Biochemistry 2020 59 1470 1473 6JW8 32237736 The crystal structure of KanD2 in complex with NADH and 3""-deamino-3""-hydroxykanamycin B 2019-04-18 2020-04-15 Kudo, F.,Kitayama, Y.,Miyanaga, A.,Hirayama, A.,Eguchi, T. Biochemical and structural analysis of a dehydrogenase, KanD2, and an aminotransferase, KanS2, that are responsible for the construction of the kanosamine moiety in kanamycin biosynthesis. Biochemistry 2020 59 1470 1473 6LCF 32246585 Crystal Structure of beta-L-arabinobiose binding protein - native 2019-11-18 2020-04-22 Miyake, M.,Terada, T.,Shimokawa, M.,Sugimoto, N.,Arakawa, T.,Shimizu, K.,Igarashi, K.,Fujita, K.,Fushinobu, S. Structural analysis of beta-L-arabinobiose-binding protein in the metabolic pathway of hydroxyproline-rich glycoproteins in Bifidobacterium longum. 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Febs Lett. 2020 594 3020 3031 7CC4 A biodegradable plastic-degrading cutinase-like enzyme from the phyllosphere yeast Pseudozyma antarctica 2020-06-16 2020-07-15 Suzuki, K.,Watanabe, T.,Kitamoto, H. A biodegradable plastic-degrading cutinase-like enzyme from the phyllosphere yeast Pseudozyma antarctica To Be Published 0 0 0 0 6KK9 33576533 A Crystal structure of OspA mutant 2019-07-24 2020-07-29 Shiga, S.,Makabe, K. Structural analysis of the beta-sheet edge of peptide self-assembly using a model protein. Proteins 2021 89 845 852 7CAP 32731397 Cyclic Lys48-linked triubiquitin 2020-06-09 2020-08-19 Hiranyakorn, M.,Yanaka, S.,Satoh, T.,Wilasri, T.,Jityuti, B.,Yagi-Utsumi, M.,Kato, K. NMR Characterization of Conformational Interconversions of Lys48-Linked Ubiquitin Chains. Int J Mol Sci 2020 21 0 0 6KT1 Crystal structure of an OspA mutant 2019-08-26 2020-08-26 Namioka, S.,Makabe, K. Crystal structure of an OspA mutant To Be Published 0 0 0 0 6LX2 32808707 Potato D-enzyme complexed with CA26 2020-02-10 2020-08-26 Imamura, K.,Matsuura, T.,Nakagawa, A.,Kitamura, S.,Kusunoki, M.,Takaha, T.,Unno, H. Structural analysis and reaction mechanism of the disproportionating enzyme (D-enzyme) from potato. Protein Sci. 2020 29 2085 2100 7CBD 32816991 Catalytic domain of Cellulomonas fimi Cel6B 2020-06-12 2020-08-26 Nakamura, A.,Ishiwata, D.,Visootsat, A.,Uchiyama, T.,Mizutani, K.,Kaneko, S.,Murata, T.,Igarashi, K.,Iino, R. Domain architecture divergence leads to functional divergence in binding and catalytic domains of bacterial and fungal cellobiohydrolases. J.Biol.Chem. 2020 295 14606 14617 6KTQ 32897601 Crystal structure of catalytic domain of homocitrate synthase from Sulfolobus acidocaldarius (SaHCS(dRAM)) in complex with alpha-ketoglutarate/Zn2+/CoA 2019-08-28 2020-09-02 Suzuki, T.,Tomita, T.,Hirayama, K.,Suzuki, M.,Kuzuyama, T.,Nishiyama, M. Involvement of subdomain II in the recognition of acetyl-CoA revealed by the crystal structure of homocitrate synthase from Sulfolobus acidocaldarius. Febs J. 2021 288 1975 1988 6KWJ 38104859 A Crystal Structure of OspA mutant 2019-09-07 2020-09-09 Kiya, M.,Shiga, S.,Ding, P.,Koide, S.,Makabe, K. beta-Strand-mediated Domain-swapping in the Absence of Hydrophobic Core Repacking. J.Mol.Biol. 2024 436 168405 168405 6KXN Crystal structure of W50A mutant of Chitiniphilus shinanonensis chitinase ChiL (CsChiL) complexed with N,N'-diacetylchitobiose 2019-09-12 2020-09-16 Ueda, M.,Sonoda, N.,Shimosaka, M.,Arai, R. Crystal structure of CsChiL, a chitinase from Chitiniphilus shinanonensis To be published 0 0 0 0 7CW1 Crystal structure of a biodegradable plastic-degrading cutinase-like enzyme from the phyllosphere yeast, Pseudozyma antarctica, solved by getting the phase from anomalous scattering of uncovalently coordinated arsenic (cacodylate). 2020-08-27 2020-09-16 Suzuki, K. 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Iscience 2020 23 101727 101727 6KYP 33205029 X-ray structure of human PPARalpha ligand binding domain-GW9662-clofibric acid co-crystals obtained by delipidation and co-crystallization 2019-09-19 2020-11-11 Kamata, S.,Oyama, T.,Saito, K.,Honda, A.,Yamamoto, Y.,Suda, K.,Ishikawa, R.,Itoh, T.,Watanabe, Y.,Shibata, T.,Uchida, K.,Suematsu, M.,Ishii, I. PPAR alpha Ligand-Binding Domain Structures with Endogenous Fatty Acids and Fibrates. Iscience 2020 23 101727 101727 6LA0 33218993 Crystal structure of AoRut 2019-11-11 2020-11-11 Makabe, K.,Hirota, R.,Shiono, Y.,Tanaka, Y.,Koseki, T. Aspergillus oryzae Rutinosidase: Biochemical and Structural Investigation. Appl.Environ.Microbiol. 2021 87 0 0 6LK7 33324389 crystal structure of Os1348 from Pseudomonas sp. Os17 2019-12-18 2020-11-11 Takeuchi, K.,Tsuchiya, W.,Fujimoto, Z.,Yamada, K.,Someya, N.,Yamazaki, T. Discovery of an Antibiotic-Related Small Protein of Biocontrol Strain Pseudomonas sp. Os17 by a Genome-Mining Strategy. Front Microbiol 2020 11 605705 605705 6LVX 33060576 Crystal structure of TLR7/Cpd-1 (SM-374527) complex 2020-02-06 2020-11-11 Tojo, S.,Zhang, Z.,Matsui, H.,Tahara, M.,Ikeguchi, M.,Kochi, M.,Kamada, M.,Shigematsu, H.,Tsutsumi, A.,Adachi, N.,Shibata, T.,Yamamoto, M.,Kikkawa, M.,Senda, T.,Isobe, Y.,Ohto, U.,Shimizu, T. Structural analysis reveals TLR7 dynamics underlying antagonism. Nat Commun 2020 11 5204 5204 6LVY 33060576 Crystal structure of TLR7/Cpd-2 (SM-360320) complex 2020-02-06 2020-11-11 Tojo, S.,Zhang, Z.,Matsui, H.,Tahara, M.,Ikeguchi, M.,Kochi, M.,Kamada, M.,Shigematsu, H.,Tsutsumi, A.,Adachi, N.,Shibata, T.,Yamamoto, M.,Kikkawa, M.,Senda, T.,Isobe, Y.,Ohto, U.,Shimizu, T. Structural analysis reveals TLR7 dynamics underlying antagonism. Nat Commun 2020 11 5204 5204 6LVZ 33060576 Crystal structure of TLR7/Cpd-3 (SM-394830) complex 2020-02-06 2020-11-11 Tojo, S.,Zhang, Z.,Matsui, H.,Tahara, M.,Ikeguchi, M.,Kochi, M.,Kamada, M.,Shigematsu, H.,Tsutsumi, A.,Adachi, N.,Shibata, T.,Yamamoto, M.,Kikkawa, M.,Senda, T.,Isobe, Y.,Ohto, U.,Shimizu, T. Structural analysis reveals TLR7 dynamics underlying antagonism. Nat Commun 2020 11 5204 5204 6LX4 33205029 X-ray structure of human PPARalpha ligand binding domain-fenofibric acid co-crystals obtained by delipidation and co-crystallization 2020-02-10 2020-11-11 Kamata, S.,Oyama, T.,Saito, K.,Honda, A.,Yamamoto, Y.,Suda, K.,Ishikawa, R.,Itoh, T.,Watanabe, Y.,Shibata, T.,Uchida, K.,Suematsu, M.,Ishii, I. PPAR alpha Ligand-Binding Domain Structures with Endogenous Fatty Acids and Fibrates. 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Iscience 2020 23 101727 101727 7CT4 33135670 Crystal structure of D-amino acid oxidase from Rasamsonia emersonii strain YA 2020-08-18 2020-11-11 Shimekake, Y.,Hirato, Y.,Funabashi, R.,Okazaki, S.,Goto, M.,Furuichi, T.,Suzuki, H.,Kera, Y.,Takahashi, S. X-ray structure analysis of a unique D-amino-acid oxidase from the thermophilic fungus Rasamsonia emersonii strain YA. Acta Crystallogr.,Sect.F 2020 76 517 523 6LDY 33303630 Structure antibody D6 in complex with methylated peptide 2019-11-23 2020-11-25 Ishii, M.,Nakakido, M.,Caaveiro, J.M.M.,Kuroda, D.,Okumura, C.J.,Maruyama, T.,Entzminger, K.,Tsumoto, K. Structural basis for antigen recognition by methylated lysine-specific antibodies. J.Biol.Chem. 2020 296 100176 100176 7CFL 33140473 X-ray structure of autolysin Acd24020 catalytic domain from Clostridium difficile 2020-06-26 2020-11-25 Sekiya, H.,Tamai, E.,Kawasaki, J.,Murakami, K.,Kamitori, S. Structural and biochemical characterizations of the novel autolysin Acd24020 from Clostridioides difficile and its full-function catalytic domain as a lytic enzyme. Mol.Microbiol. 2021 115 684 698 7C4K Ancestral L-amino acid oxidase (AncLAAO-N5) ligand free form 2020-05-18 2020-12-02 Nakano, S.,Kozuka, K.,Minamino, Y.,Karasuda, H.,Hasebe, F.,Ito, S. Ancestral L-amino acid oxidases for deracemization and stereoinversion of amino acids Commun Chem 2020 3 0 0 7C4L Anncestral L-amino acid oxidase (AncLAAO-N5) L-Gln binding form 2020-05-18 2020-12-02 Nakano, S.,Kozuka, K.,Minamino, Y.,Karasuda, H.,Hasebe, F.,Ito, S. Ancestral L-amino acid oxidases for deracemization and stereoinversion of amino acids Commun Chem 2020 3 0 0 7C4M Ancestral L-amino acid oxidase (AncLAAO-N5) L-Trp binding form 2020-05-18 2020-12-02 Nakano, S.,Kozuka, K.,Minamino, Y.,Karasuda, H.,Hasebe, F.,Ito, S. 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Acta Crystallogr.,Sect.F 2020 76 590 596 6M1W 33398074 Structure of the 2-Aminoisobutyric acid Monooxygenase Hydroxylase 2020-02-26 2021-01-06 Hibi, M.,Fukuda, D.,Kenchu, C.,Nojiri, M.,Hara, R.,Takeuchi, M.,Aburaya, S.,Aoki, W.,Mizutani, K.,Yasohara, Y.,Ueda, M.,Mikami, B.,Takahashi, S.,Ogawa, J. A three-component monooxygenase from Rhodococcus wratislaviensis may expand industrial applications of bacterial enzymes. Commun Biol 2021 4 16 16 6M5H 32888908 A class C beta-lactamase mutant - Y150F 2020-03-10 2021-01-20 Bae, D.W.,Jung, Y.E.,Jeong, B.G.,Cha, S.S. Novel inhibition mechanism of carbapenems on the ACC-1 class C beta-lactamase. Arch.Biochem.Biophys. 2020 693 108570 108570 6M5Q 32888908 A class C beta-lactamase mutant - Y150F 2020-03-11 2021-01-20 Bae, D.W.,Jung, Y.E.,Jeong, B.G.,Cha, S.S. Novel inhibition mechanism of carbapenems on the ACC-1 class C beta-lactamase. Arch.Biochem.Biophys. 2020 693 108570 108570 6LL1 Oxygen-exposed reduced terminal oxygenase in carbazole 1,9a-dioxygenase 2019-12-21 2021-01-27 Wang, Y.X.,Suzuki-Minakuchi, C.,Nojiri, H. Oxygen-exposed reduced terminal oxygenase in carbazole 1,9a-dioxygenase To Be Published 0 0 0 0 6LLF Biphenyl-2,2',3-triol-soaked resting complex of Oxy and Fd in carbazole 1,9a-dioxygenase 2019-12-23 2021-01-27 Wang, Y.X.,Suzuki-Minakuchi, C.,Nojiri, H. Biphenyl-2,2',3-triol-soaked resting complex of Oxy and Fd in carbazole 1,9a-dioxygenase To Be Published 0 0 0 0 6LLK Biphenyl-2,2',3-triol-soaked terminal oxygenase of carbazole 1,9a-dioxygenase 2019-12-23 2021-01-27 Wang, Y.X.,Suzuki-Minakuchi, C.,Nojiri, H. Biphenyl-2,2',3-triol-soaked terminal oxygenase of carbazole 1,9a-dioxygenase To Be Published 0 0 0 0 6M30 Crystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase N73F 2020-03-02 2021-02-10 Retnoningrum, D.S.,Yoshida, H.,Razani, M.D.,Meidianto, V.F.,Hartanto, A.,Artarini, A.,Ismaya, W.T. Unprecedented Role of The N73-F124 Pair in The Staphylococcus equorum MnSOD Activity. Curr Enzym Inhib 2021 0 0 0 6M30 Crystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase N73F 2020-03-02 2021-02-10 Retnoningrum, D.S.,Yoshida, H.,Razani, M.D.,Meidianto, V.F.,Hartanto, A.,Artarini, A.,Ismaya, W.T. Unprecedented Role of The N73-F124 Pair in The Staphylococcus equorum MnSOD Activity. Curr Enzym Inhib 2021 0 0 0 7DAX Crystal structure of Drosophila melanogaster Noppera-bo, glutathione S-transferase epsilon 14 (DmGSTE14), in TDP013-bound form 2020-10-18 2021-02-10 Koiwai, K.,Morohashi, K.,Inaba, K.,Ebihara, K.,Kojima, H.,Okabe, T.,Yoshino, R.,Hirokawa, T.,Nampo, T.,Fujikawa, Y.,Inoue, H.,Yumoto, F.,Senda, T.,Niwa, R. Non-steroidal inhibitors of Drosophila melanogaster steroidogenic glutathione S -transferase Noppera-bo J Pestic Sci 2021 46 75 87 7DB0 Crystal structure of Drosophila melanogaster Noppera-bo, glutathione S-transferase epsilon 14 (DmGSTE14), in dimedone-bound form 2020-10-18 2021-02-10 Koiwai, K.,Morohashi, K.,Inaba, K.,Ebihara, K.,Kojima, H.,Okabe, T.,Yoshino, R.,Hirokawa, T.,Nampo, T.,Fujikawa, Y.,Inoue, H.,Yumoto, F.,Senda, T.,Niwa, R. Non-steroidal inhibitors of Drosophila melanogaster steroidogenic glutathione S -transferase Noppera-bo J Pestic Sci 2021 46 75 87 7DB1 Crystal structure of Drosophila melanogaster Noppera-bo, glutathione S-transferase epsilon 14 (DmGSTE14), in dimedone- and glutathione-bound form 2020-10-18 2021-02-10 Koiwai, K.,Morohashi, K.,Inaba, K.,Ebihara, K.,Kojima, H.,Okabe, T.,Yoshino, R.,Hirokawa, T.,Nampo, T.,Fujikawa, Y.,Inoue, H.,Yumoto, F.,Senda, T.,Niwa, R. Non-steroidal inhibitors of Drosophila melanogaster steroidogenic glutathione S -transferase Noppera-bo J Pestic Sci 2021 46 75 87 7DB3 Crystal structure of Drosophila melanogaster Noppera-bo, glutathione S-transferase epsilon 14 (DmGSTE14), in TDP011-bound form 2020-10-18 2021-02-10 Koiwai, K.,Morohashi, K.,Inaba, K.,Ebihara, K.,Kojima, H.,Okabe, T.,Yoshino, R.,Hirokawa, T.,Nampo, T.,Fujikawa, Y.,Inoue, H.,Yumoto, F.,Senda, T.,Niwa, R. Non-steroidal inhibitors of Drosophila melanogaster steroidogenic glutathione S -transferase Noppera-bo J Pestic Sci 2021 46 75 87 7DB4 Crystal structure of Drosophila melanogaster Noppera-bo, glutathione S-transferase epsilon 14 (DmGSTE14), in TDP012- and glutathione-bound form 2020-10-18 2021-02-10 Koiwai, K.,Morohashi, K.,Inaba, K.,Ebihara, K.,Kojima, H.,Okabe, T.,Yoshino, R.,Hirokawa, T.,Nampo, T.,Fujikawa, Y.,Inoue, H.,Yumoto, F.,Senda, T.,Niwa, R. Non-steroidal inhibitors of Drosophila melanogaster steroidogenic glutathione S -transferase Noppera-bo J Pestic Sci 2021 46 75 87 6LXU Crystal structure of methionine gamma-lyase from Fusobacterium nucleatum 2020-02-12 2021-02-17 Kezuka, Y. 