3WVN
 
 | | Complex structure of VinN with L-aspartate | | Descriptor: | ASPARTIC ACID, Non-ribosomal peptide synthetase | | Authors: | Miyanaga, A, Cieslak, J, Shinohara, Y, Kudo, F, Eguchi, T. | | Deposit date: | 2014-05-30 | | Release date: | 2014-10-01 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | The crystal structure of the adenylation enzyme VinN reveals a unique beta-amino acid recognition mechanism
J.Biol.Chem., 289, 2014
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8H6S
 | | Structure of acyltransferase VinK in complex with the loading acyl carrier protein of vicenistatin PKS | | Descriptor: | MAGNESIUM ION, Malonyl-CoA-[acyl-carrier-protein] transacylase, N-[2-(acetylamino)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide, ... | | Authors: | Kawada, K, Miyanaga, A, Chisuga, T, Kudo, F, Eguchi, T. | | Deposit date: | 2022-10-18 | | Release date: | 2022-12-21 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Structural Basis of Transient Interactions of Acyltransferase VinK with the Loading Acyl Carrier Protein of the Vicenistatin Modular Polyketide Synthase.
Biochemistry, 62, 2023
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6AKD
 | | Crystal structure of IdnL7 | | Descriptor: | '5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE, AMP-dependent synthetase and ligase, GLYCEROL | | Authors: | Cieslak, J, Miyanaga, A, Kudo, F, Eguchi, T. | | Deposit date: | 2018-08-31 | | Release date: | 2019-03-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Functional and structural characterization of IdnL7, an adenylation enzyme involved in incednine biosynthesis.
Acta Crystallogr F Struct Biol Commun, 75, 2019
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7YKE
 | | Crystal structure of chondroitin ABC lyase I in complex with chondroitin disaccharide 4,6-sulfate | | Descriptor: | 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4,6-di-O-sulfo-beta-D-galactopyranose, Chondroitin sulfate ABC endolyase, MAGNESIUM ION | | Authors: | Takashima, M, Watanabe, I, Miyanaga, A, Eguchi, T. | | Deposit date: | 2022-07-22 | | Release date: | 2022-11-30 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.88 Å) | | Cite: | 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., 290, 2023
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8YYR
 | | Structure of the HitB T293G mutant | | Descriptor: | Putative ATP-dependent b-aminoacyl-ACP synthetase, [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(3~{S})-3-azanyl-3-(2-bromophenyl)propanoyl]sulfamate | | Authors: | Wang, D, Miyanaga, A, Chisuga, T, Kudo, F, Eguchi, T. | | Deposit date: | 2024-04-04 | | Release date: | 2024-06-05 | | Last modified: | 2024-08-14 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Engineering the Substrate Specificity of (S)-beta-Phenylalanine Adenylation Enzyme HitB.
Chembiochem, 25, 2024
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8YYQ
 | | Structure of the HitB F328L mutant | | Descriptor: | Putative ATP-dependent b-aminoacyl-ACP synthetase, [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(3~{S})-3-azanyl-3-(3-cyanophenyl)propanoyl]sulfamate | | Authors: | Wang, D, Miyanaga, A, Chisuga, T, Kudo, F, Eguchi, T. | | Deposit date: | 2024-04-04 | | Release date: | 2024-06-05 | | Last modified: | 2024-08-14 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Engineering the Substrate Specificity of (S)-beta-Phenylalanine Adenylation Enzyme HitB.
Chembiochem, 25, 2024
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6ABJ
 | | The apo-structure of D-lactate dehydrogenase from Pseudomonas aeruginosa | | Descriptor: | ACETATE ION, D-lactate dehydrogenase (Fermentative) | | Authors: | Furukawa, N, Miyanaga, A, Nakajima, M, Taguchi, H. | | Deposit date: | 2018-07-21 | | Release date: | 2018-09-19 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.86 Å) | | Cite: | Structural Basis of Sequential Allosteric Transitions in Tetrameric d-Lactate Dehydrogenases from Three Gram-Negative Bacteria
Biochemistry, 57, 2018
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6JML
 | | Re-refined structure of R-state L-lactate dehydrogenase fromLactobacillus casei | | Descriptor: | L-lactate dehydrogenase, SULFATE ION | | Authors: | Arai, K, Miyanaga, A, Uchikoba, H, Fushinobu, S, Taguchi, H. | | Deposit date: | 2019-03-12 | | Release date: | 2020-05-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Crystal structure of penta mutant of L-lactate dehydrogenase from Lactobacillus casei
To Be Published
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6K97
 | | Crystal structure of fusion DH domain | | Descriptor: | Fusion DH, SULFATE ION | | Authors: | Kawasaki, D, Miyanaga, A, Chisuga, T, Kudo, F, Eguchi, T. | | Deposit date: | 2019-06-14 | | Release date: | 2019-11-27 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Functional and Structural Analyses of the Split-Dehydratase Domain in the Biosynthesis of Macrolactam Polyketide Cremimycin.
