5K2M
 
 | | Bifunctional LysX/ArgX from Thermococcus kodakarensis with LysW-gamma-AAA | | Descriptor: | 2-AMINOHEXANEDIOIC ACID, ADENOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, ... | | Authors: | Yoshida, A, Tomita, T, Nishiyama, M. | | Deposit date: | 2016-05-19 | | Release date: | 2016-09-07 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.18 Å) | | Cite: | Lysine Biosynthesis of Thermococcus kodakarensis with the Capacity to Function as an Ornithine Biosynthetic System.
J. Biol. Chem., 291, 2016
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3AAW
 | | Crystal structure of aspartate kinase from Corynebacterium glutamicum in complex with lysine and threonine | | Descriptor: | Aspartokinase, Aspartokinase LysC beta subunit, LYSINE, ... | | Authors: | Yoshida, A, Tomita, T, Kuzuyama, T, Nishiyama, M. | | Deposit date: | 2009-11-27 | | Release date: | 2010-06-23 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Mechanism of concerted inhibition of {alpha}2{beta}2-type heterooligomeric aspartate kinase from Corynebacterium glutamicum
J.Biol.Chem., 285, 2010
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3AB2
 | | Crystal structure of aspartate kinase from Corynebacterium glutamicum in complex with threonine | | Descriptor: | Aspartokinase, THREONINE | | Authors: | Yoshida, A, Tomita, T, Kuzuyama, T, Nishiyama, M. | | Deposit date: | 2009-11-30 | | Release date: | 2010-06-23 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.59 Å) | | Cite: | Mechanism of concerted inhibition of {alpha}2{beta}2-type heterooligomeric aspartate kinase from Corynebacterium glutamicum
J.Biol.Chem., 285, 2010
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3AB4
 | | Crystal structure of feedback inhibition resistant mutant of aspartate kinase from Corynebacterium glutamicum in complex with lysine and threonine | | Descriptor: | Aspartokinase, LYSINE, THREONINE | | Authors: | Yoshida, A, Tomita, T, Kuzuyama, T, Nishiyama, M. | | Deposit date: | 2009-11-30 | | Release date: | 2010-06-23 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.47 Å) | | Cite: | Mechanism of concerted inhibition of {alpha}2{beta}2-type heterooligomeric aspartate kinase from Corynebacterium glutamicum
J.Biol.Chem., 285, 2010
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2ZHO
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3WWN
 | | Crystal structure of LysZ from Thermus thermophilus complex with LysW | | Descriptor: | OrfF, Putative acetylglutamate kinase-like protein, SULFATE ION, ... | | Authors: | Yoshida, A, Tomita, T, Kuzuyama, T, Nishiyama, M. | | Deposit date: | 2014-06-21 | | Release date: | 2014-11-19 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Structural insight into amino group-carrier protein-mediated lysine biosynthesis: crystal structure of the LysZ·LysW complex from Thermus thermophilus.
J.Biol.Chem., 290, 2015
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3WWM
 | | Crystal structure of LysZ from Thermus thermophilus with ADP | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, Putative acetylglutamate kinase-like protein | | Authors: | Yoshida, A, Tomita, T, Kuzuyama, T, Nishiyama, M. | | Deposit date: | 2014-06-21 | | Release date: | 2014-11-19 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Structural insight into amino group-carrier protein-mediated lysine biosynthesis: crystal structure of the LysZ·LysW complex from Thermus thermophilus.
J.Biol.Chem., 290, 2015
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3WWL
 | | Crystal structure of lysine biosynthetic amino acid carrier protein LysW from Thermus thermophilus conjugated with alpha-aminoadipate | | Descriptor: | Alpha-aminoadipate carrier protein LysW, ZINC ION | | Authors: | Yoshida, A, Tomita, T, Kuzuyama, T, Nishiyama, M. | | Deposit date: | 2014-06-21 | | Release date: | 2014-11-19 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (1.2 Å) | | Cite: | Structural insight into amino group-carrier protein-mediated lysine biosynthesis: crystal structure of the LysZ·LysW complex from Thermus thermophilus.