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Acs Chem.Biol. 2021 16 539 547 7BR5 33645532 Lysozyme-sugar complex in H2O 2020-03-26 2021-03-10 Tanaka, I.,Nishinomiya, R.,Goto, R.,Shimazaki, S.,Chatake, T. Recent structural insights into the mechanism of lysozyme hydrolysis. Acta Crystallogr D Struct Biol 2021 77 288 292 7DEQ 33645532 Lysozyme-sugar complex in D2O 2020-11-04 2021-03-10 Tanaka, I.,Nishinomiya, R.,Goto, R.,Shimazaki, S.,Chatake, T. Recent structural insights into the mechanism of lysozyme hydrolysis. Acta Crystallogr D Struct Biol 2021 77 288 292 7DER 33645532 Lysozyme alone in H2O 2020-11-04 2021-03-10 Tanaka, I.,Nishinomiya, R.,Goto, R.,Shimazaki, S.,Chatake, T. Recent structural insights into the mechanism of lysozyme hydrolysis. Acta Crystallogr D Struct Biol 2021 77 288 292 6M5Y 34735570 Structure of human galectin-1 tandem-repeat mutant with lactose 2020-03-12 2021-03-17 Nonaka, Y.,Ogawa, T.,Shoji, H.,Nishi, N.,Kamitori, S.,Nakamura, T. Crystal structure and conformational stability of a galectin-1 tandem-repeat mutant with a short linker. Glycobiology 2021 0 0 0 6M73 Crystal structure of Enterococcus hirae L-lactate oxidase in complex with D-lactate form ligand 2020-03-16 2021-03-17 Hiraka, K.,Yoshida, H.,Tsugawa, W.,Asano, R.,La Belle, J.T.,Ikebukuro, K.,Sode, K. Structure of lactate oxidase from Enterococcus hirae revealed new aspects of active site loop function: Product-inhibition mechanism and oxygen gatekeeper Protein Sci. 2022 31 0 0 6M73 Crystal structure of Enterococcus hirae L-lactate oxidase in complex with D-lactate form ligand 2020-03-16 2021-03-17 Hiraka, K.,Yoshida, H.,Tsugawa, W.,Asano, R.,La Belle, J.T.,Ikebukuro, K.,Sode, K. Structure of lactate oxidase from Enterococcus hirae revealed new aspects of active site loop function: Product-inhibition mechanism and oxygen gatekeeper Protein Sci. 2022 31 0 0 6M74 Crystal structure of Enterococcus hirae L-lactate oxidase M207L in complex with D-lactate form ligand 2020-03-16 2021-03-17 Hiraka, K.,Yoshida, H.,Tsugawa, W.,Asano, R.,La Belle, J.T.,Ikebukuro, K.,Sode, K. Structure of lactate oxidase from Enterococcus hirae revealed new aspects of active site loop function: Product-inhibition mechanism and oxygen gatekeeper Protein Sci. 2022 31 0 0 6M74 Crystal structure of Enterococcus hirae L-lactate oxidase M207L in complex with D-lactate form ligand 2020-03-16 2021-03-17 Hiraka, K.,Yoshida, H.,Tsugawa, W.,Asano, R.,La Belle, J.T.,Ikebukuro, K.,Sode, K. Structure of lactate oxidase from Enterococcus hirae revealed new aspects of active site loop function: Product-inhibition mechanism and oxygen gatekeeper Protein Sci. 2022 31 0 0 7C20 32703459 Crystal structure of Rabies virus (Nishigahara strain) phosphoprotein C-terminal domain (K214A) 2020-05-06 2021-03-17 Sugiyama, A.,Nomai, T.,Jiang, X.,Minami, M.,Yao, M.,Maenaka, K.,Ito, N.,Gooley, P.R.,Moseley, G.W.,Ose, T. Structural comparison of the C-terminal domain of functionally divergent lyssavirus P proteins. Biochem.Biophys.Res.Commun. 2020 529 507 512 7DFS 33645879 Crystal structure of a novel 4-O-alpha-L-rhamnosyl-beta-D-glucuronidase from Fusarium oxysporum 12S - Rha-GlcA complex 2020-11-09 2021-03-17 Kondo, T.,Kichijo, M.,Nakaya, M.,Takenaka, S.,Arakawa, T.,Kotake, T.,Fushinobu, S.,Sakamoto, T. Biochemical and structural characterization of a novel 4-O-alpha-l-rhamnosyl-beta-d-glucuronidase from Fusarium oxysporum. Febs J. 2021 288 4918 4938 7BOW Hydroxynitrile lyase from Parafonteria laminate 2020-03-20 2021-03-24 Nuylert, A.,Nakabayashi, M.,Yamaguchi, T.,Asano, Y. Hydroxynitrile lyase from Parafonteria laminate To Be Published 0 0 0 0 7BPO Hydroxynitrile lyase from Parafonteria laminate complexed with benzaldehyde 2020-03-23 2021-03-24 Nuylert, A.,Nakabayashi, M.,Yamaguchi, T.,Asano, Y. Hydroxynitrile lyase from Parafonteria laminate complexed with benzaldehyde To Be Published 0 0 0 0 7BR1 Hydroxynitrile lyase from Parafontaria laminate complexed with benzaldehyde prepared by cocrystallization 2020-03-26 2021-04-07 Nuylert, A.,Nakabayashi, M.,Yamaguchi, T.,Asano, Y. Hydroxynitrile lyase from Parafonteria laminate complexed with benzaldehyde prepared by cocrystallization To Be Published 0 0 0 0 7BUG Reduced oxygenase of carbazole 1,9a-dioxygenase 2020-04-06 2021-04-07 Matsuzawa, J.,Wang, Y.X.,Suzuki-Minakuchi, C.,Nojiri, H. Reduced oxygenase of carbazole 1,9a-dioxygenase To Be Published 0 0 0 0 7DDW 33794368 Crystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase S126C 2020-10-30 2021-04-07 Retnoningrum, D.S.,Yoshida, H.,Razani, M.D.,Muliadi, R.,Meidianto, V.F.,Artarini, A.,Ismaya, W.T. The role of S126 in the Staphylococcus equorum MnSOD activity and stability. J.Struct.Biol. 2021 213 107731 107731 7DDW 33794368 Crystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase S126C 2020-10-30 2021-04-07 Retnoningrum, D.S.,Yoshida, H.,Razani, M.D.,Muliadi, R.,Meidianto, V.F.,Artarini, A.,Ismaya, W.T. The role of S126 in the Staphylococcus equorum MnSOD activity and stability. J.Struct.Biol. 2021 213 107731 107731 7E0E 33769476 Crystal structure of mouse interferon alpha2 at 2.1 angstrom resolution 2021-01-27 2021-04-07 Watanabe, H.,Yabe-Wada, T.,Onai, N.,Unno, M. Detailed structure of mouse interferon alpha 2 and its interaction with Sortilin. J.Biochem. 2021 170 265 273 7BXP 2-amino-3-ketobutyrate CoA ligase from Cupriavidus necator 2020-04-20 2021-04-21 Motoyama, T.,Nakano, S.,Hasebe, F.,Miyata, R.,Kumazawa, S.,Miyoshi, N.,Ito, S. Chemoenzymatic synthesis of 3-ethyl-2,5-dimethylpyrazine by L-threonine 3-dehydrogenase and 2-amino-3-ketobutyrate CoA ligase/L-threonine aldolase Commun Chem 2021 4 108 108 7BXQ 2-amino-3-ketobutyrate CoA ligase from Cupriavidus necator L-Threonine binding form 2020-04-20 2021-04-21 Motoyama, T.,Nakano, S.,Hasebe, F.,Miyata, R.,Kumazawa, S.,Miyoshi, N.,Ito, S. Chemoenzymatic synthesis of 3-ethyl-2,5-dimethylpyrazine by L-threonine 3-dehydrogenase and 2-amino-3-ketobutyrate CoA ligase/L-threonine aldolase Commun Chem 2021 4 108 108 7BXR 2-amino-3-ketobutyrate CoA ligase from Cupriavidus necator 3-Hydroxynorvaline binding form 2020-04-20 2021-04-21 Motoyama, T.,Nakano, S.,Hasebe, F.,Miyata, R.,Kumazawa, S.,Miyoshi, N.,Ito, S. Chemoenzymatic synthesis of 3-ethyl-2,5-dimethylpyrazine by L-threonine 3-dehydrogenase and 2-amino-3-ketobutyrate CoA ligase/L-threonine aldolase Commun Chem 2021 4 108 108 7BXS 2-amino-3-ketobutyrate CoA ligase from Cupriavidus necator glycine binding form 2020-04-20 2021-04-21 Motoyama, T.,Nakano, S.,Hasebe, F.,Miyata, R.,Kumazawa, S.,Miyoshi, N.,Ito, S. Chemoenzymatic synthesis of 3-ethyl-2,5-dimethylpyrazine by L-threonine 3-dehydrogenase and 2-amino-3-ketobutyrate CoA ligase/L-threonine aldolase Commun Chem 2021 4 108 108 7CJ4 33838083 Crystal structure of homo dimeric D-allulose 3-epimerase from Methylomonas sp. 2020-07-09 2021-04-21 Yoshida, H.,Yoshihara, A.,Kato, S.,Mochizuki, S.,Akimitsu, K.,Izumori, K.,Kamitori, S. Crystal structure of a novel homodimeric l-ribulose 3-epimerase from Methylomonus sp. 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Crystal structure of a novel homodimeric l-ribulose 3-epimerase from Methylomonus sp. Febs Open Bio 2021 11 1621 1637 7CAV 33872599 Versatile cis-prenyltransferase MM_0014 from Methanosarcina mazei (crystal type: co-FG+DMAPP) 2020-06-10 2021-04-28 Okada, M.,Unno, H.,Emi, K.I.,Matsumoto, M.,Hemmi, H. A versatile cis-prenyltransferase from Methanosarcina mazei catalyzes both C- and O-prenylations. J.Biol.Chem. 2021 296 100679 100679 7CC3 33872599 Versatile cis-prenyltransferase MM_0014 from Methanosarcina mazei (crystal type: co-FG) 2020-06-16 2021-04-28 Okada, M.,Unno, H.,Emi, K.I.,Matsumoto, M.,Hemmi, H. A versatile cis-prenyltransferase from Methanosarcina mazei catalyzes both C- and O-prenylations. J.Biol.Chem. 2021 296 100679 100679 7CJ5 33838083 Crystal structure of homo dimeric D-allulose 3-epimerase from Methylomonas sp. in complex with D-fructose 2020-07-09 2021-04-28 Yoshida, H.,Yoshihara, A.,Kato, S.,Mochizuki, S.,Akimitsu, K.,Izumori, K.,Kamitori, S. Crystal structure of a novel homodimeric l-ribulose 3-epimerase from Methylomonus sp. Febs Open Bio 2021 11 1621 1637 7CUO 33716191 IclR transcription factor complexed with 4-hydroxybenzoic acid from Microbacterium hydrocarbonoxydans 2020-08-23 2021-05-05 Akiyama, T.,Sasaki, Y.,Ito, S.,Yajima, S. Structural basis of the conformational changes in Microbacterium hydrocarbonoxydans IclR transcription factor homolog due to ligand binding. Biochim Biophys Acta Proteins 2021 1869 140644 140644 7DQB 33716191 Crystal structure of an IclR homolog complexed with 4-hydroxybenzoate from Microbacterium hydrocarbonoxydans in P212121 form 2020-12-23 2021-05-05 Akiyama, T.,Sasaki, Y.,Ito, S.,Yajima, S. Structural basis of the conformational changes in Microbacterium hydrocarbonoxydans IclR transcription factor homolog due to ligand binding. Biochim Biophys Acta Proteins 2021 1869 140644 140644 7EOV 34030040 Crystal structure of mouse cytosolic sulfotransferase mSULT2A8 in complex with PAP and cholic acid 2021-04-22 2021-05-05 Teramoto, T.,Nishio, T.,Kurogi, K.,Sakakibara, Y.,Kakuta, Y. The crystal structure of mouse SULT2A8 reveals the mechanism of 7 alpha-hydroxyl, bile acid sulfation. Biochem.Biophys.Res.Commun. 