3AH3
 
 | | Crystal structure of LR5-1, 3-isopropylmalate dehydrogenase created by directed evolution | | Descriptor: | 1,2-ETHANEDIOL, Homoisocitrate dehydrogenase, SULFATE ION | | Authors: | Tomita, T, Suzuki, Y, Kuzuyama, T, Nishiyama, M. | | Deposit date: | 2010-04-13 | | Release date: | 2011-02-02 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Enhancement of the latent 3-isopropylmalate dehydrogenase activity of promiscuous homoisocitrate dehydrogenase by directed evolution
Biochem.J., 431, 2010
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3AOE
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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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6XYO
 | | Multiple system atrophy Type I alpha-synuclein filament | | Descriptor: | Alpha-synuclein | | Authors: | Schweighauser, M, Shi, Y, Tarutani, A, Kametani, F, Murzin, A.G, Ghetti, B, Matsubara, T, Tomita, T, Ando, T, Hasegawa, K, Murayama, S, Yoshida, M, Hasegawa, M, Scheres, S.H.W, Goedert, M. | | Deposit date: | 2020-01-30 | | Release date: | 2020-02-12 | | Last modified: | 2024-05-22 | | Method: | ELECTRON MICROSCOPY (2.6 Å) | | Cite: | Structures of alpha-synuclein filaments from multiple system atrophy.
Nature, 585, 2020
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6XYP
 | | Multiple system atrophy Type II-1 alpha-synuclein filament | | Descriptor: | Alpha-synuclein | | Authors: | Schweighauser, M, Shi, Y, Tarutani, A, Kametani, F, Murzin, A.G, Ghetti, B, Matsubara, T, Tomita, T, Ando, T, Hasegawa, K, Murayama, S, Yoshida, M, Hasegawa, M, Scheres, S.H.W, Goedert, M. | | Deposit date: | 2020-01-30 | | Release date: | 2020-02-12 | | Last modified: | 2024-05-22 | | Method: | ELECTRON MICROSCOPY (3.29 Å) | | Cite: | Structures of alpha-synuclein filaments from multiple system atrophy.
Nature, 585, 2020
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6XYQ
 | | Multiple system atrophy Type II-2 alpha-synuclein filament | | Descriptor: | Alpha-synuclein | | Authors: | Schweighauser, M, Shi, Y, Tarutani, A, Kametani, F, Murzin, A.G, Ghetti, B, Matsubara, T, Tomita, T, Ando, T, Hasegawa, K, Murayama, S, Yoshida, M, Hasegawa, M, Scheres, S.H.W, Goedert, M. | | Deposit date: | 2020-01-30 | | Release date: | 2020-02-12 | | Last modified: | 2024-05-22 | | Method: | ELECTRON MICROSCOPY (3.09 Å) | | Cite: | Structures of alpha-synuclein filaments from multiple system atrophy.
Nature, 585, 2020
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6IR4
 | | Crystal structure of BioU from Synechocystis sp.PCC6803 (apo form) | | Descriptor: | Slr0355 protein | | Authors: | Sakaki, K, Oishi, K, Shimizu, T, Tomita, T, Kuzuyama, T, Nishiyama, M. | | Deposit date: | 2018-11-10 | | Release date: | 2020-01-15 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | A suicide enzyme catalyzes multiple reactions for biotin biosynthesis in cyanobacteria.
Nat.Chem.Biol., 16, 2020
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6ITD
 | | Crystal structure of BioU (K124A) from Synechocystis sp.PCC6803 in complex with the analog of reaction intermediate, 3-(1-aminoethyl)-nonanedioic acid | | Descriptor: | 3-(1-AMINOETHYL)NONANEDIOIC ACID, Slr0355 protein | | Authors: | Sakaki, K, Tomita, T, Kuzuyama, T, Nishiyama, M. | | Deposit date: | 2018-11-21 | | Release date: | 2020-01-15 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | A suicide enzyme catalyzes multiple reactions for biotin biosynthesis in cyanobacteria.