Biochemistry, 58, 2019
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6ABI
 | | The apo-structure of D-lactate dehydrogenase from Fusobacterium nucleatum | | Descriptor: | D-lactate dehydrogenase, GLYCEROL, SULFATE ION | | Authors: | Furukawa, N, Miyanaga, A, Nakajima, M, Taguchi, H. | | Deposit date: | 2018-07-21 | | Release date: | 2018-09-19 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Structural Basis of Sequential Allosteric Transitions in Tetrameric d-Lactate Dehydrogenases from Three Gram-Negative Bacteria
Biochemistry, 57, 2018
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5ZDM
 | | The ligand-free structure of FomD | | Descriptor: | CALCIUM ION, FomD, GLYCEROL | | Authors: | Sato, S, Miyanaga, A, Kudo, F, Eguchi, T. | | Deposit date: | 2018-02-23 | | Release date: | 2018-07-25 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.38 Å) | | Cite: | Biochemical and Structural Analysis of FomD That Catalyzes the Hydrolysis of Cytidylyl ( S)-2-Hydroxypropylphosphonate in Fosfomycin Biosynthesis.
Biochemistry, 57, 2018
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5JJQ
 | | Crystal structure of IdnL1 | | Descriptor: | 5'-O-[(R)-{[(3S)-3-aminobutanoyl]oxy}(hydroxy)phosphoryl]adenosine, AMP-dependent synthetase and ligase, CHLORIDE ION | | Authors: | Cieslak, J, Miyanaga, A, Kudo, F, Eguchi, T. | | Deposit date: | 2016-04-25 | | Release date: | 2017-03-22 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Biochemical characterization and structural insight into aliphatic beta-amino acid adenylation enzymes IdnL1 and CmiS6
Proteins, 85, 2017
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5JJP
 | | Crystal structure of CmiS6 | | Descriptor: | Nonribosomal peptide synthase | | Authors: | Cieslak, J, Miyanaga, A, Kudo, F, Eguchi, T. | | Deposit date: | 2016-04-25 | | Release date: | 2017-03-22 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Biochemical characterization and structural insight into aliphatic beta-amino acid adenylation enzymes IdnL1 and CmiS6
Proteins, 85, 2017
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7VEE
 | | The ligand-free structure of GfsA KSQ-AT didomain | | Descriptor: | GLYCEROL, Polyketide synthase | | Authors: | Chisuga, T, Miyanaga, A, Nagai, A, Kudo, F, Eguchi, T. | | Deposit date: | 2021-09-08 | | Release date: | 2022-01-12 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.55 Å) | | Cite: | Structural Insight into the Reaction Mechanism of Ketosynthase-Like Decarboxylase in a Loading Module of Modular Polyketide Synthases.
Acs Chem.Biol., 17, 2022
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6JW6
 | | The crystal structure of KanD2 in complex with NAD | | Descriptor: | Dehydrogenase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE | | Authors: | Kudo, F, Kitayama, Y, Miyanaga, A, Hirayama, A, Eguchi, T. | | Deposit date: | 2019-04-18 | | Release date: | 2020-04-15 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | 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, 59, 2020
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8IN9
 | | The structure of the GfsA KSQ-AT didomain in complex with the GfsA ACP domain | | Descriptor: | N-[2-(acetylamino)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide, Polyketide synthase | | Authors: | Chisuga, T, Murakami, S, Miyanaga, A, Kudo, F, Eguchi, T. | | Deposit date: | 2023-03-09 | | Release date: | 2023-05-31 | | Last modified: | 2023-06-28 | | Method: | X-RAY DIFFRACTION (3.4 Å) | | Cite: | 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., 18, 2023
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7VEF
 | | The structure of GfsA KSQ-AT didomain in complex with a malonate substrate analog | | Descriptor: | GLYCEROL, N-(2-acetamidoethyl)-2-nitro-ethanamide, Polyketide synthase | | Authors: | Chisuga, T, Miyanaga, A, Nagai, A, Kudo, F, Eguchi, T. | | Deposit date: | 2021-09-08 | | Release date: | 2022-01-12 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.65 Å) | | Cite: | Structural Insight into the Reaction Mechanism of Ketosynthase-Like Decarboxylase in a Loading Module of Modular Polyketide Synthases.
