8GYJ
 
 | | Crystal structure of Fic25 complexed with PLP-(5S,6S)-N2-acetyl-DADH adduct from Streptomyces ficellus | | Descriptor: | (2~{S},5~{S},6~{S})-2-acetamido-6-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-5,7-bis(oxidanyl)heptanoic acid, DegT/DnrJ/EryC1/StrS family aminotransferase, GLYCEROL, ... | | Authors: | Kurosawa, S, Yoshida, A, Tomita, T, Nishiyama, M. | | Deposit date: | 2022-09-22 | | Release date: | 2023-02-22 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.82 Å) | | Cite: | Mechanisms of Sugar Aminotransferase-like Enzymes to Synthesize Stereoisomers of Non-proteinogenic Amino Acids in Natural Product Biosynthesis.
Acs Chem.Biol., 18, 2023
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2ZUW
 | | Crystal structure of Galacto-N-biose/Lacto-N-biose I phosphorylase in complex with GlcNAc and sulfate | | Descriptor: | 2-acetamido-2-deoxy-alpha-D-glucopyranose, GLYCEROL, Lacto-N-biose phosphorylase, ... | | Authors: | Hidaka, M, Nishimoto, M, Kitaoka, M, Wakagi, T, Shoun, H, Fushinobu, S. | | Deposit date: | 2008-10-28 | | Release date: | 2008-12-30 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.11 Å) | | Cite: | The crystal structure of galacto-N-biose/lacto-N-biose I phosphorylase: A large deformation of a tim barrel scaffold
J.Biol.Chem., 284, 2009
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2ZHO
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2ZUT
 | | Crystal structure of Galacto-N-biose/Lacto-N-biose I phosphorylase in complex with GalNAc | | Descriptor: | 2-acetamido-2-deoxy-alpha-D-galactopyranose, GLYCEROL, Lacto-N-biose phosphorylase, ... | | Authors: | Hidaka, M, Nishimoto, M, Kitaoka, M, Wakagi, T, Shoun, H, Fushinobu, S. | | Deposit date: | 2008-10-28 | | Release date: | 2008-12-30 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | The crystal structure of galacto-N-biose/lacto-N-biose I phosphorylase: A large deformation of a tim barrel scaffold
J.Biol.Chem., 284, 2009
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6K0H
 | | Crystal Structure of UDP-glucose 4-epimerase from Bifidobacterium longum in complex with NAD+ and UDP-GlcNAc | | Descriptor: | DI(HYDROXYETHYL)ETHER, MAGNESIUM ION, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... | | Authors: | Nam, Y.-W, Nishimoto, M, Arakawa, T, Kitaoka, M, Fushinobu, S. | | Deposit date: | 2019-05-06 | | Release date: | 2019-08-07 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural basis for broad substrate specificity of UDP-glucose 4-epimerase in the human milk oligosaccharide catabolic pathway of Bifidobacterium longum.
Sci Rep, 9, 2019
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6K0I
 | | Crystal Structure of UDP-glucose 4-epimerase from Bifidobacterium longum in complex with NAD+ and UDP-Glc | | Descriptor: | NICOTINAMIDE-ADENINE-DINUCLEOTIDE, UDP-glucose 4-epimerase, URIDINE-5'-DIPHOSPHATE-GLUCOSE | | Authors: | Nam, Y.-W, Nishimoto, M, Arakawa, T, Kitaoka, M, Fushinobu, S. | | Deposit date: | 2019-05-06 | | Release date: | 2019-08-07 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structural basis for broad substrate specificity of UDP-glucose 4-epimerase in the human milk oligosaccharide catabolic pathway of Bifidobacterium longum.
Sci Rep, 9, 2019
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6K0G
 | | Crystal Structure of UDP-glucose 4-epimerase from Bifidobacterium longum in complex with NAD+ and UDP | | Descriptor: | MAGNESIUM ION, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, UDP-glucose 4-epimerase, ... | | Authors: | Nam, Y.-W, Nishimoto, M, Arakawa, T, Kitaoka, M, Fushinobu, S. | | Deposit date: | 2019-05-06 | | Release date: | 2019-08-07 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structural basis for broad substrate specificity of UDP-glucose 4-epimerase in the human milk oligosaccharide catabolic pathway of Bifidobacterium longum.