2021 562 15 20 7EFQ 33919837 Crystal structure of hPPARgamma ligand binding domain complexed with rosiglitazone-based fluorescence probe 2021-03-23 2021-05-12 Yoshikawa, C.,Ishida, H.,Ohashi, N.,Itoh, T. Synthesis of a Coumarin-Based PPAR gamma Fluorescence Probe for Competitive Binding Assay. Int J Mol Sci 2021 22 0 0 7CQC 33950020 The NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicus S2P homolog with the PA14 tag inserted between the residues 181 and 184 2020-08-10 2021-05-19 Tamura-Sakaguchi, R.,Aruga, R.,Hirose, M.,Ekimoto, T.,Miyake, T.,Hizukuri, Y.,Oi, R.,Kaneko, M.K.,Kato, Y.,Akiyama, Y.,Ikeguchi, M.,Iwasaki, K.,Nogi, T. Moving toward generalizable NZ-1 labeling for 3D structure determination with optimized epitope-tag insertion. Acta Crystallogr D Struct Biol 2021 77 645 662 7C3A 34196618 Ferredoxin reductase in carbazole 1,9a-dioxygenase 2020-05-11 2021-05-26 Ashikawa, Y.,Fujimoto, Z.,Inoue, K.,Yamane, H.,Nojiri, H. Crystal structure of the ferredoxin reductase component of carbazole 1,9a-dioxygenase from Janthinobacterium sp. J3. Acta Crystallogr D Struct Biol 2021 77 921 932 7C8M 33938220 Crystal structure of IscU wild-type 2020-06-03 2021-05-26 Kunichika, K.,Nakamura, R.,Fujishiro, T.,Takahashi, Y. The Structure of the Dimeric State of IscU Harboring Two Adjacent [2Fe-2S] Clusters Provides Mechanistic Insights into Cluster Conversion to [4Fe-4S]. Biochemistry 2021 60 1569 1572 7D5R 33971157 Structure of the Ca2+-bound C646A mutant of peptidylarginine deiminase type III (PAD3) 2020-09-28 2021-06-02 Funabashi, K.,Sawata, M.,Nagai, A.,Akimoto, M.,Mashimo, R.,Takahara, H.,Kizawa, K.,Thompson, P.R.,Ite, K.,Kitanishi, K.,Unno, M. Structures of human peptidylarginine deiminase type III provide insights into substrate recognition and inhibitor design. Arch.Biochem.Biophys. 2021 708 108911 108911 7CES 35395703 Crystal structure of L-cycloserine-bound form of cysteine desulfurase SufS H121A from Bacillus subtilis 2020-06-24 2021-06-30 Nakamura, R.,Ogawa, S.,Takahashi, Y.,Fujishiro, T. Cycloserine enantiomers inhibit PLP-dependent cysteine desulfurase SufS via distinct mechanisms. Febs J. 2022 0 0 0 7DE4 34101368 Hybrid cluster protein (HCP) from Escherichia coli 2020-11-02 2021-06-30 Fujishiro, T.,Ooi, M.,Takaoka, K. Crystal structure of Escherichia coli class II hybrid cluster protein, HCP, reveals a [4Fe-4S] cluster at the N-terminal protrusion. Febs J. 2021 288 6752 6768 7DTM 34242022 Crystal structure of metallo-beta-lactamase IMP-1 in complex with citrate. 2021-01-06 2021-08-04 Yamaguchi, Y.,Kato, K.,Ichimaru, Y.,Jin, W.,Sakai, M.,Abe, M.,Wachino, J.I.,Arakawa, Y.,Miyagi, Y.,Imai, M.,Fukuishi, N.,Yamagata, Y.,Otsuka, M.,Fujita, M.,Kurosaki, H. Crystal Structures of Metallo-beta-Lactamase (IMP-1) and Its D120E Mutant in Complexes with Citrate and the Inhibitory Effect of the Benzyl Group in Citrate Monobenzyl Ester. J.Med.Chem. 2021 64 10019 10026 7DTN 34242022 Crystal structure of metallo-beta-lactamase IMP-1 mutant (D120E) in complex with citrate. 2021-01-06 2021-08-04 Yamaguchi, Y.,Kato, K.,Ichimaru, Y.,Jin, W.,Sakai, M.,Abe, M.,Wachino, J.I.,Arakawa, Y.,Miyagi, Y.,Imai, M.,Fukuishi, N.,Yamagata, Y.,Otsuka, M.,Fujita, M.,Kurosaki, H. Crystal Structures of Metallo-beta-Lactamase (IMP-1) and Its D120E Mutant in Complexes with Citrate and the Inhibitory Effect of the Benzyl Group in Citrate Monobenzyl Ester. J.Med.Chem. 2021 64 10019 10026 7ESK 34303708 Crystal structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase from Fusarium oxysporum 12S, Ligand free form 2021-05-11 2021-08-04 Kondo, T.,Kichijo, M.,Maruta, A.,Nakaya, M.,Takenaka, S.,Arakawa, T.,Fushinobu, S.,Sakamoto, T. Structural and functional analysis of gum arabic l-rhamnose-alpha-1,4-d-glucuronate lyase establishes a novel polysaccharide lyase family. J.Biol.Chem. 2021 297 101001 101001 7ESL 34303708 Crystal structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase from Fusarium oxysporum 12S, N247A N-glycan free form 2021-05-11 2021-08-04 Kondo, T.,Kichijo, M.,Maruta, A.,Nakaya, M.,Takenaka, S.,Arakawa, T.,Fushinobu, S.,Sakamoto, T. Structural and functional analysis of gum arabic l-rhamnose-alpha-1,4-d-glucuronate lyase establishes a novel polysaccharide lyase family. J.Biol.Chem. 2021 297 101001 101001 7ESN 34303708 Crystal structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase from Fusarium oxysporum 12S, H105F Rha-GlcA complex 2021-05-11 2021-08-04 Kondo, T.,Kichijo, M.,Maruta, A.,Nakaya, M.,Takenaka, S.,Arakawa, T.,Fushinobu, S.,Sakamoto, T. Structural and functional analysis of gum arabic l-rhamnose-alpha-1,4-d-glucuronate lyase establishes a novel polysaccharide lyase family. J.Biol.Chem. 2021 297 101001 101001 7EIH 34358565 Ancestral L-Lys oxidase (ligand free form) 2021-03-31 2021-08-11 Sugiura, S.,Nakano, S.,Niwa, M.,Hasebe, F.,Matsui, D.,Ito, S. Catalytic mechanism of ancestral L-lysine oxidase assigned by sequence data mining. J.Biol.Chem. 2021 297 101043 101043 7EII 34358565 Ancestral L-Lys oxidase K387A variant (L-Lys binding form) 2021-03-31 2021-08-11 Sugiura, S.,Nakano, S.,Niwa, M.,Hasebe, F.,Matsui, D.,Ito, S. Catalytic mechanism of ancestral L-lysine oxidase assigned by sequence data mining. J.Biol.Chem. 2021 297 101043 101043 7EPR 34254784 Partial Consensus L-threonine 3-dehydrogenase (C-Change) 2021-04-27 2021-08-11 Kozuka, K.,Nakano, S.,Asano, Y.,Ito, S. Partial Consensus Design and Enhancement of Protein Function by Secondary-Structure-Guided Consensus Mutations. Biochemistry 2021 60 2309 2319 7EPS 34254784 Partial Consensus L-threonine 3-dehydrogenase (E-change) 2021-04-27 2021-08-11 Kozuka, K.,Nakano, S.,Asano, Y.,Ito, S. Partial Consensus Design and Enhancement of Protein Function by Secondary-Structure-Guided Consensus Mutations. Biochemistry 2021 60 2309 2319 7CSM Crystal structure of Sulfurisphaera tokodaii O6-methylguanine methyltransferase C120S variant 2020-08-15 2021-08-18 Kikuchi, M.,Yamauchi, T.,Iizuka, Y.,Tsunoda, M. Roles of the hydroxy group of tyrosine in crystal structures of Sulfurisphaera tokodaii O6-methylguanine-DNA methyltransferase. Acta Crystallogr.,Sect.F 2021 77 444 451 7CYM 34364873 Crystal structure of LI-Cadherin EC1-4 2020-09-03 2021-08-18 Yui, A.,Caaveiro, J.M.M.,Kuroda, D.,Nakakido, M.,Nagatoishi, S.,Goda, S.,Maruno, T.,Uchiyama, S.,Tsumoto, K. Mechanism of dimerization and structural features of human LI-cadherin. J.Biol.Chem. 2021 297 101054 101054 7EIR 34392362 Crystal structure of chondroitin ABC lyase I in complex with chondroitin disaccharide 6S 2021-03-31 2021-08-25 Takashima, M.,Watanabe, I.,Miyanaga, A.,Eguchi, T. Substrate specificity of Chondroitinase ABC I based on analyses of biochemical reactions and crystal structures in complex with disaccharides. Glycobiology 2021 31 1571 1581 7EIS 34392362 Crystal structure of chondroitin ABC lyase I in complex with chondroitin disaccharide 0S 2021-03-31 2021-08-25 Takashima, M.,Watanabe, I.,Miyanaga, A.,Eguchi, T. Substrate specificity of Chondroitinase ABC I based on analyses of biochemical reactions and crystal structures in complex with disaccharides. Glycobiology 2021 31 1571 1581 7F2R 34473106 Crystal structure of VinK-VinL covalent complex formed with a pantetheineamide cross-linking probe 2021-06-14 2021-09-01 Miyanaga, A.,Ouchi, R.,Kudo, F.,Eguchi, T. Complex structure of the acyltransferase VinK and the carrier protein VinL with a pantetheine cross-linking probe. Acta Crystallogr.,Sect.F 2021 77 294 302 7D4V Crystal structure of Sulfurisphaera tokodaii O6-methylguanine methyltransferase Y91F/C120S variant 2020-09-24 2021-09-29 Kikuchi, M.,Yamauchi, T.,Iizuka, Y.,Tsunoda, M. Roles of the hydroxy group of tyrosine in crystal structures of Sulfurisphaera tokodaii O6-methylguanine-DNA methyltransferase. Acta Crystallogr.,Sect.F 2021 77 444 451 7D5M Crystal structure of inositol dehydrogenase homolog complexed with NAD+ from Azotobacter vinelandii 2020-09-27 2021-09-29 Fukano, K.,Ono, T.,Suzuki, M.,Takenoya, M.,Ito, S.,Sasaki, Y.,Yajima, S. Crystal structure of inositol dehydrogenase complexed with NAD+ from Azotobacter vinelandii To Be Published 0 0 0 0 7DXS 34559526 Crystal structure of the ap1h peptide homodimer. 2021-01-20 2021-09-29 Yagi, S.,Padhi, A.K.,Vucinic, J.,Barbe, S.,Schiex, T.,Nakagawa, R.,Simoncini, D.,Zhang, K.Y.J.,Tagami, S. Seven Amino Acid Types Suffice to Create the Core Fold of RNA Polymerase. J.Am.Chem.Soc. 2021 143 15998 16006 7DXT 34559526 Crystal structure of the chemically synthesized mk2h peptide homodimer 2021-01-20 2021-09-29 Yagi, S.,Padhi, A.K.,Vucinic, J.,Barbe, S.,Schiex, T.,Nakagawa, R.,Simoncini, D.,Zhang, K.Y.J.,Tagami, S. Seven Amino Acid Types Suffice to Create the Core Fold of RNA Polymerase. J.Am.Chem.Soc. 2021 143 15998 16006 7DT6 34225167 Crystal structure of V30M mutated transthyretin in complex with purpurin 2021-01-04 2021-10-13 Kitakami, R.,Inui, K.,Nakagawa, Y.,Sawai, Y.,Katayama, W.,Yokoyama, T.,Okada, T.,Kanamitsu, K.,Nakagawa, S.,Toyooka, N.,Mizuguchi, M. Inhibitory activities of anthraquinone and xanthone derivatives against transthyretin amyloidogenesis. Bioorg.Med.Chem. 2021 44 116292 116292 7DDM Crystal Structure of PenA39 beta-Lactamase 2020-10-29 2021-11-03 Nukaga, M.,Becka, S.A.,Zeiser, E.T.,Hoshino, Y.,LiPuma, J.J.,Papp-Wallace, K.M. Frameshift mutations in genes encoding PBP3 and PBP4 trigger an unusual, extreme beta-lactam resistance phenotype in Burkholderia multivorans To Be Published 0 0 0 0 7V1V 34688653 Difructose dianhydride I synthase/hydrolase (alphaFFase1) from Bifidobacterium dentium, ligand-free form 2021-08-06 2021-11-03 Kashima, T.,Okumura, K.,Ishiwata, A.,Kaieda, M.,Terada, T.,Arakawa, T.,Yamada, C.,Shimizu, K.,Tanaka, K.,Kitaoka, M.,Ito, Y.,Fujita, K.,Fushinobu, S. Identification of difructose dianhydride I synthase/hydrolase from an oral bacterium establishes a novel glycoside hydrolase family. J.Biol.Chem. 2021 297 101324 101324 7EXW 34735571 GH127 beta-L-arabinofuranosidase HypBA1 covalently complexed with alpha-L-arabinofuranosylamide 2021-05-28 2021-11-17 Maruyama, S.,Sawano, K.,Amaki, S.,Suzuki, T.,Narita, S.,Kimura, K.,Arakawa, T.,Yamada, C.,Ito, Y.,Dohmae, N.,Fujita, K.,Ishiwata, A.,Fushinobu, S. Substrate complex structure, active site labeling and catalytic role of the zinc ion in cysteine glycosidase. Glycobiology 2022 32 171 180 7DQQ Crystal structure of Sulfurisphaera tokodaii O6-methylguanine methyltransferase Y91F/C120S variant in complex with O6-methyldeoxyguanosine 2020-12-24 2021-12-15 Kikuchi, M.,Yamauchi, T.,Iizuka, Y.,Tsunoda, M. Roles of the hydroxy group of tyrosine in crystal structures of Sulfurisphaera tokodaii O6-methylguanine-DNA methyltransferase. Acta Crystallogr.,Sect.F 2021 77 444 451 7DQT Crystal structure of O6-methylguanine methyltransferase Y91F variant 2020-12-24 2021-12-15 Kikuchi, M.,Yamauchi, T.,Iizuka, Y.,Tsunoda, M. Roles of the hydroxy group of tyrosine in crystal structures of Sulfurisphaera tokodaii O6-methylguanine-DNA methyltransferase. Acta Crystallogr.,Sect.F 2021 77 444 451 7E1P Crystal structure of Sulfurisphaera tokodaii O6-methylguanine methyltransferase C120S variant in complex with O6-methyldeoxyguanosine 2021-02-03 2021-12-15 Kikuchi, M.,Yamauchi, T.,Iizuka, Y.,Tsunoda, M. Roles of the hydroxy group of tyrosine in crystal structures of Sulfurisphaera tokodaii O6-methylguanine-DNA methyltransferase. Acta Crystallogr.,Sect.F 2021 77 444 451 7FB7 34801826 Crystal structure of human UHRF1 TTD in complex with 5-amino-2,4-dimethylpyridine 2021-07-08 2022-01-05 Kori, S.,Shibahashi, Y.,Ekimoto, T.,Nishiyama, A.,Yoshimi, S.,Yamaguchi, K.,Nagatoishi, S.,Ohta, M.,Tsumoto, K.,Nakanishi, M.,Defossez, P.A.,Ikeguchi, M.,Arita, K. Structure-based screening combined with computational and biochemical analyses identified the inhibitor targeting the binding of DNA Ligase 1 to UHRF1. Bioorg.Med.Chem. 2021 52 116500 116500 7VEE 34985877 The ligand-free structure of GfsA KSQ-AT didomain 2021-09-08 2022-01-12 Chisuga, T.,Nagai, A.,Miyanaga, A.,Goto, E.,Kishikawa, K.,Kudo, F.,Eguchi, T. Structural Insight into the Reaction Mechanism of Ketosynthase-Like Decarboxylase in a Loading Module of Modular Polyketide Synthases. Acs Chem.Biol. 2022 17 198 206 7VEF 34985877 The structure of GfsA KSQ-AT didomain in complex with a malonate substrate analog 2021-09-08 2022-01-12 Chisuga, T.,Nagai, A.,Miyanaga, A.,Goto, E.,Kishikawa, K.,Kudo, F.,Eguchi, T. Structural Insight