Nat.Chem.Biol., 16, 2020
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4YB4
 | | Crystal structure of homoisocitrate dehydrogenase from Thermus thermophilus in complex with homoisocitrate, magnesium ion (II) and NADH | | Descriptor: | (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylic acid, 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, GLYCEROL, ... | | Authors: | Takahashi, K, Tomita, T, Kuzuyama, T, Nishiyama, M. | | Deposit date: | 2015-02-18 | | Release date: | 2016-03-09 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Structure of homoisocitrate dehydrogenase from Thermus thermophilus in complex with homoisocitrate, magnesium(II) and NADH
To Be Published
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8HAR
 | | SAH-bound C-Methyltransferase Fur6 from Streptomyces sp. KO-3988 | | Descriptor: | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, Fur6, S-ADENOSYL-L-HOMOCYSTEINE | | Authors: | Noguchi, T, Nagata, R, Tomita, T, Kuzuyama, T. | | Deposit date: | 2022-10-26 | | Release date: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.12 Å) | | Cite: | Reductive biosynthesis of meroterpenoids via transient diazotization
To Be Published
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4Y1P
 | | Crystal structure of 3-isopropylmalate dehydrogenase (Saci_0600) from Sulfolobus acidocaldarius complex with 3-isopropylmalate and Mg2+ | | Descriptor: | 3-ISOPROPYLMALIC ACID, 3-isopropylmalate dehydrogenase, MAGNESIUM ION, ... | | Authors: | Takahashi, K, Tomita, T, Kuzuyama, T, Nishiyama, M. | | Deposit date: | 2015-02-08 | | Release date: | 2016-03-09 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Characterization of two beta-decarboxylating dehydrogenases from Sulfolobus acidocaldarius
Extremophiles, 20, 2016
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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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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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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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5HN5
 | | Crystal structure of beta-decarboxylating dehydrogenase (TK0280) from Thermococcus kodakarensis complexed with Mn and isocitrate | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, Homoisocitrate dehydrogenase, ISOCITRIC ACID, ... | | 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 (2.55 Å) | | Cite: | Structure and function of an ancestral-type beta-decarboxylating dehydrogenase from Thermococcus kodakarensis
Biochem. J., 474, 2017
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5HN6
 | | Crystal structure of beta-decarboxylating dehydrogenase (TK0280) from Thermococcus kodakarensis complexed with Mn and 3-isopropylmalate | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 3-ISOPROPYLMALIC ACID, Homoisocitrate dehydrogenase, ... | | 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 (2.5 Å) | | Cite: | Structure and function of an ancestral-type beta-decarboxylating dehydrogenase from Thermococcus kodakarensis
Biochem. J., 474, 2017
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5HN3
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5EIN
 | | Crystal structure of C148A mutant of LysY from Thermus thermophilus in complex with NADP+ and LysW-gamma-aminoadipic acid | | Descriptor: | Alpha-aminoadipate carrier protein LysW, FORMIC ACID, N-acetyl-gamma-glutamyl-phosphate/N-acetyl-gamma-aminoadipyl-phosphate reductase, ... | | Authors: | Shimizu, T, Tomita, T, Nishiyama, M. | | Deposit date: | 2015-10-30 | | Release date: | 2016-03-23 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Crystal Structure of the LysYLysW Complex from Thermus thermophilus.
J.Biol.Chem., 291, 2016
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5EIO
 | | Crystal structure of LysY from Thermus thermophilus complexed with NADP+ and LysW-gamma-aminoadipic semialdehyde | | Descriptor: | ACETIC ACID, N-acetyl-gamma-glutamyl-phosphate/N-acetyl-gamma-aminoadipyl-phosphate reductase, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, ... | | Authors: | Shimizu, T, Tomita, T, Nishiyama, M. | | Deposit date: | 2015-10-30 | | Release date: | 2016-03-23 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal Structure of the LysYLysW Complex from Thermus thermophilus.
J.Biol.Chem., 291, 2016
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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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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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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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