Acs Chem.Biol., 17, 2022
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6JW8
 | | The crystal structure of KanD2 in complex with NADH and 3"-deamino-3"-hydroxykanamycin B | | Descriptor: | (2S,3R,4S,5S,6R)-2-[(1S,2S,3R,4S,6R)-3-[(2R,3R,4R,5S,6R)-6-(aminomethyl)-3-azanyl-4,5-bis(oxidanyl)oxan-2-yl]oxy-4,6-bis(azanyl)-2-oxidanyl-cyclohexyl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol, 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, Dehydrogenase | | Authors: | Kudo, F, Kitayama, Y, Miyanaga, A, Hirayama, A, Eguchi, T. | | Deposit date: | 2019-04-18 | | Release date: | 2020-04-15 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | 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, 59, 2020
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6JW7
 | | The crystal structure of KanD2 in complex with NADH and 3"-deamino-3"-hydroxykanamycin A | | Descriptor: | (2R,3S,4S,5R,6R)-2-(aminomethyl)-6-[(1R,2S,3S,4R,6S)-4,6-bis(azanyl)-3-[(2S,3R,4S,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-oxidanyl-cyclohexyl]oxy-oxane-3,4,5-triol, 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, Dehydrogenase | | Authors: | Kudo, F, Kitayama, Y, Miyanaga, A, Hirayama, A, Eguchi, T. | | Deposit date: | 2019-04-18 | | Release date: | 2020-04-15 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.36 Å) | | Cite: | 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, 59, 2020
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2DEP
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5H40
 | | Crystal Structure of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans in complex with sophorose | | Descriptor: | CALCIUM ION, GLYCEROL, Uncharacterized protein, ... | | Authors: | Nakajima, M, Tanaka, N, Furukawa, N, Nihira, T, Kodutsumi, Y, Takahashi, Y, Sugimoto, N, Miyanaga, A, Fushinobu, S, Taguchi, H, Nakai, H. | | Deposit date: | 2016-10-28 | | Release date: | 2017-03-01 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Mechanistic insight into the substrate specificity of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans
Sci Rep, 7, 2017
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5H41
 | | Crystal Structure of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans in complex with sophorose, isofagomine, sulfate ion | | Descriptor: | 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE, SULFATE ION, Uncharacterized protein, ... | | Authors: | Nakajima, M, Tanaka, N, Furukawa, N, Nihira, T, Kodutsumi, Y, Takahashi, Y, Sugimoto, N, Miyanaga, A, Fushinobu, S, Taguchi, H, Nakai, H. | | Deposit date: | 2016-10-28 | | Release date: | 2017-03-01 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Mechanistic insight into the substrate specificity of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans
Sci Rep, 7, 2017
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5H42
 | | Crystal Structure of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans in complex with alpha-d-glucose-1-phosphate | | Descriptor: | 1-O-phosphono-alpha-D-glucopyranose, Uncharacterized protein, alpha-D-glucopyranose | | Authors: | Nakajima, M, Tanaka, N, Furukawa, N, Nihira, T, Kodutsumi, Y, Takahashi, Y, Sugimoto, N, Miyanaga, A, Fushinobu, S, Taguchi, H, Nakai, H. | | Deposit date: | 2016-10-28 | | Release date: | 2017-03-01 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Mechanistic insight into the substrate specificity of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans
Sci Rep, 7, 2017
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5H3Z
 | | Crystal Structure of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans | | Descriptor: | CALCIUM ION, DI(HYDROXYETHYL)ETHER, GLYCEROL, ... | | Authors: | Nakajima, M, Tanaka, N, Furukawa, N, Nihira, T, Kodutsumi, Y, Takahashi, Y, Sugimoto, N, Miyanaga, A, Fushinobu, S, Taguchi, H, Nakai, H. | | Deposit date: | 2016-10-28 | | Release date: | 2017-03-01 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Mechanistic insight into the substrate specificity of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans
Sci Rep, 7, 2017
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6J9T
 | | Complex structure of Lactobacillus casei lactate dehydrogenase with fructose-1,6-bisphosphate | | Descriptor: | 1,6-di-O-phosphono-beta-D-fructofuranose, L-lactate dehydrogenase, SULFATE ION | | Authors: | Arai, K, Miyanaga, A, Uchikoba, H, Fushinobu, S, Taguchi, H. | | Deposit date: | 2019-01-24 | | Release date: | 2019-02-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Crystal structure of penta mutant of L-lactate dehydrogenase from Lactobacillus casei
To Be Published
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