into the Reaction Mechanism of Ketosynthase-Like Decarboxylase in a Loading Module of Modular Polyketide Synthases. Acs Chem.Biol. 2022 17 198 206 7FFH 35039506 Diarylpentanoid-producing polyketide synthase (N199L mutant) 2021-07-23 2022-01-19 Wang, X.H.,Gao, B.W.,Nakashima, Y.,Mori, T.,Zhang, Z.X.,Kodama, T.,Lee, Y.E.,Zhang, Z.K.,Wong, C.P.,Liu, Q.Q.,Qi, B.W.,Wang, J.,Li, J.,Liu, X.,Abe, I.,Morita, H.,Tu, P.F.,Shi, S.P. Identification of a diarylpentanoid-producing polyketide synthase revealing an unusual biosynthetic pathway of 2-(2-phenylethyl)chromones in agarwood. Nat Commun 2022 13 348 348 7EBU 35172816 Crystal structure of Aedes aegypti Noppera-bo, glutathione S-transferase epsilon 8, in Daidzein- and glutathione-bound form 2021-03-11 2022-01-26 Inaba, K.,Ebihara, K.,Senda, M.,Yoshino, R.,Sakuma, C.,Koiwai, K.,Takaya, D.,Watanabe, C.,Watanabe, A.,Kawashima, Y.,Fukuzawa, K.,Imamura, R.,Kojima, H.,Okabe, T.,Uemura, N.,Kasai, S.,Kanuka, H.,Nishimura, T.,Watanabe, K.,Inoue, H.,Fujikawa, Y.,Honma, T.,Hirokawa, T.,Senda, T.,Niwa, R. Molecular action of larvicidal flavonoids on ecdysteroidogenic glutathione S-transferase Noppera-bo in Aedes aegypti. Bmc Biol. 2022 20 43 43 7EBW 35172816 Crystal structure of Aedes aegypti Noppera-bo, glutathione S-transferase epsilon 8, in desmethylglycitein and glutathione-bound form 2021-03-11 2022-01-26 Inaba, K.,Ebihara, K.,Senda, M.,Yoshino, R.,Sakuma, C.,Koiwai, K.,Takaya, D.,Watanabe, C.,Watanabe, A.,Kawashima, Y.,Fukuzawa, K.,Imamura, R.,Kojima, H.,Okabe, T.,Uemura, N.,Kasai, S.,Kanuka, H.,Nishimura, T.,Watanabe, K.,Inoue, H.,Fujikawa, Y.,Honma, T.,Hirokawa, T.,Senda, T.,Niwa, R. Molecular action of larvicidal flavonoids on ecdysteroidogenic glutathione S-transferase Noppera-bo in Aedes aegypti. Bmc Biol. 2022 20 43 43 7V6I 35092420 Crystal structure of lacto-N-biosidase BsaX from Bifidobacterium saguini, lacto-N-biose complex 2021-08-20 2022-02-09 Yamada, C.,Katayama, T.,Fushinobu, S. Crystal structures of glycoside hydrolase family 136 lacto-N-biosidases from monkey gut- and human adult gut bacteria. Biosci.Biotechnol.Biochem. 2022 86 464 475 7V6M 35092420 Crystal structure of lacto-N-biosidase TnX from Tynzenella nexilis, lacto-N-biose complex 2021-08-20 2022-02-09 Yamada, C.,Katayama, T.,Fushinobu, S. Crystal structures of glycoside hydrolase family 136 lacto-N-biosidases from monkey gut- and human adult gut bacteria. Biosci.Biotechnol.Biochem. 2022 86 464 475 7VB3 35101448 Crystal structure of hydroxynitrile lyase from Linum usitatissimum 2021-08-30 2022-02-09 Zheng, D.,Nakabayashi, M.,Asano, Y. Structural characterization of Linum usitatissimum hydroxynitrile lyase: A new cyanohydrin decomposition mechanism involving a cyano-zinc complex. J.Biol.Chem. 2022 298 101650 101650 7VB5 35101448 Crystal structure of hydroxynitrile lyase from Linum usitatissimum complexed with acetone cyanohydrin 2021-08-30 2022-02-09 Zheng, D.,Nakabayashi, M.,Asano, Y. Structural characterization of Linum usitatissimum hydroxynitrile lyase: A new cyanohydrin decomposition mechanism involving a cyano-zinc complex. J.Biol.Chem. 2022 298 101650 101650 7VC6 35120929 The structure of beta-xylosidase from Phanerochaete chrysosporium(PcBxl3) 2021-09-01 2022-02-09 Kojima, K.,Sunagawa, N.,Mikkelsen, N.E.,Hansson, H.,Karkehabadi, S.,Samejima, M.,Sandgren, M.,Igarashi, K. Comparison of glycoside hydrolase family 3 beta-xylosidases from basidiomycetes and ascomycetes reveals evolutionarily distinct xylan degradation systems. J.Biol.Chem. 2022 298 101670 101670 7VC7 35120929 The structure of beta-xylosidase from Phanerochaete chrysosporium(PcBxl3) 2021-09-01 2022-02-09 Kojima, K.,Sunagawa, N.,Mikkelsen, N.E.,Hansson, H.,Karkehabadi, S.,Samejima, M.,Sandgren, M.,Igarashi, K. Comparison of glycoside hydrolase family 3 beta-xylosidases from basidiomycetes and ascomycetes reveals evolutionarily distinct xylan degradation systems. J.Biol.Chem. 2022 298 101670 101670 7VGO 35094218 Hen egg lysozyme 2021-09-17 2022-02-23 Oda, M.,Sano, T.,Kamatari, Y.O.,Abe, Y.,Ikura, T.,Ito, N. Structural Analysis of Hen Egg Lysozyme Refolded after Denaturation at Acidic pH. Protein J. 2022 41 71 78 7E6D 35395703 Crystal structure of cysteine desulfurase SufS R376A from Bacillus subtilis 2021-02-22 2022-03-02 Nakamura, R.,Ogawa, S.,Takahashi, Y.,Fujishiro, T. Cycloserine enantiomers inhibit PLP-dependent cysteine desulfurase SufS via distinct mechanisms. Febs J. 2022 289 5947 5970 7E6E 35395703 Crystal structure of PMP-bound form of cysteine desulfurase SufS R376A from Bacillus subtilis in D-cycloserine-inhibition 2021-02-22 2022-03-02 Nakamura, R.,Ogawa, S.,Takahashi, Y.,Fujishiro, T. Cycloserine enantiomers inhibit PLP-dependent cysteine desulfurase SufS via distinct mechanisms. Febs J. 2022 289 5947 5970 7E9X Trehalase of Arabidopsis thaliana acid mutant -D380A 2021-03-05 2022-03-09 Taguchi, Y.,Saburi, W.,Yu, J.,Imai, R.,Yao, M.,Mori, H. pH-dependent alteration of substrate specificity of plant trehalase and its molecular mechanism To Be Published 0 0 0 0 7VCO 35267055 Frischella perrara beta-fructofuranosidase 2021-09-03 2022-03-09 Kubota, A.,Kawai, R.,Li, D.,Kozono, T.,Sasaki, N.,Nishikawa, A.,Fujii, T.,Tochio, T.,Tonozuka, T. Enzymatic and structural characterization of beta-fructofuranosidase from the honeybee gut bacterium Frischella perrara. Appl.Microbiol.Biotechnol. 2022 106 2455 2470 7VCP 35267055 Frischella perrara beta-fructofuranosidase in complex with fructose 2021-09-03 2022-03-09 Kubota, A.,Kawai, R.,Li, D.,Kozono, T.,Sasaki, N.,Nishikawa, A.,Fujii, T.,Tochio, T.,Tonozuka, T. Enzymatic and structural characterization of beta-fructofuranosidase from the honeybee gut bacterium Frischella perrara. Appl.Microbiol.Biotechnol. 2022 106 2455 2470 7VKW 35065074 The apo structure of beta-1,2-glucosyltransferase from Ignavibacterium album 2021-10-01 2022-03-09 Kobayashi, K.,Shimizu, H.,Tanaka, N.,Kuramochi, K.,Nakai, H.,Nakajima, M.,Taguchi, H. Characterization and structural analyses of a novel glycosyltransferase acting on the beta-1,2-glucosidic linkages. J.Biol.Chem. 2022 298 101606 101606 7VKX 35065074 The complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with glucose 2021-10-01 2022-03-09 Kobayashi, K.,Shimizu, H.,Tanaka, N.,Kuramochi, K.,Nakai, H.,Nakajima, M.,Taguchi, H. Characterization and structural analyses of a novel glycosyltransferase acting on the beta-1,2-glucosidic linkages. J.Biol.Chem. 2022 298 101606 101606 7VKY 35065074 The complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with sophorose 2021-10-01 2022-03-09 Kobayashi, K.,Shimizu, H.,Tanaka, N.,Kuramochi, K.,Nakai, H.,Nakajima, M.,Taguchi, H. 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J.Biol.Chem. 2022 298 101606 101606 7VL2 35065074 The complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with ethyl alpha-D-Glucoside 2021-10-01 2022-03-09 Kobayashi, K.,Shimizu, H.,Tanaka, N.,Kuramochi, K.,Nakai, H.,Nakajima, M.,Taguchi, H. Characterization and structural analyses of a novel glycosyltransferase acting on the beta-1,2-glucosidic linkages. J.Biol.Chem. 2022 298 101606 101606 7VL3 35065074 The complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with phenyl alpha-D-glucoside 2021-10-01 2022-03-09 Kobayashi, K.,Shimizu, H.,Tanaka, N.,Kuramochi, K.,Nakai, H.,Nakajima, M.,Taguchi, H. Characterization and structural analyses of a novel glycosyltransferase acting on the beta-1,2-glucosidic linkages. 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J.Biol.Chem. 2022 298 101606 101606 7VL6 35065074 The complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with arbutin 2021-10-01 2022-03-09 Kobayashi, K.,Shimizu, H.,Tanaka, N.,Kuramochi, K.,Nakai, H.,Nakajima, M.,Taguchi, H. Characterization and structural analyses of a novel glycosyltransferase acting on the beta-1,2-glucosidic linkages. J.Biol.Chem. 2022 298 101606 101606 7VL7 35065074 The complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with esculin 2021-10-01 2022-03-09 Kobayashi, K.,Shimizu, H.,Tanaka, N.,Kuramochi, K.,Nakai, H.,Nakajima, M.,Taguchi, H. Characterization and structural analyses of a novel glycosyltransferase acting on the beta-1,2-glucosidic linkages. J.Biol.Chem. 2022 298 101606 101606 7EI7 RNA kink-turn motif with 2-aminopurine 2021-03-30 2022-03-30 Kondo, J.,Saisu, S. 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Bioorg.Med.Chem.Lett. 2022 64 128676 128676 7WNP 35546796 Crystallographic structure of copper amine oxidase from Arthrobacter glibiformis at pD 7.4 determined by both X-ray and neutron diffraction data at 1.72 angstrom resolution. 2022-01-19 2022-04-20 Murakawa, T.,Kurihara, K.,Adachi, M.,Kusaka, K.,Tanizawa, K.,Okajima, T. Re-evaluation of protein neutron crystallography with and without X-ray/neutron joint refinement. Iucrj 2022 9 342 348 7WNP 35546796 Crystallographic structure of copper amine oxidase from Arthrobacter glibiformis at pD 7.4 determined by both X-ray and neutron diffraction data at 1.72 angstrom resolution. 2022-01-19 2022-04-20 Murakawa, T.,Kurihara, K.,Adachi, M.,Kusaka, K.,Tanizawa, K.,Okajima, T. Re-evaluation of protein neutron crystallography with and without X-ray/neutron joint refinement. Iucrj 2022 9 342 348 7X87 35065074 The complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with sophotetraose observed as sophorose 2022-03-11 2022-04-20 Kobayashi, K.,Shimizu, H.,Tanaka, N.,Kuramochi, K.,Nakai, H.,Nakajima, M.,Taguchi, H. Characterization and structural analyses of a novel glycosyltransferase acting on the beta-1,2-glucosidic linkages. J Biol Chem 2022 298 101606 0 7ECQ Crystal structure of FAM3A 2021-03-13 2022-04-27 Chang, Z.,Shi, C. High Resolution Crystal Structure of FAM3A shed lights on its function on beta-oxidation To Be Published 0 0 0 0 7V91 35652665 Crystal Structure of the Catalytic Domain of a Family GH19 Chitinase from Gazyumaru, Ficus microcarpa 2021-08-24 2022-04-27 Kozome, D.,Uechi, K.,Taira, T.,Fukada, H.,Kubota, T.,Ishikawa, K. Structural Analysis and Construction of a Thermostable Antifungal Chitinase. Appl.Environ.Microbiol. 2022 88 0 0 7XIT 36184946 Crystal structure of engineered HIV-1 Reverse Transcriptase RNase H domain complexed with nitrofuran methoxy(methoxycarbonyl)phenyl ester 2022-04-14 2022-04-27 Lu, H.,Komukai, Y.,Usami, K.,Guo, Y.,Qiao, X.,Nukaga, M.,Hoshino, T. Computational and Crystallographic Analysis of Binding Structures of Inhibitory Compounds for HIV-1 RNase H Activity. J.Chem.Inf.Model. 2022 62 6762 6774 7XJ7 36184946 Crystal structure of engineered HIV-1 Reverse Transcriptase RNase H domain complexed with nitrofuran methoxy(methoxycarbonyl)phenyl ester 2022-04-15 2022-04-27 Lu, H.,Komukai, Y.,Usami, K.,Guo, Y.,Qiao, X.,Nukaga, M.,Hoshino, T. Computational and Crystallographic Analysis of Binding Structures of Inhibitory Compounds for HIV-1 RNase H Activity. J.Chem.Inf.Model. 