J.Biol.Chem., 290, 2015
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2DTJ
 | | Crystal structure of regulatory subunit of aspartate kinase from Corynebacterium glutamicum | | Descriptor: | Aspartokinase, CITRIC ACID, THREONINE | | Authors: | Yoshida, A, Tomita, T, Fushinobu, S, Kuzuyama, T, Nishiyama, M. | | Deposit date: | 2006-07-12 | | Release date: | 2007-05-01 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.58 Å) | | Cite: | Structural Insight into Concerted Inhibition of alpha(2)beta(2)-Type Aspartate Kinase from Corynebacterium glutamicum
J.Mol.Biol., 368, 2007
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2DT9
 | | Crystal structure of the regulatory subunit of aspartate kinase from Thermus flavus | | Descriptor: | ACETATE ION, Aspartokinase, THREONINE | | Authors: | Yoshida, A, Tomita, T, Fushinobu, S, Kuzuyama, T, Nishiyama, M. | | Deposit date: | 2006-07-11 | | Release date: | 2007-07-17 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.15 Å) | | Cite: | Crystal structures of the regulatory subunit of Thr-sensitive aspartate kinase from Thermus thermophilus
Febs J., 276, 2009
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8GYI
 | | Crystal structure of Fic25 (holo form) from Streptomyces ficellus | | Descriptor: | DegT/DnrJ/EryC1/StrS family aminotransferase, GLYCEROL, IMIDAZOLE, ... | | 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 (1.93 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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8GYH
 | | Crystal structure of Fic25 (apo form) from Streptomyces ficellus | | Descriptor: | DegT/DnrJ/EryC1/StrS family aminotransferase, GLYCEROL, IMIDAZOLE | | Authors: | Kurosawa, S, Yoshida, A, Tomita, T, Nishiyama, M. | | Deposit date: | 2022-09-22 | | Release date: | 2023-02-22 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (1.8 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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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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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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7W63
 | | Crystal structure of minor pilin TcpB from Vibrio cholerae | | Descriptor: | SULFATE ION, Toxin-coregulated pilus biosynthesis protein B | | Authors: | Oki, H, Kawahara, K, Iimori, M, Imoto, Y, Maruno, T, Uchiyama, S, Muroga, Y, Yoshida, A, Yoshida, T, Ohkubo, T, Matsuda, S, Iida, T, Nakamura, S. | | Deposit date: | 2021-12-01 | | Release date: | 2022-11-09 | | Last modified: | 2022-11-16 | | Method: | X-RAY DIFFRACTION (2.32 Å) | | Cite: | Structural basis for the toxin-coregulated pilus-dependent secretion of Vibrio cholerae colonization factor.
Sci Adv, 8, 2022
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7W65
 | | Crystal structure of minor pilin TcpB from Vibrio cholerae complexed with secreted protein TcpF | | Descriptor: | Toxin coregulated pilus biosynthesis protein F, Toxin-coregulated pilus biosynthesis protein B | | Authors: | Oki, H, Kawahara, K, Iimori, M, Imoto, Y, Maruno, T, Uchiyama, S, Muroga, Y, Yoshida, A, Yoshida, T, Ohkubo, T, Matsuda, S, Iida, T, Nakamura, S. | | Deposit date: | 2021-12-01 | | Release date: | 2022-11-09 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (4.05 Å) | | Cite: | Structural basis for the toxin-coregulated pilus-dependent secretion of Vibrio cholerae colonization factor.
Sci Adv, 8, 2022
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7W64
 | | Crystal structure of minor pilin TcpB from Vibrio cholerae complexed with N-terminal peptide fragment of TcpF | | Descriptor: | CALCIUM ION, CHLORIDE ION, PENTAETHYLENE GLYCOL, ... | | Authors: | Oki, H, Kawahara, K, Iimori, M, Imoto, Y, Maruno, T, Uchiyama, S, Muroga, Y, Yoshida, A, Yoshida, T, Ohkubo, T, Matsuda, S, Iida, T, Nakamura, S. | | Deposit date: | 2021-12-01 | | Release date: | 2022-11-09 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structural basis for the toxin-coregulated pilus-dependent secretion of Vibrio cholerae colonization factor.
