5WSY
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![BU of 5wsy by Molmil](/molmil-images/mine/5wsy) | The complex structure of SAV606 with N-carboxymethyl-3-aminobutyrate | Descriptor: | (3~{R})-3-(2-hydroxy-2-oxoethylamino)butanoic acid, Uncharacterized protein | Authors: | Chisuga, T, Miyanaga, A, Kudo, F, Eguchi, T. | Deposit date: | 2016-12-08 | Release date: | 2017-05-31 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Structural analysis of the dual-function thioesterase SAV606 unravels the mechanism of Michael addition of glycine to an alpha , beta-unsaturated thioester. J. Biol. Chem., 292, 2017
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8YYQ
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![BU of 8yyq by Molmil](/molmil-images/mine/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 | Method: | X-RAY DIFFRACTION (1.95 Å) | Cite: | Engineering the Substrate Specificity of (S)-beta-Phenylalanine Adenylation Enzyme HitB. Chembiochem, 2024
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8YYR
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![BU of 8yyr by Molmil](/molmil-images/mine/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 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Engineering the Substrate Specificity of (S)-beta-Phenylalanine Adenylation Enzyme HitB. Chembiochem, 2024
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8K4R
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![BU of 8k4r by Molmil](/molmil-images/mine/8k4r) | Structure of VinM-VinL complex | Descriptor: | Acyl-carrier-protein, Non-ribosomal peptide synthetase, SODIUM ION, ... | Authors: | Miyanaga, A, Nagata, K, Nakajima, J, Chisuga, T, Kudo, F, Eguchi, T. | Deposit date: | 2023-07-20 | Release date: | 2023-11-01 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Structural Basis of Amide-Forming Adenylation Enzyme VinM in Vicenistatin Biosynthesis. Acs Chem.Biol., 18, 2023
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7YKE
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![BU of 7yke by Molmil](/molmil-images/mine/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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8H6S
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![BU of 8h6s by Molmil](/molmil-images/mine/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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8IN9
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![BU of 8in9 by Molmil](/molmil-images/mine/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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5Y1I
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![BU of 5y1i by Molmil](/molmil-images/mine/5y1i) | The crystal structure of GfsF | Descriptor: | Cytochrome P450, DI(HYDROXYETHYL)ETHER, PROTOPORPHYRIN IX CONTAINING FE, ... | Authors: | Miyanaga, A, Kudo, F, Eguchi, T. | Deposit date: | 2017-07-20 | Release date: | 2017-09-13 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Substrate Recognition by a Dual-Function P450 Monooxygenase GfsF Involved in FD-891 Biosynthesis Chembiochem, 18, 2017
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5WSX
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![BU of 5wsx by Molmil](/molmil-images/mine/5wsx) | The crystal structure of SAV606 | Descriptor: | Uncharacterized protein | Authors: | Chisuga, T, Miyanaga, A, Kudo, F, Eguchi, T. | Deposit date: | 2016-12-08 | Release date: | 2017-05-31 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Structural analysis of the dual-function thioesterase SAV606 unravels the mechanism of Michael addition of glycine to an alpha , beta-unsaturated thioester. J. Biol. Chem., 292, 2017
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4ZM3
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![BU of 4zm3 by Molmil](/molmil-images/mine/4zm3) | Crystal structure of PLP-Dependent 3-Aminobenzoate Synthase PctV wild-type | Descriptor: | Aminotransferase, DI(HYDROXYETHYL)ETHER, PYRIDOXAL-5'-PHOSPHATE, ... | Authors: | Hirayama, A, Miyanaga, A, Kudo, F, Eguchi, T. | Deposit date: | 2015-05-02 | Release date: | 2015-10-14 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.27 Å) | Cite: | Mechanism-Based Trapping of the Quinonoid Intermediate by Using the K276R Mutant of PLP-Dependent 3-Aminobenzoate Synthase PctV in the Biosynthesis of Pactamycin. Chembiochem, 16, 2015
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4ZM4
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![BU of 4zm4 by Molmil](/molmil-images/mine/4zm4) | Complex structure of PctV K276R mutant with PMP and 3-dehydroshkimate | Descriptor: | (3E,4R,5R)-4,5-dihydroxy-3-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}cyclohex-1-ene-1-carboxylic acid, Aminotransferase, PYRIDOXAL-5'-PHOSPHATE | Authors: | Hirayama, A, Miyanaga, A, Kudo, F, Eguchi, T. | Deposit date: | 2015-05-02 | Release date: | 2015-10-14 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Mechanism-Based Trapping of the Quinonoid Intermediate by Using the K276R Mutant of PLP-Dependent 3-Aminobenzoate Synthase PctV in the Biosynthesis of Pactamycin. Chembiochem, 16, 2015
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5JJQ
