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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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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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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7DQ5
 | | Crystal structure of HitB in complex with (S)-beta-phenylalanine sulfamoyladenosine | | Descriptor: | CALCIUM ION, 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-phenyl-propanoyl]sulfamate | | Authors: | Kudo, F, Takahashi, S, Miyanaga, A, Nakazawa, Y, Eguchi, T. | | Deposit date: | 2020-12-22 | | Release date: | 2021-03-03 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.45 Å) | | Cite: | Mutational Biosynthesis of Hitachimycin Analogs Controlled by the beta-Amino Acid-Selective Adenylation Enzyme HitB.
Acs Chem.Biol., 16, 2021
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7DQ6
 | | Crystal structure of HitB in complex with (S)-beta-3-Br-phenylalanine sulfamoyladenosine | | Descriptor: | CALCIUM ION, Putative ATP-dependent b-aminoacyl-ACP synthetase, [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl N-[(3S)-3-azanyl-3-(3-bromophenyl)propanoyl]sulfamate | | Authors: | Kudo, F, Takahashi, S, Miyanaga, A, Nakazawa, Y, Eguchi, T. | | Deposit date: | 2020-12-22 | | Release date: | 2021-03-03 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Mutational Biosynthesis of Hitachimycin Analogs Controlled by the beta-Amino Acid-Selective Adenylation Enzyme HitB.
Acs Chem.Biol., 16, 2021
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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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7CL2
 | | The crystal structure of KanJ | | Descriptor: | GLYCEROL, Kanamycin B dioxygenase, NICKEL (II) ION, ... | | Authors: | Kitayama, Y, Miyanaga, A, Kudo, F, Eguchi, T. | | Deposit date: | 2020-07-20 | | Release date: | 2021-01-13 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Stepwise Post-glycosylation Modification of Sugar Moieties in Kanamycin Biosynthesis.
Chembiochem, 22, 2021
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7CL5
 | | The crystal structure of KanJ in complex with kanamycin B and N-oxalylglycine | | Descriptor: | (1R,2S,3S,4R,6S)-4,6-DIAMINO-3-[(3-AMINO-3-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-2-HYDROXYCYCLOHEXYL 2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSIDE, Kanamycin B dioxygenase, N-OXALYLGLYCINE, ... | | Authors: | Kitayama, Y, Miyanaga, A, Kudo, F, Eguchi, T. | | Deposit date: | 2020-07-20 | | Release date: | 2021-01-13 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Stepwise Post-glycosylation Modification of Sugar Moieties in Kanamycin Biosynthesis.
Chembiochem, 22, 2021
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7CL4
 | | The crystal structure of KanJ in complex with N-oxalylglycine | | Descriptor: | Kanamycin B dioxygenase, N-OXALYLGLYCINE, NICKEL (II) ION | | Authors: | Kitayama, Y, Miyanaga, A, Kudo, F, Eguchi, T. | | Deposit date: | 2020-07-20 | | Release date: | 2021-01-13 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.25 Å) | | Cite: | Stepwise Post-glycosylation Modification of Sugar Moieties in Kanamycin Biosynthesis.
Chembiochem, 22, 2021
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7CL6
 | | The crystal structure of KanJ in complex with neamine and N-oxalylglycine | | Descriptor: | (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside, Kanamycin B dioxygenase, N-OXALYLGLYCINE, ... | | Authors: | Kitayama, Y, Miyanaga, A, Kudo, F, Eguchi, T. | | Deposit date: | 2020-07-20 | | Release date: | 2021-01-13 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.44 Å) | | Cite: | Stepwise Post-glycosylation Modification of Sugar Moieties in Kanamycin Biosynthesis.
Chembiochem, 22, 2021
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7CL3
 | | The crystal structure of KanJ in complex with kanamycin B | | Descriptor: | (1R,2S,3S,4R,6S)-4,6-DIAMINO-3-[(3-AMINO-3-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-2-HYDROXYCYCLOHEXYL 2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSIDE, Kanamycin B dioxygenase, NICKEL (II) ION, ... | | Authors: | Kitayama, Y, Miyanaga, A, Kudo, F, Eguchi, T. | | Deposit date: | 2020-07-20 | | Release date: | 2021-01-13 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Stepwise Post-glycosylation Modification of Sugar Moieties in Kanamycin Biosynthesis.
Chembiochem, 22, 2021
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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: | 2024-10-16 | | 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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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: | 2024-10-23 | | 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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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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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: | 2024-10-30 | | 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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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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5CZC
 | | The structure of VinK | | Descriptor: | CALCIUM ION, GLYCEROL, Malonyl-CoA-[acyl-carrier-protein] transacylase | | Authors: | Miyanaga, A, Iwasawa, S, Shinohara, Y, Kudo, F, Eguchi, T. | | Deposit date: | 2015-07-31 | | Release date: | 2016-02-03 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structure-based analysis of the molecular interactions between acyltransferase and acyl carrier protein in vicenistatin biosynthesis.
Proc.Natl.Acad.Sci.USA, 113, 2016
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5CZD
 | | The complex structure of VinK with VinL | | Descriptor: | 1,1'-ethane-1,2-diyldipyrrolidine-2,5-dione, 4'-PHOSPHOPANTETHEINE, Acyl-carrier-protein, ... | | Authors: | Miyanaga, A, Iwasawa, S, Shinohara, Y, Kudo, F, Eguchi, T. | | Deposit date: | 2015-07-31 | | Release date: | 2016-02-03 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.34 Å) | | Cite: | Structure-based analysis of the molecular interactions between acyltransferase and acyl carrier protein in vicenistatin biosynthesis.
Proc.Natl.Acad.Sci.USA, 113, 2016
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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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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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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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5ZK4
 | | The structure of DSZS acyltransferase with carrier protein | | Descriptor: | DisA protein, DisD protein, N-[2-(acetylamino)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide, ... | | Authors: | Miyanaga, A, Ouchi, R, Kudo, F, Eguchi, T. | | Deposit date: | 2018-03-23 | | Release date: | 2018-06-13 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.03 Å) | | Cite: | Structural basis of protein-protein interactions between a trans-acting acyltransferase and acyl carrier protein in polyketide disorazole biosynthesis
J. Am. Chem. Soc., 140, 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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