2022 62 6762 6774 7EPQ 34214602 Crystal structure of exopolyphosphatase (PPX) from Porphyromonas gingivalis in complex with sulfate and magnesium ions 2021-04-27 2022-05-11 Zhang, A.,Lu, Z.,Xu, Y.,Qi, T.,Li, W.,Zhang, L.,Cui, Z. The structure of exopolyphosphatase (PPX) from Porphyromonas gingivalis in complex with substrate analogs and magnesium ions reveals the basis for polyphosphate processivity. J.Struct.Biol. 2021 213 107767 107767 7F76 Crystal Structure of FMN-dependent NADPH-quinone reductase (azoR) from Bacillus cohnii 2021-06-28 2022-05-11 Yoneda, K.,Sakuraba, H.,Ohshima, T. Crystal Structure of FMN-dependent NADPH-quinone reductase (azoR) from Bacillus cohnii To Be Published 0 0 0 0 7FAO 35054886 Top7 surface mutant K42A Q43A K46A K57S K58S, and I68R 2021-07-07 2022-05-18 Ito, Y.,Araki, T.,Shiga, S.,Konno, H.,Makabe, K. Surface Engineering of Top7 to Facilitate Structure Determination. Int J Mol Sci 2022 23 0 0 7WGN 35563117 X-ray structure of human PPAR delta ligand binding domain-pemafibrate co-crystals obtained by co-crystallization 2021-12-28 2022-05-25 Honda, A.,Kamata, S.,Akahane, M.,Machida, Y.,Uchii, K.,Shiiyama, Y.,Habu, Y.,Miyawaki, S.,Kaneko, C.,Oyama, T.,Ishii, I. Functional and Structural Insights into Human PPAR alpha / delta / gamma Subtype Selectivity of Bezafibrate, Fenofibric Acid, and Pemafibrate. Int J Mol Sci 2022 23 0 0 7WGO 35563117 X-ray structure of human PPAR gamma ligand binding domain-bezafibrate co-rystals obtained by co-crystallization 2021-12-28 2022-05-25 Honda, A.,Kamata, S.,Akahane, M.,Machida, Y.,Uchii, K.,Shiiyama, Y.,Habu, Y.,Miyawaki, S.,Kaneko, C.,Oyama, T.,Ishii, I. Functional and Structural Insights into Human PPAR alpha / delta / gamma Subtype Selectivity of Bezafibrate, Fenofibric Acid, and Pemafibrate. Int J Mol Sci 2022 23 0 0 7WGQ 35563117 X-ray structure of human PPAR gamma ligand binding domain-pemafibrate co-crystals obtained by co-crystallization 2021-12-28 2022-05-25 Honda, A.,Kamata, S.,Akahane, M.,Machida, Y.,Uchii, K.,Shiiyama, Y.,Habu, Y.,Miyawaki, S.,Kaneko, C.,Oyama, T.,Ishii, I. Functional and Structural Insights into Human PPAR alpha / delta / gamma Subtype Selectivity of Bezafibrate, Fenofibric Acid, and Pemafibrate. Int J Mol Sci 2022 23 0 0 7VOS 35594350 High-resolution neutron and X-ray joint refined structure of high-potential iron-sulfur protein in the oxidized state 2021-10-14 2022-06-01 Hanazono, Y.,Hirano, Y.,Takeda, K.,Kusaka, K.,Tamada, T.,Miki, K. Revisiting the concept of peptide bond planarity in an iron-sulfur protein by neutron structure analysis. 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J.Struct.Biol. 2022 214 107874 107874 7F4B 35835834 The crystal structure of the immature apo-enzyme of homoserine dehydrogenase from the hyperthermophilic archaeon Sulfurisphaera tokodaii. 2021-06-18 2022-06-22 Kubota, T.,Kurihara, E.,Watanabe, K.,Ogata, K.,Kaneko, R.,Goto, M.,Ohshima, T.,Yoshimune, K. Conformational changes in the catalytic region are responsible for heat-induced activation of hyperthermophilic homoserine dehydrogenase. Commun Biol 2022 5 704 704 7XKM 35641885 Crystal structure of DNA-Ag(I) rod comprising a one-dimensional array of 11 silver ions 2022-04-20 2022-07-06 Atsugi, T.,Ono, A.,Tasaka, M.,Eguchi, N.,Fujiwara, S.,Kondo, J. A Novel Ag I -DNA Rod Comprising a One-Dimensional Array of 11 Silver Ions within a Double Helical Structure. Angew.Chem.Int.Ed.Engl. 2022 61 0 0 7FDD 38104859 A Crystal structure of OspA mutant 2021-07-16 2022-07-20 Kiya, M.,Shiga, S.,Ding, P.,Koide, S.,Makabe, K. beta-Strand-mediated Domain-swapping in the Absence of Hydrophobic Core Repacking. J.Mol.Biol. 2024 436 168405 168405 7FJR 38104859 Structure of a mutant of OspA 2021-08-04 2022-08-10 Kiya, M.,Shiga, S.,Ding, P.,Koide, S.,Makabe, K. beta-Strand-mediated Domain-swapping in the Absence of Hydrophobic Core Repacking. J.Mol.Biol. 2024 436 168405 168405 7EOZ The structure of rice Defective Pollen Wall (DPW) in the complex with its cofactor NADP 2021-04-24 2022-08-24 Wang, W.,Li, G.,Wang, J.,Yan, L.M. Defective Pollen Wall Bridges Lipid and Sugar Metabolisms in Plant Male Reproductive Development To Be Published 0 0 0 0 7WUX 35998388 Crystal structure of AziU3/U2 complexed with (5S,6S)-O7-sulfo DADH from Streptomyces sahachiroi 2022-02-09 2022-09-07 Kurosawa, S.,Hasebe, F.,Okamura, H.,Yoshida, A.,Matsuda, K.,Sone, Y.,Tomita, T.,Shinada, T.,Takikawa, H.,Kuzuyama, T.,Kosono, S.,Nishiyama, M. Molecular Basis for Enzymatic Aziridine Formation via Sulfate Elimination. J.Am.Chem.Soc. 2022 144 16164 16170 7XTL 36106687 Crystal structure of the C-terminal domain of human N-acetylglucosaminyltransferase IVa 2022-05-17 2022-09-28 Oka, N.,Mori, S.,Ikegaya, M.,Park, E.Y.,Miyazaki, T. Crystal structure and sugar-binding ability of the C-terminal domain of N-acetylglucosaminyltransferase IV establish a new carbohydrate-binding module family. Glycobiology 2022 32 1153 1163 7Y8V 36302388 Crystal structure of AlbEF homolog mutant (AlbF-H54A/H58A) from Quasibacillus thermotolerans 2022-06-24 2022-10-12 Ishida, K.,Nakamura, A.,Kojima, S. Crystal structure of the AlbEF complex involved in subtilosin A biosynthesis. Structure 2022 30 1637 0 7W81 35500652 Crystal structure of the heme-bound form of the linker-NEAT3 region of IsdH from Staphylococcus aureus 2021-12-07 2022-10-19 Valenciano-Bellido, S.,Caaveiro, J.M.M.,Morante, K.,Sushko, T.,Nakakido, M.,Nagatoishi, S.,Tsumoto, K. Structure and role of the linker domain of the iron surface-determinant protein IsdH in heme transportation in Staphylococcus aureus. J.Biol.Chem. 2022 298 101995 101995 7YBD 36166824 Crystal structure of sliding DNA clamp of Clostridioides difficile 2022-06-29 2022-10-19 Hishiki, A.,Okazaki, S.,Hara, K.,Hashimoto, H. Crystal structure of the sliding DNA clamp from the Gram-positive anaerobic bacterium Clostridioides difficile. J.Biochem. 2022 173 13 20 7X5G 36454022 Nrf2 (A510Y)-MafG heterodimer bound with CsMBE2 2022-03-04 2022-11-09 Sengoku, T.,Shiina, M.,Suzuki, K.,Hamada, K.,Sato, K.,Uchiyama, A.,Kobayashi, S.,Oguni, A.,Itaya, H.,Kasahara, K.,Moriwaki, H.,Watanabe, C.,Honma, T.,Okada, C.,Baba, S.,Ohta, T.,Motohashi, H.,Yamamoto, M.,Ogata, K. Structural basis of transcription regulation by CNC family transcription factor, Nrf2. Nucleic Acids Res. 2022 50 12543 12557 7XAR 36229406 Crystal structure of 3C-like protease from SARS-CoV-2 in complex with covalent inhibitor 2022-03-18 2022-11-09 Hirose, Y.,Shindo, N.,Mori, M.,Onitsuka, S.,Isogai, H.,Hamada, R.,Hiramoto, T.,Ochi, J.,Takahashi, D.,Ueda, T.,Caaveiro, J.M.M.,Yoshida, Y.,Ohdo, S.,Matsunaga, N.,Toba, S.,Sasaki, M.,Orba, Y.,Sawa, H.,Sato, A.,Kawanishi, E.,Ojida, A. Discovery of Chlorofluoroacetamide-Based Covalent Inhibitors for Severe Acute Respiratory Syndrome Coronavirus 2 3CL Protease. J.Med.Chem. 2022 65 13852 13865 7Y4K 36508422 Crystal structure of Ricin A chain bound with N2-(2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)glycyl-L-phenylalanyl-N6-((benzyloxy)carbonyl)-L-ornitine 2022-06-15 2022-11-16 Saito, R.,Goto, M.,Katakura, S.,Ohba, T.,Kawata, R.,Nagatsu, K.,Higashi, S.,Kurisu, K.,Matsumoto, K.,Ohtsuka, K. Pterin-based small molecule inhibitor capable of binding to the secondary pocket in the active site of ricin-toxin A chain. Plos One 2022 17 0 0 7Y4M 36508422 Crystal structure of Ricin A chain bound with N2-(2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)glycyl-L-phenylalanyl-N6-((benzyloxy)carbonyl)-L-lysine 2022-06-15 2022-11-16 Saito, R.,Goto, M.,Katakura, S.,Ohba, T.,Kawata, R.,Nagatsu, K.,Higashi, S.,Kurisu, K.,Matsumoto, K.,Ohtsuka, K. Pterin-based small molecule inhibitor capable of binding to the secondary pocket in the active site of ricin-toxin A chain. Plos One 2022 17 0 0 7YKE 36478634 Crystal structure of chondroitin ABC lyase I in complex with chondroitin disaccharide 4,6-sulfate 2022-07-22 2022-11-30 Watanabe, I.,Miyanaga, A.,Hoshi, H.,Suzuki, K.,Eguchi, T. Biochemical and crystallographic assessments of the effect of 4,6-O-disulfated disaccharide moieties in chondroitin sulfate E on chondroitinase ABC I activity. Febs J. 2023 290 2379 2393 7W6W 36701098 Crystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase L169W 2021-12-02 2022-12-07 Retnoningrum, D.S.,Yoshida, H.,Pajatiwi, I.,Muliadi, R.,Utami, R.A.,Artarini, A.,Ismaya, W.T. Introducing Intermolecular Interaction to Strengthen the Stability of MnSOD Dimer. Appl.Biochem.Biotechnol. 2023 195 4537 4551 7W6W 36701098 Crystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase L169W 2021-12-02 2022-12-07 Retnoningrum, D.S.,Yoshida, H.,Pajatiwi, I.,Muliadi, R.,Utami, R.A.,Artarini, A.,Ismaya, W.T. Introducing Intermolecular Interaction to Strengthen the Stability of MnSOD Dimer. Appl.Biochem.Biotechnol. 2023 195 4537 4551 7WRR 36441206 X-ray structure of Thermus thermophilus HB8 transketorase in complex with TPP and MES 2022-01-27 2022-12-07 Yoshihara, A.,Takamatsu, Y.,Mochizuki, S.,Yoshida, H.,Masui, R.,Izumori, K.,Kamitori, S. Structural and biochemical characterizations of Thermus thermophilus HB8 transketolase producing a heptulose. Appl.Microbiol.Biotechnol. 2023 107 233 245 7WRT 36441206 X-ray structure ofThermus thermophilus HB8 transketorase demonstrate in complex with TPP and D-erythrose-4-phosphate 2022-01-27 2022-12-07 Yoshihara, A.,Takamatsu, Y.,Mochizuki, S.,Yoshida, H.,Masui, R.,Izumori, K.,Kamitori, S. Structural and biochemical characterizations of Thermus thermophilus HB8 transketolase producing a heptulose. Appl.Microbiol.Biotechnol. 2023 107 233 245 7XZS 35998389 Crystal structure of Ricin A chain bound with (2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)-L-tyrosine 2022-06-03 2022-12-21 Goto, M.,Higashi, S.,Ohba, T.,Kawata, R.,Nagatsu, K.,Suzuki, S.,Anslyn, E.V.,Saito, R. Conformational change in ricin toxin A-Chain: A critical factor for inhibitor binding to the secondary pocket. Biochem.Biophys.Res.Commun. 2022 627 1 4 7XZT 35998389 Crystal structure of Ricin A chain bound with (2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)-D-tyrosine 2022-06-03 2022-12-21 Goto, M.,Higashi, S.,Ohba, T.,Kawata, R.,Nagatsu, K.,Suzuki, S.,Anslyn, E.V.,Saito, R. Conformational change in ricin toxin A-Chain: A critical factor for inhibitor binding to the secondary pocket. 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Biochem.Biophys.Res.Commun. 2022 627 1 4 7Y02 35998389 Crystal structure of Ricin A chain bound with (S)-2-(2-amino-4-oxo-3,4-dihydropteridine-7-carboxamido)-3-(4-fluorophenyl)propanoic acid 2022-06-03 2022-12-21 Goto, M.,Higashi, S.,Ohba, T.,Kawata, R.,Nagatsu, K.,Suzuki, S.,Anslyn, E.V.,Saito, R. Conformational change in ricin toxin A-Chain: A critical factor for inhibitor binding to the secondary pocket. Biochem.Biophys.Res.Commun. 2022 627 1 4 7Y03 35998389 Crystal structure of Ricin A chain bound with (S)-2-(2-amino-4-oxo-3,4-dihydropteridine-7-carboxamido)-2-phenylacetic acid 2022-06-03 2022-12-21 Goto, M.,Higashi, S.,Ohba, T.,Kawata, R.,Nagatsu, K.,Suzuki, S.,Anslyn, E.V.,Saito, R. Conformational change in ricin toxin A-Chain: A critical factor for inhibitor binding to the secondary pocket. Biochem.Biophys.Res.Commun. 2022 627 1 4 7Y05 35998389 Crystal structure of Ricin A chain bound with (R)-2-(2-amino-4-oxo-3,4-dihydropteridine-7-carboxamido)-2-phenylacetic acid 2022-06-03 2022-12-21 Goto, M.,Higashi, S.,Ohba, T.,Kawata, R.,Nagatsu, K.,Suzuki, S.,Anslyn, E.V.,Saito, R. Conformational change in ricin toxin A-Chain: A critical factor for inhibitor binding to the secondary pocket. Biochem.Biophys.Res.Commun. 2022 627 1 4 7Y06 35998389 Crystal structure of Ricin A chain bound with (S)-2-(2-amino-4-oxo-3,4-dihydropteridine-7-carboxamido)-4-phenylbutanoic acid 2022-06-03 2022-12-21 Goto, M.,Higashi, S.,Ohba, T.,Kawata, R.,Nagatsu, K.,Suzuki, S.,Anslyn, E.V.,Saito, R. Conformational change in ricin toxin A-Chain: A critical factor for inhibitor binding to the secondary pocket. Biochem.Biophys.Res.Commun. 