Sci Rep, 9, 2019
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3A3U
 | | Crystal structure of MqnD (TTHA1568), a menaquinone biosynthetic enzyme from Thermus thermophilus HB8 | | Descriptor: | 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL, L(+)-TARTARIC ACID, Menaquinone biosynthetic enzyme, ... | | Authors: | Arai, R, Nishino, A, Nagano, K, Uchikubo-Kamo, T, Katsura, K, Nishimoto, M, Toyama, M, Terada, T, Kuramitsu, S, Murayama, K, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2009-06-20 | | Release date: | 2009-07-14 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Crystal structure of MqnD (TTHA1568), a menaquinone biosynthetic enzyme from Thermus thermophilus HB8.
J.Struct.Biol., 168, 2009
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7C9R
 | | STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF THIORHODOVIBRIO STRAIN 970 | | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},24~{E},26~{E})-2,31-dimethoxy-2,6,10,14,19,23,27,31-octamethyl-dotriaconta-6,8,10,12,14,16,18,20,22,24,26-undecaene, Alpha subunit 1 of light-harvesting 1 complex, ... | | Authors: | Tani, K, Kanno, R, Makino, Y, Hall, M, Takenouchi, M, Imanishi, M, Yu, L.-J, Overmann, J, Madigan, M.T, Kimura, Y, Mizoguchi, A, Humbel, B.M, Wang-Otomo, Z.-Y. | | Deposit date: | 2020-06-07 | | Release date: | 2020-10-07 | | Last modified: | 2020-10-14 | | Method: | ELECTRON MICROSCOPY (2.82 Å) | | Cite: | Cryo-EM structure of a Ca 2+ -bound photosynthetic LH1-RC complex containing multiple alpha beta-polypeptides.
Nat Commun, 11, 2020
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2Z1Y
 | | Crystal structure of LysN, alpha-aminoadipate aminotransferase (complexed with N-(5'-phosphopyridoxyl)-L-leucine), from Thermus thermophilus HB27 | | Descriptor: | Alpha-aminodipate aminotransferase, LEUCINE, PYRIDOXAL-5'-PHOSPHATE | | Authors: | Tomita, T, Miyazaki, T, Miyagawa, T, Fushinobu, S, Kuzuyama, T, Nishiyama, M. | | Deposit date: | 2007-05-16 | | Release date: | 2008-06-03 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | Mechanism of broad substrate specificity of alpha-aminoadipate aminotransferase from Thermus thermophilus
To be Published
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6KTQ
 | | Crystal structure of catalytic domain of homocitrate synthase from Sulfolobus acidocaldarius (SaHCS(dRAM)) in complex with alpha-ketoglutarate/Zn2+/CoA | | Descriptor: | 2-OXOGLUTARIC ACID, COENZYME A, Homocitrate synthase, ... | | Authors: | Suzuki, T, Tomita, T, Kuzuyama, T, Nishiyama, M. | | Deposit date: | 2019-08-28 | | Release date: | 2020-09-02 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.98 Å) | | Cite: | Involvement of subdomain II in the recognition of acetyl-CoA revealed by the crystal structure of homocitrate synthase from Sulfolobus acidocaldarius.
Febs J., 288, 2021
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1ET7
 | | CRYSTAL STRUCTURE OF NITRITE REDUCTASE HIS255ASP MUTANT FROM ALCALIGENES FAECALIS S-6 | | Descriptor: | CADMIUM ION, COPPER (II) ION, NITRITE REDUCTASE | | Authors: | Boulanger, M.J, Kukimoto, M, Nishiyama, M, Horinouchi, S, Murphy, M.E.P. | | Deposit date: | 2000-04-12 | | Release date: | 2000-08-24 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Catalytic roles for two water bridged residues (Asp-98 and His-255) in the active site of copper-containing nitrite reductase.