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![BU of 5jjq by Molmil](/molmil-images/mine/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
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![BU of 5jjp by Molmil](/molmil-images/mine/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
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![BU of 7vee by Molmil](/molmil-images/mine/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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7VEF
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![BU of 7vef by Molmil](/molmil-images/mine/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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2D2X
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![BU of 2d2x by Molmil](/molmil-images/mine/2d2x) | Crystal structure of 2-deoxy-scyllo-inosose synthase | Descriptor: | 2-deoxy-scyllo-inosose synthase, COBALT (II) ION, GLYCEROL, ... | Authors: | Nango, E, Kumasaka, T, Tanaka, N, Kakinuma, K, Eguchi, T. | Deposit date: | 2005-09-20 | Release date: | 2006-10-03 | Last modified: | 2011-07-13 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Structure of 2-deoxy-scyllo-inosose synthase, a key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics, in complex with a mechanism-based inhibitor and NAD+ Proteins, 70, 2008
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6K96
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![BU of 6k96 by Molmil](/molmil-images/mine/6k96) | Crystal structure of Ari2 | Descriptor: | Five-membered-cyclitol-phosphate synthase, GLYCEROL, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... | Authors: | Miyanaga, A, Tsunoda, T, Kudo, F, Eguchi, T. | Deposit date: | 2019-06-14 | Release date: | 2019-12-25 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Stereochemistry in the Reaction of themyo-Inositol Phosphate Synthase Ortholog Ari2 during Aristeromycin Biosynthesis. Biochemistry, 58, 2019
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6M01
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![BU of 6m01 by Molmil](/molmil-images/mine/6m01) | The structure of HitB-HitD complex | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, GLYCEROL, N-[2-(acetylamino)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide, ... | Authors: | Miyanaga, A, Kurihara, S, Kudo, F, Eguchi, T. | Deposit date: | 2020-02-19 | Release date: | 2020-07-08 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Structural Characterization of Complex of Adenylation Domain and Carrier Protein by Using Pantetheine Cross-Linking Probe. Acs Chem.Biol., 15, 2020
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5ZDN
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![BU of 5zdn by Molmil](/molmil-images/mine/5zdn) | The complex structure of FomD with CDP | Descriptor: | CYTIDINE-5'-DIPHOSPHATE, 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 (2.02 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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5ZDM
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![BU of 5zdm by Molmil](/molmil-images/mine/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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6J38
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![BU of 6j38 by Molmil](/molmil-images/mine/6j38) | Crystal structure of CmiS2 | Descriptor: | FAD-dependent glycine oxydase, FLAVIN-ADENINE DINUCLEOTIDE | Authors: | Kawasaki, D, Chisuga, T, Miyanaga, A, Kudo, F, Eguchi, T. | Deposit date: | 2019-01-04 | Release date: | 2019-06-12 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Structural Analysis of the Glycine Oxidase Homologue CmiS2 Reveals a Unique Substrate Recognition Mechanism for Formation of a beta-Amino Acid Starter Unit in Cremimycin Biosynthesis. Biochemistry, 58, 2019
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6J39
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![BU of 6j39 by Molmil](/molmil-images/mine/6j39) | Crystal structure of CmiS2 with inhibitor | Descriptor: | (3R)-3-[(carboxymethyl)sulfanyl]nonanoic acid, FAD-dependent glycine oxydase, FLAVIN-ADENINE DINUCLEOTIDE | Authors: | Kawasaki, D, Chisuga, T, Miyanaga, A, Kudo, F, Eguchi, T. | Deposit date: | 2019-01-04 | Release date: | 2019-06-12 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.45 Å) | Cite: | Structural Analysis of the Glycine Oxidase Homologue CmiS2 Reveals a Unique Substrate Recognition Mechanism for Formation of a beta-Amino Acid Starter Unit in Cremimycin Biosynthesis. Biochemistry, 58, 2019
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6K97
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![BU of 6k97 by Molmil](/molmil-images/mine/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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6JW6
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![BU of 6jw6 by Molmil](/molmil-images/mine/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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6JW8
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![BU of 6jw8 by Molmil](/molmil-images/mine/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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