2022 627 1 4 7Y07 35998389 Crystal structure of Ricin A chain bound with (S)-2-amino-N-(1-hydroxy-3-phenylpropan-2-yl)-4-oxo-3,4-dihydropteridine-7-carboxamide 2022-06-03 2022-12-21 Goto, M.,Higashi, S.,Ohba, T.,Kawata, R.,Nagatsu, K.,Suzuki, S.,Anslyn, E.V.,Saito, R. Conformational change in ricin toxin A-Chain: A critical factor for inhibitor binding to the secondary pocket. Biochem.Biophys.Res.Commun. 2022 627 1 4 8H6S 36512613 Structure of acyltransferase VinK in complex with the loading acyl carrier protein of vicenistatin PKS 2022-10-18 2022-12-21 Miyanaga, A.,Kawada, K.,Chisuga, T.,Kudo, F.,Eguchi, T. Structural Basis of Transient Interactions of Acyltransferase VinK with the Loading Acyl Carrier Protein of the Vicenistatin Modular Polyketide Synthase. Biochemistry 2023 62 17 21 7WDU 36864192 6-sulfo-beta-D-N-acetylglucosaminidase from Bifidobacterium bifidum in complex with PUGNAc-6S 2021-12-22 2022-12-28 Katoh, T.,Yamada, C.,Wallace, M.D.,Yoshida, A.,Gotoh, A.,Arai, M.,Maeshibu, T.,Kashima, T.,Hagenbeek, A.,Ojima, M.N.,Takada, H.,Sakanaka, M.,Shimizu, H.,Nishiyama, K.,Ashida, H.,Hirose, J.,Suarez-Diez, M.,Nishiyama, M.,Kimura, I.,Stubbs, K.A.,Fushinobu, S.,Katayama, T. A bacterial sulfoglycosidase highlights mucin O-glycan breakdown in the gut ecosystem. Nat.Chem.Biol. 2023 19 778 789 7WZU 36519431 Crystal structure of metallo-beta-lactamase IMP-6. 2022-02-19 2023-01-04 Yamaguchi, Y.,Kato, K.,Ichimaru, Y.,Uenosono, Y.,Tawara, S.,Ito, R.,Matsuse, N.,Wachino, J.I.,Toma-Fukai, S.,Jin, W.,Arakawa, Y.,Otsuka, M.,Fujita, M.,Fukuishi, N.,Sugiura, K.,Imai, M.,Kurosaki, H. Difference in the Inhibitory Effect of Thiol Compounds and Demetallation Rates from the Zn(II) Active Site of Metallo-beta-lactamases (IMP-1 and IMP-6) Associated with a Single Amino Acid Substitution. Acs Infect Dis. 2023 9 65 78 7X7I Ancestral L-Lys oxidase (AncLLysO-2) ligand free form 2022-03-09 2023-01-18 Motoyama, T.,Yamamoto, Y.,Ishida, C.,Hasebe, F.,Kawamura, Y.,Shigeta, Y.,Ito, S.,Nakano, S. Reaction Mechanism of Ancestral l-Lys alpha-Oxidase from Caulobacter Species Studied by Biochemical, Structural, and Computational Analysis Acs Omega 2022 7 44407 44419 7X7J Ancestral L-Lys oxidase (AncLLysO-2) L-Lys binding form 2022-03-09 2023-01-18 Motoyama, T.,Yamamoto, Y.,Ishida, C.,Hasebe, F.,Kawamura, Y.,Shigeta, Y.,Ito, S.,Nakano, S. Reaction Mechanism of Ancestral l-Lys alpha-Oxidase from Caulobacter Species Studied by Biochemical, Structural, and Computational Analysis Acs Omega 2022 7 44407 44419 7X7K Ancestral L-Lys oxidase (AncLLysO-2) L-Arg binding form 2022-03-09 2023-01-18 Motoyama, T.,Yamamoto, Y.,Ishida, C.,Hasebe, F.,Kawamura, Y.,Shigeta, Y.,Ito, S.,Nakano, S. Reaction Mechanism of Ancestral l-Lys alpha-Oxidase from Caulobacter Species Studied by Biochemical, Structural, and Computational Analysis Acs Omega 2022 7 44407 44419 8HBR 36598352 The C-terminal domain of Spiral2 2022-10-30 2023-01-18 Ohno, M.,Higuchi, Y.,Hayashi, I. Crystal structure of the C-terminal domain of the plant-specific microtubule-associated protein Spiral2. Acta Crystallogr.,Sect.F 2023 79 17 22 7WNK 36701098 Crystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase K38R and A121E 2022-01-18 2023-01-25 Retnoningrum, D.S.,Yoshida, H.,Pajatiwi, I.,Muliadi, R.,Utami, R.A.,Artarini, A.,Ismaya, W.T. Introducing Intermolecular Interaction to Strengthen the Stability of MnSOD Dimer. Appl.Biochem.Biotechnol. 2023 195 4537 4551 7WNK 36701098 Crystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase K38R and A121E 2022-01-18 2023-01-25 Retnoningrum, D.S.,Yoshida, H.,Pajatiwi, I.,Muliadi, R.,Utami, R.A.,Artarini, A.,Ismaya, W.T. Introducing Intermolecular Interaction to Strengthen the Stability of MnSOD Dimer. Appl.Biochem.Biotechnol. 2023 195 4537 4551 7WNL 36701098 Crystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase K38R and A121Y 2022-01-18 2023-01-25 Retnoningrum, D.S.,Yoshida, H.,Pajatiwi, I.,Muliadi, R.,Utami, R.A.,Artarini, A.,Ismaya, W.T. Introducing Intermolecular Interaction to Strengthen the Stability of MnSOD Dimer. Appl.Biochem.Biotechnol. 2023 195 4537 4551 7WNL 36701098 Crystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase K38R and A121Y 2022-01-18 2023-01-25 Retnoningrum, D.S.,Yoshida, H.,Pajatiwi, I.,Muliadi, R.,Utami, R.A.,Artarini, A.,Ismaya, W.T. Introducing Intermolecular Interaction to Strengthen the Stability of MnSOD Dimer. Appl.Biochem.Biotechnol. 2023 195 4537 4551 8GYH 36669120 Crystal structure of Fic25 (apo form) from Streptomyces ficellus 2022-09-22 2023-02-22 Kurosawa, S.,Okamura, H.,Yoshida, A.,Tomita, T.,Sone, Y.,Hasebe, F.,Shinada, T.,Takikawa, H.,Kosono, S.,Nishiyama, M. Mechanisms of Sugar Aminotransferase-like Enzymes to Synthesize Stereoisomers of Non-proteinogenic Amino Acids in Natural Product Biosynthesis. Acs Chem.Biol. 2023 18 385 395 8GYI 36669120 Crystal structure of Fic25 (holo form) from Streptomyces ficellus 2022-09-22 2023-02-22 Kurosawa, S.,Okamura, H.,Yoshida, A.,Tomita, T.,Sone, Y.,Hasebe, F.,Shinada, T.,Takikawa, H.,Kosono, S.,Nishiyama, M. Mechanisms of Sugar Aminotransferase-like Enzymes to Synthesize Stereoisomers of Non-proteinogenic Amino Acids in Natural Product Biosynthesis. Acs Chem.Biol. 2023 18 385 395 8GYJ 36669120 Crystal structure of Fic25 complexed with PLP-(5S,6S)-N2-acetyl-DADH adduct from Streptomyces ficellus 2022-09-22 2023-02-22 Kurosawa, S.,Okamura, H.,Yoshida, A.,Tomita, T.,Sone, Y.,Hasebe, F.,Shinada, T.,Takikawa, H.,Kosono, S.,Nishiyama, M. Mechanisms of Sugar Aminotransferase-like Enzymes to Synthesize Stereoisomers of Non-proteinogenic Amino Acids in Natural Product Biosynthesis. Acs Chem.Biol. 2023 18 385 395 7X2B 36943649 Red fluorescent protein from Diadumene lineata 2022-02-25 2023-03-01 Horiuchi, Y.,Makabe, K.,Laskaratou, D.,Hatori, K.,Sliwa, M.,Mizuno, H.,Hotta, J.I. Cloning and structural basis of fluorescent protein color variants from identical species of sea anemone, Diadumene lineata. Photochem Photobiol Sci 2023 22 1591 1601 8HUY 36862095 N-acetyl-(R)-beta-phenylalanine acylase 2022-12-24 2023-03-15 Kato, Y.,Kawasaki, H.,Nakamatsu, T.,Matsuda, N.,Natsume, R. Expression, purification and crystallization of N-acetyl-(R)-beta-phenylalanine acylases derived from Burkholderia sp. AJ110349 and Variovorax sp. AJ110348 and structure determination of the Burkholderia enzyme. Acta Crystallogr.,Sect.F 2023 79 70 78 8I59 36862095 N-acetyl-(R)-beta-phenylalanine acylase, selenomethionyl derivative 2023-01-24 2023-03-15 Kato, Y.,Kawasaki, H.,Nakamatsu, T.,Matsuda, N.,Natsume, R. Expression, purification and crystallization of N-acetyl-(R)-beta-phenylalanine acylases derived from Burkholderia sp. AJ110349 and Variovorax sp. AJ110348 and structure determination of the Burkholderia enzyme. Acta Crystallogr.,Sect.F 2023 79 70 78 8I5A 36862095 N-acetyl-(R)-beta-phenylalanine acylase, 2.75 angstrom resolution 2023-01-24 2023-03-15 Kato, Y.,Kawasaki, H.,Nakamatsu, T.,Matsuda, N.,Natsume, R. Expression, purification and crystallization of N-acetyl-(R)-beta-phenylalanine acylases derived from Burkholderia sp. AJ110349 and Variovorax sp. AJ110348 and structure determination of the Burkholderia enzyme. Acta Crystallogr.,Sect.F 2023 79 70 78 7XE9 35755825 T4 lysozyme mutant-S44C/C54T/N68C/A93C/C97A/T115C, DMSO 20% 2022-03-30 2023-03-22 Hiromoto, T.,Ikura, T.,Honjo, E.,Blaber, M.,Kuroki, R.,Tamada, T. Creation of Cross-Linked Crystals With Intermolecular Disulfide Bonds Connecting Symmetry-Related Molecules Allows Retention of Tertiary Structure in Different Solvent Conditions. Front Mol Biosci 2022 9 908394 908394 7XEA 35755825 T4 lysozyme mutant-S44C/C54T/N68C/A93C/C97A/T115C, DMSO 40%, and then backsoaking 2022-03-30 2023-03-22 Hiromoto, T.,Ikura, T.,Honjo, E.,Blaber, M.,Kuroki, R.,Tamada, T. Creation of Cross-Linked Crystals With Intermolecular Disulfide Bonds Connecting Symmetry-Related Molecules Allows Retention of Tertiary Structure in Different Solvent Conditions. Front Mol Biosci 2022 9 908394 908394 7XUY 35777133 Crystal structure of 5-chloro-2-hydroxymuconate tautomerase CnbG 2022-05-20 2023-03-29 Ma, H.L.,Ding, M.,Guo, L.,Li, D.F. Structural insights into the substrate specificity of 5-chloro-2-hydroxymuconate tautomerase CnbG. Biochem.Biophys.Res.Commun. 2022 620 42 48 7XEK SufS with D-cysteine for 6 h 2022-03-31 2023-04-05 Nakamura, R.,Takahashi, Y.,Fujishiro, T. X-ray crystallographic snapshots of the thioazolidine formation upon the PLP during inhibition of SufS by D-cysteine to be published 0 0 0 0 8HYE 36918121 Structure of amino acid dehydrogenase-2752 with ligand 2023-01-06 2023-04-05 Maeno, M.,Ohmori, T.,Nukada, D.,Sakuraba, H.,Satomura, T.,Ohshima, T. Two different alanine dehydrogenases from Geobacillus kaustophilus: Their biochemical characteristics and differential expression in vegetative cells and spores. Biochim Biophys Acta Proteins 2023 1871 140904 140904 6NBJ Qri7 2018-12-07 2023-04-26 Stec, B. Discovery of the Universal tRNA Binding Mode for the TsaD-like Components of the t6A tRNA Modification Pathway Biophysica 2023 3 0 0 7YGO 36716510 DNA duplex containing 5OHU-Hg(II)-T base pairs 2022-07-12 2023-05-24 Torigoe, H.,Kondo, J.,Arakawa, F. Specific binding of Hg 2+ to mismatched base pairs involving 5-hydroxyuracil in duplex DNA. J.Inorg.Biochem. 2023 241 112125 112125 7XLI 37330175 Crystal structure of IsdB linker-NEAT2 bound to a nanobody (VHH) 2022-04-21 2023-05-31 Valenciano-Bellido, S.,Caaveiro, J.M.M.,Nakakido, M.,Kuroda, D.,Aikawa, C.,Nakagawa, I.,Tsumoto, K. Targeting hemoglobin receptors IsdH and IsdB of Staphylococcus aureus with a single VHH antibody inhibits bacterial growth. J.Biol.Chem. 2023 299 104927 104927 7XVX Neutron crystal structure of human macrophage migration inhibitory factor 2022-05-25 2023-05-31 Ezawa, T.,Nakagaki, T.,Sugishima, K.,Ishida, T.,Hirano, Y.,Kusaka, K.,Tamada, T.,Odaka, M.,Wakui, H.,Matsumura, H. Neutron crystal structure of human macrophage migration inhibitory factor To Be Published 0 0 0 0 7XVX Neutron crystal structure of human macrophage migration inhibitory factor 2022-05-25 2023-05-31 Ezawa, T.,Nakagaki, T.,Sugishima, K.,Ishida, T.,Hirano, Y.,Kusaka, K.,Tamada, T.,Odaka, M.,Wakui, H.,Matsumura, H. Neutron crystal structure of human macrophage migration inhibitory factor To Be Published 0 0 0 0 8IN9 37216195 The structure of the GfsA KSQ-AT didomain in complex with the GfsA ACP domain 2023-03-09 2023-05-31 Chisuga, T.,Murakami, S.,Miyanaga, A.,Kudo, F.,Eguchi, T. Structure-Based Analysis of Transient Interactions between Ketosynthase-like Decarboxylase and Acyl Carrier Protein in a Loading Module of Modular Polyketide Synthase. Acs Chem.Biol. 2023 18 1398 1404 8GSY 37071018 X-ray structure of Clostridium perfringens pili protein B N-terminal domain 2022-09-07 2023-06-07 Tamai, E.,Yamada, M.,Ishida, T.,Arimura, N.,Matsunami, R.,Sekiya, H.,Kamitori, S. Structural and biochemical characterization of Clostridium perfringens pili protein B collagen-binding domains. Febs Lett. 2023 597 1345 1354 8IBR 38046823 Crystal structure of GH42 beta-galactosidase BiBga42A from Bifidobacterium longum subspecies infantis in complex with glycerol 2023-02-10 2023-06-07 Gotoh, A.,Hidaka, M.,Sakurama, H.,Nishimoto, M.,Kitaoka, M.,Sakanaka, M.,Fushinobu, S.,Katayama, T. Substrate recognition mode of a glycoside hydrolase family 42 beta-galactosidase from Bifidobacterium longum subspecies infantis ( Bi Bga42A) revealed by crystallographic and mutational analyses. Microbiome Res Rep 2023 2 20 20 8IBS 38046823 Crystal structure of GH42 beta-galactosidase BiBga42A from Bifidobacterium longum subspecies infantis E160A/E318A mutant in complex with galactose 2023-02-10 2023-06-07 