Sci Adv, 8, 2022
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5XOY
 | | Crystal structure of LysK from Thermus thermophilus in complex with Lysine | | Descriptor: | LYSINE, SULFATE ION, [LysW]-lysine hydrolase | | Authors: | Tomita, T, Fujita, S, Hasebe, F, Cho, S.-H, Yoshida, A, Kuzuyama, T, Nishiyama, M. | | Deposit date: | 2017-05-31 | | Release date: | 2017-09-13 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.39 Å) | | Cite: | Crystal structure of LysK, an enzyme catalyzing the last step of lysine biosynthesis in Thermus thermophilus, in complex with lysine: Insight into the mechanism for recognition of the amino-group carrier protein, LysW
Biochem. Biophys. Res. Commun., 491, 2017
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7WUX
 | | Crystal structure of AziU3/U2 complexed with (5S,6S)-O7-sulfo DADH from Streptomyces sahachiroi | | Descriptor: | (2S,5S,6S)-2,6-bis(azanyl)-5-oxidanyl-7-sulfooxy-heptanoic acid, 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE, AziU2, ... | | Authors: | Kurosawa, S, Yoshida, A, Tomita, T, Nishiyama, M. | | Deposit date: | 2022-02-09 | | Release date: | 2022-09-07 | | Last modified: | 2022-09-21 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Molecular Basis for Enzymatic Aziridine Formation via Sulfate Elimination.
J.Am.Chem.Soc., 144, 2022
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7WUW
 | | Crystal structure of AziU3/U2 from Streptomyces sahachiroi | | Descriptor: | AziU2, AziU3, MAGNESIUM ION, ... | | Authors: | Kurosawa, S, Yoshida, A, Tomita, T, Nishiyama, M. | | Deposit date: | 2022-02-09 | | Release date: | 2022-09-07 | | Last modified: | 2022-09-21 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | Molecular Basis for Enzymatic Aziridine Formation via Sulfate Elimination.
J.Am.Chem.Soc., 144, 2022
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9API
 | | THE S VARIANT OF HUMAN ALPHA1-ANTITRYPSIN, STRUCTURE AND IMPLICATIONS FOR FUNCTION AND METABOLISM | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ALPHA 1-ANTITRYPSIN, ... | | Authors: | Loebermann, H, Tokuoka, R, Deisenhofer, J, Huber, R. | | Deposit date: | 1988-09-08 | | Release date: | 1990-10-15 | | Last modified: | 2024-01-10 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | The S variant of human alpha 1-antitrypsin, structure and implications for function and metabolism.
Protein Eng., 2, 1989
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7WDT
 | | 6-sulfo-beta-D-N-acetylglucosaminidase from Bifidobacterium bifidum in complex with GlcNAc-6S | | Descriptor: | 2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose, 2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose, Beta-N-acetylhexosaminidase, ... | | Authors: | Yamada, C, Kashima, T, Fushinobu, S, Katoh, T, Katayama, T. | | Deposit date: | 2021-12-22 | | Release date: | 2022-12-28 | | Last modified: | 2023-06-14 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | A bacterial sulfoglycosidase highlights mucin O-glycan breakdown in the gut ecosystem.
Nat.Chem.Biol., 19, 2023
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7WDU
 | | 6-sulfo-beta-D-N-acetylglucosaminidase from Bifidobacterium bifidum in complex with PUGNAc-6S | | Descriptor: | Beta-N-acetylhexosaminidase, CALCIUM ION, [[(3R,4R,5S,6R)-3-acetamido-4,5-bis(oxidanyl)-6-(sulfooxymethyl)oxan-2-ylidene]amino] N-phenylcarbamate | | Authors: | Kashima, T, Yamada, C, Fushinobu, S, Katoh, T, Katayama, T. | | Deposit date: | 2021-12-22 | | Release date: | 2022-12-28 | | Last modified: | 2023-06-14 | | Method: | X-RAY DIFFRACTION (2.23 Å) | | Cite: | A bacterial sulfoglycosidase highlights mucin O-glycan breakdown in the gut ecosystem.
Nat.Chem.Biol., 19, 2023
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5HN4
 | | Crystal structure of beta-decarboxylating dehydrogenase (TK0280) from Thermococcus kodakarensis complexed with Mn and homoisocitrate | | Descriptor: | (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylic acid, Homoisocitrate dehydrogenase, IMIDAZOLE, ... | | Authors: | Shimizu, T, Tomita, T, Nishiyama, M. | | Deposit date: | 2016-01-18 | | Release date: | 2016-12-07 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.64 Å) | | Cite: | Structure and function of an ancestral-type beta-decarboxylating dehydrogenase from Thermococcus kodakarensis
Biochem. J., 474, 2017
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