J.Biol.Chem., 275, 2000
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4YGB
 | | Crystal structure of ERGIC-53/MCFD2, monoclinic calcium-free form | | Descriptor: | CALCIUM ION, GLYCEROL, Multiple coagulation factor deficiency protein 2, ... | | Authors: | Satoh, T, Nishio, M, Yagi-Utsumi, M, Suzuki, K, Anzai, T, Mizushima, T, Kamiya, Y, Kato, K. | | Deposit date: | 2015-02-26 | | Release date: | 2016-04-06 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Crystallographic snapshots of the EF-hand protein MCFD2 complexed with the intracellular lectin ERGIC-53 involved in glycoprotein transport.
Acta Crystallogr.,Sect.F, 76, 2020
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1ET5
 | | CRYSTAL STRUCTURE OF NITRITE REDUCTASE ASP98ASN MUTANT FROM ALCALIGENES FAECALIS S-6 | | Descriptor: | COPPER (II) ION, NITRITE REDUCTASE, ZINC ION | | Authors: | Boulanger, M.J, Kukimoto, M, Nishiyama, M, Horinouchi, S, Murphy, M.E.P. | | Deposit date: | 2000-04-12 | | Release date: | 2000-08-24 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Catalytic roles for two water bridged residues (Asp-98 and His-255) in the active site of copper-containing nitrite reductase.
J.Biol.Chem., 275, 2000
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2J40
 | | 1-pyrroline-5-carboxylate dehydrogenase from Thermus thermophilus with bound inhibitor L-proline and NAD. | | Descriptor: | (4R)-2-METHYLPENTANE-2,4-DIOL, (4S)-2-METHYL-2,4-PENTANEDIOL, 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE, ... | | Authors: | Inagaki, E, Sakamoto, K, Nishio, M, Yokoyama, S. | | Deposit date: | 2006-08-24 | | Release date: | 2007-10-02 | | Last modified: | 2023-12-13 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Crystal Structure of Ternary Complex of Delta1-Pyrroline-5-Carboxylate Dehydrogenase with Substrate Mimic and Co-Factoer
To be Published
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1ZRN
 | | INTERMEDIATE STRUCTURE OF L-2-HALOACID DEHALOGENASE WITH MONOCHLOROACETATE | | Descriptor: | ACETIC ACID, L-2-HALOACID DEHALOGENASE | | Authors: | Li, Y.-F, Hata, Y, Fujii, T, Hisano, T, Nishihara, M, Kurihara, T, Esaki, N. | | Deposit date: | 1998-03-03 | | Release date: | 1999-03-23 | | Last modified: | 2023-08-09 | | Method: | X-RAY DIFFRACTION (1.83 Å) | | Cite: | Crystal structures of reaction intermediates of L-2-haloacid dehalogenase and implications for the reaction mechanism.
J.Biol.Chem., 273, 1998
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2J5N
 | | 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE FROM THERMUS THERMOPHIRUS WITH BOUND INHIBITOR GLYCINE AND NAD. | | Descriptor: | (4R)-2-METHYLPENTANE-2,4-DIOL, (4S)-2-METHYL-2,4-PENTANEDIOL, 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE, ... | | Authors: | Inagaki, E, Sakamoto, K, Nishio, M, Yokoyama, S. | | Deposit date: | 2006-09-19 | | Release date: | 2007-10-16 | | Last modified: | 2023-12-13 | | Method: | X-RAY DIFFRACTION (1.63 Å) | | Cite: | Crystal Structure of Ternary Complex of Delta1-Pyrroline-5-Carboxylate Dehydrogenase with Substrate Mimic and Co-Factoer
To be Published
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1ZRM
 | | CRYSTAL STRUCTURE OF THE REACTION INTERMEDIATE OF L-2-HALOACID DEHALOGENASE WITH 2-CHLORO-N-BUTYRATE | | Descriptor: | L-2-HALOACID DEHALOGENASE, butanoic acid | | Authors: | Li, Y.-F, Hata, Y, Fujii, T, Hisano, T, Nishihara, M, Kurihara, T, Esaki, N. | | Deposit date: | 1998-03-03 | | Release date: | 1999-03-23 | | Last modified: | 2023-08-09 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Crystal structures of reaction intermediates of L-2-haloacid dehalogenase and implications for the reaction mechanism.