Gotoh, A.,Hidaka, M.,Sakurama, H.,Nishimoto, M.,Kitaoka, M.,Sakanaka, M.,Fushinobu, S.,Katayama, T. Substrate recognition mode of a glycoside hydrolase family 42 beta-galactosidase from Bifidobacterium longum subspecies infantis ( Bi Bga42A) revealed by crystallographic and mutational analyses. Microbiome Res Rep 2023 2 20 20 8IBT 38046823 Crystal structure of GH42 beta-galactosidase BiBga42A from Bifidobacterium longum subspecies infantis E318S mutant in complex with lacto-N-tetraose 2023-02-10 2023-06-07 Gotoh, A.,Hidaka, M.,Sakurama, H.,Nishimoto, M.,Kitaoka, M.,Sakanaka, M.,Fushinobu, S.,Katayama, T. Substrate recognition mode of a glycoside hydrolase family 42 beta-galactosidase from Bifidobacterium longum subspecies infantis ( Bi Bga42A) revealed by crystallographic and mutational analyses. Microbiome Res Rep 2023 2 20 20 8IU8 37269952 Crystal structure of GH66 endodextranase from Flavobacterium johnsoniae 2023-03-24 2023-06-14 Nakamura, S.,Kurata, R.,Tonozuka, T.,Funane, K.,Park, E.Y.,Miyazaki, T. Bacteroidota polysaccharide utilization system for branched dextran exopolysaccharides from lactic acid bacteria. J.Biol.Chem. 2023 299 104885 104885 8IU9 37269952 Crystal structure of GH66 endodextranase from Flavobacterium johnsoniae in complex with glucose 2023-03-24 2023-06-14 Nakamura, S.,Kurata, R.,Tonozuka, T.,Funane, K.,Park, E.Y.,Miyazaki, T. Bacteroidota polysaccharide utilization system for branched dextran exopolysaccharides from lactic acid bacteria. J.Biol.Chem. 2023 299 104885 104885 8IUA 37269952 Crystal structure of GH66 endodextranase from Flavobacterium johnsoniae in complex with isomaltose 2023-03-24 2023-06-14 Nakamura, S.,Kurata, R.,Tonozuka, T.,Funane, K.,Park, E.Y.,Miyazaki, T. Bacteroidota polysaccharide utilization system for branched dextran exopolysaccharides from lactic acid bacteria. J.Biol.Chem. 2023 299 104885 104885 8IUB 37269952 Crystal structure of GH66 endodextranase from Flavobacterium johnsoniae in complex with isomaltotriose 2023-03-24 2023-06-14 Nakamura, S.,Kurata, R.,Tonozuka, T.,Funane, K.,Park, E.Y.,Miyazaki, T. Bacteroidota polysaccharide utilization system for branched dextran exopolysaccharides from lactic acid bacteria. J.Biol.Chem. 2023 299 104885 104885 8IUC 37269952 Crystal structure of GH65 alpha-1,2-glucosidase from Flavobacterium johnsoniae in complex with isomaltose 2023-03-24 2023-06-14 Nakamura, S.,Kurata, R.,Tonozuka, T.,Funane, K.,Park, E.Y.,Miyazaki, T. Bacteroidota polysaccharide utilization system for branched dextran exopolysaccharides from lactic acid bacteria. J.Biol.Chem. 2023 299 104885 104885 7YRP Crystal structure of VIM-28 metallo-beta-lactamase 2022-08-10 2023-06-21 Shimizu-Ibuka, A.,Sato, H. Crystal structure of VIM-28 metallo-beta-lactamase To Be Published 0 0 0 0 8J50 37438884 Crystal structure of Flavihumibacter petaseus GH31 alpha-galactosidase 2023-04-21 2023-07-26 Ikegaya, M.,Park, E.Y.,Miyazaki, T. Structure-function analysis of bacterial GH31 alpha-galactosidases specific for alpha-(1→4)-galactobiose. Febs J. 2023 290 4984 4998 8J51 37438884 Crystal structure of Flavihumibacter petaseus GH31 alpha-galactosidase in complex with galactose 2023-04-21 2023-07-26 Ikegaya, M.,Park, E.Y.,Miyazaki, T. Structure-function analysis of bacterial GH31 alpha-galactosidases specific for alpha-(1→4)-galactobiose. Febs J. 2023 290 4984 4998 8J52 37438884 Crystal structure of Flavihumibacter petaseus GH31 alpha-galactosidase mutant D304A in complex with alpha-1,4-galactobiose 2023-04-21 2023-07-26 Ikegaya, M.,Park, E.Y.,Miyazaki, T. Structure-function analysis of bacterial GH31 alpha-galactosidases specific for alpha-(1→4)-galactobiose. Febs J. 2023 290 4984 4998 8J53 37438884 Crystal structure of Bacteroides salyersiae GH31 alpha-galactosidase 2023-04-21 2023-07-26 Ikegaya, M.,Park, E.Y.,Miyazaki, T. Structure-function analysis of bacterial GH31 alpha-galactosidases specific for alpha-(1→4)-galactobiose. Febs J. 2023 290 4984 4998 7YQS 38382672 Neutron structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase from Fusarium oxysporum 12S, L-Rha complex 2022-08-08 2023-08-09 Yano, N.,Kondo, T.,Kusaka, K.,Arakawa, T.,Sakamoto, T.,Fushinobu, S. Charge neutralization and beta-elimination cleavage mechanism of family 42 L-rhamnose-alpha-1,4-D-glucuronate lyase revealed using neutron crystallography. J.Biol.Chem. 2024 300 105774 105774 7YQS 38382672 Neutron structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase from Fusarium oxysporum 12S, L-Rha complex 2022-08-08 2023-08-09 Yano, N.,Kondo, T.,Kusaka, K.,Arakawa, T.,Sakamoto, T.,Fushinobu, S. Charge neutralization and beta-elimination cleavage mechanism of family 42 L-rhamnose-alpha-1,4-D-glucuronate lyase revealed using neutron crystallography. J.Biol.Chem. 2024 300 105774 105774 8HUM 37627519 X-ray structure of human PPAR gamma ligand binding domain-lanifibranor-SRC1 coactivator peptide co-crystals obtained by co-crystallization 2022-12-24 2023-08-09 Kamata, S.,Honda, A.,Ishikawa, R.,Akahane, M.,Fujita, A.,Kaneko, C.,Miyawaki, S.,Habu, Y.,Shiiyama, Y.,Uchii, K.,Machida, Y.,Oyama, T.,Ishii, I. Functional and Structural Insights into the Human PPAR alpha / delta / gamma Targeting Preferences of Anti-NASH Investigational Drugs, Lanifibranor, Seladelpar, and Elafibranor. Antioxidants 2023 12 0 0 8HUN 37627519 X-ray structure of human PPAR alpha ligand binding domain-seladelpar co-crystals obtained by cross-seeding 2022-12-24 2023-08-09 Kamata, S.,Honda, A.,Ishikawa, R.,Akahane, M.,Fujita, A.,Kaneko, C.,Miyawaki, S.,Habu, Y.,Shiiyama, Y.,Uchii, K.,Machida, Y.,Oyama, T.,Ishii, I. Functional and Structural Insights into the Human PPAR alpha / delta / gamma Targeting Preferences of Anti-NASH Investigational Drugs, Lanifibranor, Seladelpar, and Elafibranor. Antioxidants 2023 12 0 0 8JPW Crystal Structure of Single-chain L-Glutamate Oxidase Mutant from Streptomyces sp. X-119-6 2023-06-13 2023-08-09 Yamaguchi, H.,Takahashi, K.,Tatsumi, M.,Tagami, U.,Mizukoshi, T.,Miyano, H.,Sugiki, M. Development of a novel single-chain l-glutamate oxidase from Streptomyces sp. X-119-6 by inserting flexible linkers Enzyme.Microb.Technol. 2023 170 110287 0 8H29 37030501 Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with L-threonine 2022-10-05 2023-08-16 Ikushiro, H.,Murakami, T.,Takahashi, A.,Katayama, A.,Sawai, T.,Goto, H.,Koolath, S.,Murai, Y.,Monde, K.,Miyahara, I.,Kamiya, N.,Yano, T. Structural insights into the substrate recognition of serine palmitoyltransferase from Sphingobacterium multivorum. J.Biol.Chem. 2023 299 104684 104684 8HHV 37726269 endo-alpha-D-arabinanase EndoMA1 from Microbacterium arabinogalactanolyticum 2022-11-17 2023-08-16 Shimokawa, M.,Ishiwata, A.,Kashima, T.,Nakashima, C.,Li, J.,Fukushima, R.,Sawai, N.,Nakamori, M.,Tanaka, Y.,Kudo, A.,Morikami, S.,Iwanaga, N.,Akai, G.,Shimizu, N.,Arakawa, T.,Yamada, C.,Kitahara, K.,Tanaka, K.,Ito, Y.,Fushinobu, S.,Fujita, K. Identification and characterization of endo-alpha-, exo-alpha-, and exo-beta-D-arabinofuranosidases degrading lipoarabinomannan and arabinogalactan of mycobacteria. Nat Commun 2023 14 5803 5803 8I34 37517696 The crystal structure of EPD-BCP1 from a marine sponge 2023-01-16 2023-08-16 Kawasaki, S.,Kaneko, T.,Asano, T.,Maoka, T.,Takaichi, S.,Shomura, Y. An ependymin-related blue carotenoprotein decorates marine blue sponge. J.Biol.Chem. 2023 299 105110 105110 8IC6 37726269 exo-beta-D-arabinanase ExoMA2 from Microbacterium arabinogalactanolyticum in complex with Tris 2023-02-10 2023-08-16 Shimokawa, M.,Ishiwata, A.,Kashima, T.,Nakashima, C.,Li, J.,Fukushima, R.,Sawai, N.,Nakamori, M.,Tanaka, Y.,Kudo, A.,Morikami, S.,Iwanaga, N.,Akai, G.,Shimizu, N.,Arakawa, T.,Yamada, C.,Kitahara, K.,Tanaka, K.,Ito, Y.,Fushinobu, S.,Fujita, K. Identification and characterization of endo-alpha-, exo-alpha-, and exo-beta-D-arabinofuranosidases degrading lipoarabinomannan and arabinogalactan of mycobacteria. Nat Commun 2023 14 5803 5803 8J1C 37524275 Structure of amino acid dehydrogenase in complex with NADP 2023-04-12 2023-08-16 Kawakami, R.,Takami, N.,Hayashi, J.,Yoneda, K.,Ohmori, T.,Ohshima, T.,Sakuraba, H. First crystal structure of an NADP + -dependent l-arginine dehydrogenase belonging to the mu-crystallin family. Int.J.Biol.Macromol. 2023 249 126070 126070 8J1G 37524275 Structure of amino acid dehydrogenase in complex with NADPH 2023-04-12 2023-08-16 Kawakami, R.,Takami, N.,Hayashi, J.,Yoneda, K.,Ohmori, T.,Ohshima, T.,Sakuraba, H. First crystal structure of an NADP + -dependent l-arginine dehydrogenase belonging to the mu-crystallin family. Int.J.Biol.Macromol. 2023 249 126070 126070 8H7C 37695900 Crystal structure of a de novo enzyme, ferric enterobactin esterase Syn-F4 (K4T) - Pt derivative 2022-10-19 2023-09-20 Kurihara, K.,Umezawa, K.,Donnelly, A.E.,Sperling, B.,Liao, G.,Hecht, M.H.,Arai, R. Crystal structure and activity of a de novo enzyme, ferric enterobactin esterase Syn-F4. Proc.Natl.Acad.Sci.USA 2023 120 0 0 8H7E 37695900 Crystal structure of a de novo enzyme, ferric enterobactin esterase Syn-F4 (K4T) at 2.0 angstrom resolution 2022-10-19 2023-09-20 Kurihara, K.,Umezawa, K.,Donnelly, A.E.,Sperling, B.,Liao, G.,Hecht, M.H.,Arai, R. Crystal structure and activity of a de novo enzyme, ferric enterobactin esterase Syn-F4. Proc.Natl.Acad.Sci.USA 2023 120 0 0 8I7P 37259593 Crystal structure of Ricin A chain bound with N2-(2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)glycyl-L-tyrosine 2023-02-01 2023-09-20 Goto, M.,Sakamoto, N.,Higashi, S.,Kawata, R.,Nagatsu, K.,Saito, R. Crystal structure of ricin toxin A chain complexed with a highly potent pterin-based small-molecular inhibitor. J Enzyme Inhib Med Chem 2023 38 2219038 2219038 8J6G Neutron structure of copper amine oxidase from Arthrobacter globiformis anaerobically reduced by phenylethylamine at pD 9.0 2023-04-25 2023-09-20 Murakawa, T.,Kurihara, K.,Shoji, M.,Yano, N.,Kusaka, K.,Kawano, Y.,Suzuki, M.,Shigeta, Y.,Yano, T.,Adachi, M.,Tanizawa, K.,Okajima, T. Neutron Crystallography of a Semiquinone Radical Intermediate of Copper Amine Oxidase Reveals a Substrate-Assisted Conformational Change of the Peptidyl Quinone Cofactor Acs Catalysis 2023 0 12403 12413 8J6G Neutron structure of copper amine oxidase from Arthrobacter globiformis anaerobically reduced by phenylethylamine at pD 9.0 2023-04-25 2023-09-20 Murakawa, T.,Kurihara, K.,Shoji, M.,Yano, N.,Kusaka, K.,Kawano, Y.,Suzuki, M.,Shigeta, Y.,Yano, T.,Adachi, M.,Tanizawa, K.,Okajima, T. Neutron Crystallography of a Semiquinone Radical Intermediate of Copper Amine Oxidase Reveals a Substrate-Assisted Conformational Change of the Peptidyl Quinone Cofactor Acs Catalysis 2023 0 12403 12413 8GOS 36823935 Crystal structure of fluorescent protein RasM 2022-08-25 2023-09-27 Tsubouchi, M.,Ishii, N.,Kagotani, Y.,Shimizu, R.,Fujita, T.,Adachi, M.,Itakura, R. Beat-frequency-resolved two-dimensional electronic spectroscopy: disentangling vibrational coherences in artificial fluorescent proteins with sub-10-fs visible laser pulses. Opt Express 2023 31 6890 6906 8H62 37716701 Crystal structure of Internalin A from Listeria monocytogenes with human E-cadherin EC12 2022-10-14 2023-10-04 Yamazaki, T.,Nagatoishi, S.,Yamawaki, T.,Nozawa, T.,Matsunaga, R.,Nakakido, M.,Caaveiro, J.M.M.,Nakagawa, I.,Tsumoto, K. Anti-InlA single-domain antibodies that inhibit the cell invasion of Listeria monocytogenes. J.Biol.Chem. 2023 299 105254 105254 8H63 37716701 Crystal structure of Internalin A from Listeria monocytogenes with nanobody VHH10 bound 2022-10-15 2023-10-04 Yamazaki, T.,Nagatoishi, S.,Yamawaki, T.,Nozawa, T.,Matsunaga, R.,Nakakido, M.,Caaveiro, J.M.M.,Nakagawa, I.,Tsumoto, K. Anti-InlA single-domain antibodies that inhibit the cell invasion of Listeria monocytogenes. J.Biol.Chem. 2023 299 105254 105254 8JHE 37737277 Hyper-thermostable ancestral L-amino acid oxidase 2 (HTAncLAAO2) 2023-05-23 2023-10-04 Kawamura, Y.,Ishida, C.,Miyata, R.,Miyata, A.,Hayashi, S.,Fujinami, D.,Ito, S.,Nakano, S. Structural and functional analysis of hyper-thermostable ancestral L-amino acid oxidase that can convert Trp derivatives to D-forms by chemoenzymatic reaction. Commun Chem 2023 6 200 200 8H2K Cellodextrin phosphorylase from Clostridium thermocellum mutant - all cysteine residues were substituted with serines 2022-10-06 2023-10-11 Kuga, T.,Sunagawa, N.,Igarashi, K. 11 cysteine-to-serine mutations improve stability of cellodextrin phosphorylase from Clostridium thermocellum To Be Published 0 0 0 0 8H2V Cellodextrin phosphorylase from Clostridium thermocellum mutant - all cysteine residues were substituted with serines 2022-10-07 2023-10-11 Kuga, T.,Sunagawa, N.,Igarashi, K. 11 cysteine-to-serine mutations improve stability of cellodextrin phosphorylase from Clostridium thermocellum To Be Published 0 0 0 0 8H2W Cellodextrin phosphorylase from Clostridium thermocellum mutant - all cysteine residues were substituted with serines 2022-10-07 2023-10-11 Kuga, T.,Sunagawa, N.,Igarashi, K. 11 cysteine-to-serine mutations improve stability of cellodextrin phosphorylase from Clostridium thermocellum To Be Published 0 0 0 0 8JE9 37793172 Crystal structure of CGL1 from Crassostrea gigas, mannobiose-bound form (CGL1/Man(alpha)1-2Man) 2023-05-15 2023-10-25 Hatakeyama, T.,Masuda, K.,Kudo, M.,Tanaka, K.,Takeuchi, A.,Unno, H. Mannose oligosaccharide recognition of CGL1, a mannose-specific lectin containing DM9 motifs from Crassostrea gigas, revealed by X-ray crystallographic analysis. J.Biochem. 2023 175 35 41 8JEA 37793172 Crystal structure of CGL1 from Crassostrea gigas, mannotriose-bound form (CGL1/Man(alpha)1-2Man(alpha)1-2Man) 2023-05-15 2023-10-25 Hatakeyama, T.,Masuda, K.,Kudo, M.,Tanaka, K.,Takeuchi, A.,Unno, H. Mannose oligosaccharide recognition of CGL1, a mannose-specific lectin containing DM9 motifs from Crassostrea gigas, revealed by X-ray crystallographic analysis. J.Biochem. 2023 175 35 41 8JEB 37793172 Crystal structure of CGL1 from Crassostrea gigas, mannotetraose-bound form (CGL1/Man(alpha)1-2Man(alpha)1-2Man(alpha)1-6Man) 2023-05-15 2023-10-25 Hatakeyama, T.,Masuda, K.,Kudo, M.,Tanaka, K.,Takeuchi, A.,Unno, H. Mannose oligosaccharide recognition of CGL1, a mannose-specific lectin containing DM9 motifs from Crassostrea gigas, revealed by X-ray crystallographic analysis. J.Biochem. 2023 175 35 41 8WL7 37820454 X-ray structure of Enterobacter cloacae allose-binding protein in complex with D-allose 2023-09-29 2023-10-25 Kamitori, S. X-ray structures of Enterobacter cloacae allose-binding protein in complexes with monosaccharides demonstrate its unique recognition mechanism for high affinity to allose. Biochem.Biophys.Res.Commun. 2023 682 187 192 8WL9 37820454 X-ray structure of Enterobacter cloacae allose-binding protein in complex with D-ribose 2023-09-29 2023-10-25 Kamitori, S. X-ray structures of Enterobacter cloacae allose-binding protein in complexes with monosaccharides demonstrate its unique recognition mechanism for high affinity to allose. Biochem.Biophys.Res.Commun. 2023 682 187 192 8WLB 37820454 X-ray structure of Enterobacter cloacae allose-binding protein in complex with D-psicose 2023-09-29 2023-10-25 Kamitori, S. X-ray structures of Enterobacter cloacae allose-binding protein in complexes with monosaccharides demonstrate its unique recognition mechanism for high affinity to allose. Biochem.Biophys.Res.Commun. 2023 682 187 192 8K4R 37870408 Structure of VinM-VinL complex 2023-07-20 2023-11-01 Miyanaga, A.,Nagata, K.,Nakajima, J.,Chisuga, T.,Kudo, F.,Eguchi, T. Structural Basis of Amide-Forming Adenylation Enzyme VinM in Vicenistatin Biosynthesis. Acs Chem.Biol. 2023 18 2343 2348 8HMM 37818702 Crystal structure of AoRhaA 2022-12-05 2023-12-06 Makabe, K.,Ishida, N.,Kanezaki, N.,Shiono, Y.,Koseki, T. Aspergillus oryzae alpha-l-rhamnosidase: Crystal structure and insight into the substrate specificity. Proteins 2024 92 236 245 8IHW X-ray crystal structure of D43R mutant of endo-1,4-beta glucanase from Eisenia fetida 2023-02-24 2023-12-06 Kuroki, C.,Hirano, Y.,Nakazawa, M.,Sakamoto, T.,Tamada, T.,Ueda, M. A single mutation Asp43Arg was increased 2.5-fold the catalytic activity and maintained the stability of cold-adapted endo-1,4-beta glucanase (Ef-EG2) from Eisenia fetida. Curr Res Biotechnol 2023 5 0 0 8JQP 38029967 Protocatecuate hydroxylase from Xylophilus ampelinus complexed with 3,4-dihydroxybenzoate 2023-06-14 2023-12-06 Katsuki, N.,Fukushima, R.,Doi, Y.,Masuo, S.,Arakawa, T.,Yamada, C.,Fushinobu, S.,Takaya, N. Protocatechuate hydroxylase is a novel group A flavoprotein monooxygenase with a unique substrate recognition mechanism. J.Biol.Chem. 2023 300 105508 105508 8JQQ 38029967 Protocatecuate hydroxylase from Xylophilus ampelinus C347T mutant 2023-06-14 2023-12-06 Katsuki, N.,Fukushima, R.,Doi, Y.,Masuo, S.,Arakawa, T.,Yamada, C.,Fushinobu, S.,Takaya, N. Protocatechuate hydroxylase is a novel group A flavoprotein monooxygenase with a unique substrate recognition mechanism. J.Biol.Chem. 2023 300 105508 105508 8JD8 38108885 Crystal structure of Citrus limon Cu-Zn superoxide dismutase 2023-05-12 2023-12-27 Utami, R.A.,Yoshida, H.,Kartadinata, L.H.,Abdillah, V.A.,Faratilla, C.R.,Retnoningrum, D.S.,Ismaya, W.T. Direct relationship between dimeric form and activity in the acidic copper-zinc superoxide dismutase from lemon. Acta Crystallogr.,Sect.F 2023 79 301 307 8JD8 38108885 Crystal structure of Citrus limon Cu-Zn superoxide dismutase 2023-05-12 2023-12-27 Utami, R.A.,Yoshida, H.,Kartadinata, L.H.,Abdillah, V.A.,Faratilla, C.R.,Retnoningrum, D.S.,Ismaya, W.T. Direct relationship between dimeric form and activity in the acidic copper-zinc superoxide dismutase from lemon. Acta Crystallogr.,Sect.F 2023 79 301 307 8I52 Crystal structure of VIM-2 metallo-beta-lactamase in complex with 10-HHIA 2023-01-23 2024-01-10 Wachino, J. Crystal structure of VIM-2 Metallo-beta-lactamase in complex with 10-HHIA To Be Published 0 0 0 0 8X6R 38176113 KRasG12C in complex with inhibitor 2023-11-21 2024-01-17 Imaizumi, T.,Shimada, I.,Satake, Y.,Yamaki, S.,Koike, T.,Nigawara, T.,Kaneko, O.,Amano, Y.,Mori, K.,Yamanaka, Y.,Nakayama, A.,Nishizono, Y.,Shimazaki, M.,Nagashima, T.,Kuramoto, K. Discovery of ASP6918, a KRAS G12C inhibitor: Synthesis and structure-activity relationships of 1-{2,7-diazaspiro[3.5]non-2-yl}prop-2-en-1-one derivatives as covalent inhibitors with good potency and oral activity for the treatment of solid tumors. Bioorg.Med.Chem. 2023 98 117581 117581 8X38 Crystal Structure of Decarboxylative Vanillate 1-Hydroxylase from Phanerochaete chrysosporium 2023-11-12 2024-01-24 Mori, R.,Suzuki, H.,Ishida, T.,Igarashi, K.,Kato, M.,Shimizu, M. Decarboxylative Vanillate 1-Hydroxylase from Phanerochaete chrysosporium To Be Published 0 0 0 0 8I57 Uroporphyrin III (UPIII)-bound CfbA 2023-01-24 2024-01-31 Ogawa, S.,Hikita, M.,Fujishiro, T. Substrate selectivity of CfbA To be published 0 0 0 0 8I74 Crystal structure of decarboxylated osteocalcin at pH 8.5 2023-01-31 2024-01-31 Mizuguchi, M.,Yokoyama, T.,Otani, T.,Kuribara, S.,Nabeshima, Y.,Obita, T.,Hirata, M.,Kawano, K. Crystal structures of decarboxylated osteocalcin and implications for the interaction with its receptor To Be Published 0 0 0 0 8I75 Crystal structure of decarboxylated osteocalcin at pH 2.0 2023-01-31 2024-01-31 Mizuguchi, M.,Yokoyama, T.,Otani, T.,Kuribara, S.,Nabeshima, Y.,Obita, T.,Hirata, M.,Kawano, K. Crystal structures of decarboxylated osteocalcin and implications for the interaction with its receptor To Be Published 0 0 0 0 8I76 Crystal structure of decarboxylated osteocalcin at pH 2.0 without glycerol 2023-01-31 2024-01-31 Mizuguchi, M.,Yokoyama, T.,Otani, T.,Kuribara, S.,Nabeshima, Y.,Obita, T.,Hirata, M.,Kawano, K. Crystal structures of decarboxylated osteocalcin and implications for the interaction with its receptor To Be Published 0 0 0 0 7YPD Discovery and characterization of a new carbonyl reductase from Rhodotorula toluroides reducing fluoroketones, and X-ray analysis of the variant by rational engineering 2022-08-03 2024-02-07 Watanabe, Y.,Asano, Y.,Hibi, M. Discovery and characterization of a new carbonyl reductase from Rhodotorula toluroides reducing fluoroketones, and X-ray analysis of the variant by rational engineering To Be Published 0 0 0 0 8XX9 Rhodothermus marinus alpha-amylase RmGH13_47A CBM48-A-B-C domains 2024-01-18 2024-02-07 Miyasaka, Y.,Yokoyama, K.,Kozono, T.,Kitano, Y.,Miyazaki, T.,Sakaguchi, M.,Nishikawa, A.,Tonozuka, T. Structural basis for the recognition of alpha-1,6-branched alpha-glucan by GH13_47 alpha-amylase from Rhodothermus marinus Proteins 2024 0 0 0 8K9P 38232298 Neutron X-ray joint structure of pseudoazurin from Alcaligenes faecalis 2023-08-01 2024-02-14 Fukuda, Y.,Lintuluoto, M.,Kurihara, K.,Hasegawa, K.,Inoue, T.,Tamada, T. Overlooked Hydrogen Bond in a Blue Copper Protein Uncovered by Neutron and Sub- angstrom ngstrom Resolution X-ray Crystallography. Biochemistry 2024 63 339 347 8K9P 38232298 Neutron X-ray joint structure of pseudoazurin from Alcaligenes faecalis 2023-08-01 2024-02-14 Fukuda, Y.,Lintuluoto, M.,Kurihara, K.,Hasegawa, K.,Inoue, T.,Tamada, T. Overlooked Hydrogen Bond in a Blue Copper Protein Uncovered by Neutron and Sub- angstrom ngstrom Resolution X-ray Crystallography. Biochemistry 2024 63 339 347 8WY1 38300345 The structure of cyclization domain in cyclic beta-1,2-glucan synthase from Thermoanaerobacter italicus 2023-10-30 2024-02-14 Tanaka, N.,Saito, R.,Kobayashi, K.,Nakai, H.,Kamo, S.,Kuramochi, K.,Taguchi, H.,Nakajima, M.,Masaike, T. Functional and structural analysis of a cyclization domain in a cyclic beta-1,2-glucan synthase. Appl.Microbiol.Biotechnol. 2024 108 187 187 8IOX Escherichia coli OpgD mutant-D388N 2023-03-13 2024-03-13 Motouchi, S.,Nakajima, M. Novel glycoside hydrolase family enzymes from Escherichia coli associating with osmo-regulated periplasmic glucan synthesis To Be Published 0 0 0 0 8IP1 Escherichia coli OpgD mutant-D388N with beta-1,2-glucan 2023-03-13 2024-03-13 Motouchi, S.,Nakajima, M. Novel glycoside hydrolase family enzymes from Escherichia coli associating with osmo-regulated periplasmic glucan synthesis To Be Published 0 0 0 0 8IP2 Escherichia coli OpgG mutant-D361N with beta-1,2-glucan 2023-03-13 2024-03-13 Motouchi, S.,Nakajima, M. Novel glycoside hydrolase family enzymes from Escherichia coli associating with osmo-regulated periplasmic glucan synthesis To Be Published 0 0 0 0 8WWY 38442163 Crystal structure of mouse TIFA/TIFAB heterodimer 2023-10-27 2024-03-13 Nakamura, T.,Ohyama, C.,Sakamoto, M.,Toma, T.,Tateishi, H.,Matsuo, M.,Chirifu, M.,Ikemizu, S.,Morioka, H.,Fujita, M.,Inoue, J.I.,Yamagata, Y. TIFAB regulates the TIFA-TRAF6 signaling pathway involved in innate immunity by forming a heterodimer complex with TIFA. Proc.Natl.Acad.Sci.USA 2024 121 0 0 8J82 GaHNL-12gen (artificial S-hydroxynitrile lyase generated by GAOptimizer) 2023-04-29 2024-04-03 Ozawa, H.,Unno, I.,Sekine, R.,Chisuga, T.,Ito, S.,Nakano, S. Development of evolutionary algorithm-based protein redesign method Cell Rep Phys Sci 2024 5 0 0