J.Biol.Chem., 273, 1998
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4YGE
 | | Crystal structure of ERGIC-53/MCFD2, trigonal calcium-bound form 2 | | Descriptor: | CALCIUM ION, CHLORIDE ION, Multiple coagulation factor deficiency protein 2, ... | | Authors: | Satoh, T, Nishio, M, Yagi-Utsumi, M, Suzuki, K, Anzai, T, Mizushima, T, Kamiya, Y, Kato, K. | | Deposit date: | 2015-02-26 | | Release date: | 2016-04-06 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.05 Å) | | Cite: | Crystallographic snapshots of the EF-hand protein MCFD2 complexed with the intracellular lectin ERGIC-53 involved in glycoprotein transport.
Acta Crystallogr.,Sect.F, 76, 2020
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4YGC
 | | Crystal structure of ERGIC-53/MCFD2, monoclinic calcium-bound form 1 | | Descriptor: | CALCIUM ION, CHLORIDE ION, Multiple coagulation factor deficiency protein 2, ... | | Authors: | Satoh, T, Nishio, M, Yagi-Utsumi, M, Suzuki, K, Anzai, T, Mizushima, T, Kamiya, Y, Kato, K. | | Deposit date: | 2015-02-26 | | Release date: | 2016-04-06 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Crystallographic snapshots of the EF-hand protein MCFD2 complexed with the intracellular lectin ERGIC-53 involved in glycoprotein transport.
Acta Crystallogr.,Sect.F, 76, 2020
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4YGD
 | | Crystal structure of ERGIC-53/MCFD2, monoclinic calcium-bound form 2 | | Descriptor: | CALCIUM ION, CHLORIDE ION, Multiple coagulation factor deficiency protein 2, ... | | Authors: | Satoh, T, Nishio, M, Yagi-Utsumi, M, Suzuki, K, Anzai, T, Mizushima, T, Kamiya, Y, Kato, K. | | Deposit date: | 2015-02-26 | | Release date: | 2016-04-06 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.51 Å) | | Cite: | Crystallographic snapshots of the EF-hand protein MCFD2 complexed with the intracellular lectin ERGIC-53 involved in glycoprotein transport.
Acta Crystallogr.,Sect.F, 76, 2020
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1ET8
 | | CRYSTAL STRUCTURE OF NITRITE REDUCTASE HIS255ASN MUTANT FROM ALCALIGENES FAECALIS | | Descriptor: | COPPER (II) ION, NITRITE REDUCTASE, ZINC ION | | Authors: | Boulanger, M.J, Kukimoto, M, Nishiyama, M, Horinouchi, S, Murphy, M.E.P. | | Deposit date: | 2000-04-12 | | Release date: | 2000-08-24 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Catalytic roles for two water bridged residues (Asp-98 and His-255) in the active site of copper-containing nitrite reductase.
J.Biol.Chem., 275, 2000
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5GUD
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5GUE
 | | Crystal structure of CotB2 (GGSPP/Mg2+-Bound Form) from Streptomyces melanosporofaciens | | Descriptor: | Cyclooctat-9-en-7-ol synthase, MAGNESIUM ION, phosphonooxy-[(10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenyl]sulfanyl-phosphinic acid | | Authors: | Tomita, T, Kim, S.-Y, Ozaki, T, Yoshida, A, Kuzuyama, T, Nishiyama, M. | | Deposit date: | 2016-08-28 | | Release date: | 2017-06-07 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structural Insights into the CotB2-Catalyzed Cyclization of Geranylgeranyl Diphosphate to the Diterpene Cyclooctat-9-en-7-ol
ACS Chem. Biol., 12, 2017
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5GUC
 | | Crystal structure of CotB2 (apo form) from Streptomyces melanosporofaciens | | Descriptor: | Cyclooctat-9-en-7-ol synthase, FORMIC ACID | | Authors: | Tomita, T, Kim, S.-Y, Ozaki, T, Yoshida, A, Kuzuyama, T, Nishiyama, M. | | Deposit date: | 2016-08-28 | | Release date: | 2017-06-07 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structural Insights into the CotB2-Catalyzed Cyclization of Geranylgeranyl Diphosphate to the Diterpene Cyclooctat-9-en-7-ol
ACS Chem. Biol., 12, 2017
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