7EXV
 
 | | GH127 beta-L-arabinofuranosidase HypBA1 covalently complexed with beta-L-arabinofuranoylamide | | Descriptor: | 2-bromanyl-N-[(2S,3R,4R,5S)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]ethanamide, Non-reducing end beta-L-arabinofuranosidase, ZINC ION | | Authors: | Sawano, K, Arakawa, T, Yamada, C, Fujita, K, Fushinobu, S. | | Deposit date: | 2021-05-28 | | Release date: | 2021-11-17 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Substrate complex structure, active site labeling and catalytic role of the zinc ion in cysteine glycosidase.
Glycobiology, 32, 2022
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8HR3
 | | [D-Cys5,Asp7,Val8,D-Lys16]-STp(5-17) | | Descriptor: | DCY-CYS-ASP-VAL-CYS-CYS-ASN-PRO-ALA-CYS-ALA-DLY-CYS | | Authors: | Shimamoto, S, Hidaka, Y, Yoshino, S, Goto, M. | | Deposit date: | 2022-12-14 | | Release date: | 2023-09-20 | | Method: | SOLUTION NMR | | Cite: | The Molecular Basis of Heat-Stable Enterotoxin for Vaccine Development and Cancer Cell Detection.
Molecules, 28, 2023
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7BZL
 | | GH127 beta-L-arabinofuranosidase HypBA1 covalently complexed with beta-L-arabinofuranose-configured cyclophellitol | | Descriptor: | (1S,2S,3R,4R)-3-(hydroxymethyl)cyclopentane-1,2,4-triol, Non-reducing end beta-L-arabinofuranosidase, ZINC ION | | Authors: | Amaki, S, McGregor, N.G.S, Arakawa, T, Yamada, C, Borlandelli, V, Overkleeft, H.S, Davies, G.J, Fushinobu, S. | | Deposit date: | 2020-04-28 | | Release date: | 2021-01-27 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Cysteine Nucleophiles in Glycosidase Catalysis: Application of a Covalent beta-l-Arabinofuranosidase Inhibitor.
Angew.Chem.Int.Ed.Engl., 60, 2021
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8HR4
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3AO9
 | | Crystal structure of the C-terminal domain of sequence-specific ribonuclease | | Descriptor: | CADMIUM ION, Colicin-E5 | | Authors: | Inoue, S, Fushinobu, S, Ogawa, T, Hidaka, M, Masaki, H, Yajima, S. | | Deposit date: | 2010-09-22 | | Release date: | 2011-09-28 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Identification of the catalytic residues of sequence-specific and histidine-free ribonuclease colicin E5
J.Biochem., 152, 2012
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8WOV
 | | Crystal structure of Arabidopsis thaliana UDP-glucose 4-epimerase 2 (AtUGE2) complexed with UDP, G233A mutant | | Descriptor: | NICOTINAMIDE-ADENINE-DINUCLEOTIDE, UDP-glucose 4-epimerase 2, URIDINE-5'-DIPHOSPHATE | | Authors: | Matsumoto, M, Umezawa, A, Kotake, T, Fushinobu, S. | | Deposit date: | 2023-10-07 | | Release date: | 2024-05-15 | | Last modified: | 2024-07-10 | | Method: | X-RAY DIFFRACTION (2.25 Å) | | Cite: | Cytosolic UDP-L-arabinose synthesis by bifunctional UDP-glucose 4-epimerases in Arabidopsis.
Plant J., 119, 2024
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8WOP
 | | Crystal structure of Arabidopsis thaliana UDP-glucose 4-epimerase 2 (AtUGE2) complexed with UDP, wild-type | | Descriptor: | NICOTINAMIDE-ADENINE-DINUCLEOTIDE, UDP-glucose 4-epimerase 2, URIDINE-5'-DIPHOSPHATE | | Authors: | Matsumoto, M, Umezawa, A, Kotake, T, Fushinobu, S. | | Deposit date: | 2023-10-07 | | Release date: | 2024-05-08 | | Last modified: | 2024-07-10 | | Method: | X-RAY DIFFRACTION (2.35 Å) | | Cite: | Cytosolic UDP-L-arabinose synthesis by bifunctional UDP-glucose 4-epimerases in Arabidopsis.
Plant J., 119, 2024
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8HHV
 | | endo-alpha-D-arabinanase EndoMA1 from Microbacterium arabinogalactanolyticum | | Descriptor: | CALCIUM ION, GLYCEROL, SODIUM ION, ... | | Authors: | Nakashima, C, Li, J, Arakawa, T, Yamada, C, Ishiwata, A, Fujita, K, Fushinobu, S. | | Deposit date: | 2022-11-17 | | Release date: | 2023-08-16 | | Last modified: | 2023-09-27 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Identification and characterization of endo-alpha-, exo-alpha-, and exo-beta-D-arabinofuranosidases degrading lipoarabinomannan and arabinogalactan of mycobacteria.
Nat Commun, 14, 2023
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8WOW
 | | Crystal structure of Arabidopsis thaliana UDP-glucose 4-epimerase 2 (AtUGE2) complexed with UDP, I160L/G233A mutant | | Descriptor: | NICOTINAMIDE-ADENINE-DINUCLEOTIDE, SULFATE ION, UDP-glucose 4-epimerase 2, ... | | Authors: | Matsumoto, M, Umezawa, A, Kotake, T, Fushinobu, S. | | Deposit date: | 2023-10-08 | | Release date: | 2024-05-15 | | Last modified: | 2024-07-10 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Cytosolic UDP-L-arabinose synthesis by bifunctional UDP-glucose 4-epimerases in Arabidopsis.
Plant J., 119, 2024
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5WZN
 | | Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - GalNAc complex | | Descriptor: | 2-acetamido-2-deoxy-alpha-D-galactopyranose, Alpha-N-acetylgalactosaminidase, CALCIUM ION, ... | | Authors: | Sato, M, Arakawa, T, Ashida, H, Fushinobu, S. | | Deposit date: | 2017-01-18 | | Release date: | 2017-06-07 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | The first crystal structure of a family 129 glycoside hydrolase from a probiotic bacterium reveals critical residues and metal cofactors
J. Biol. Chem., 292, 2017
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5WZP
 | | Alpha-N-acetylgalactosaminidase NagBb from Bifidobacterium bifidum - ligand free | | Descriptor: | Alpha-N-acetylgalactosaminidase, CALCIUM ION, ZINC ION | | Authors: | Sato, M, Arakawa, T, Ashida, H, Fushinobu, S. | | Deposit date: | 2017-01-18 | | Release date: | 2017-06-07 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.64 Å) | | Cite: | The first crystal structure of a family 129 glycoside hydrolase from a probiotic bacterium reveals critical residues and metal cofactors
J. Biol. Chem., 292, 2017
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5Z76
 | | Artificial L-threonine 3-dehydrogenase designed by full consensus design | | Descriptor: | Artificial L-threonine 3-dehydrogenase | | Authors: | Nakano, S, Motoyama, T, Miyashita, Y, Ishizuka, Y, Matsuo, N, Tokiwa, H, Shinoda, S, Asano, Y, Ito, S. | | Deposit date: | 2018-01-27 | | Release date: | 2018-08-22 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Benchmark Analysis of Native and Artificial NAD+-Dependent Enzymes Generated by a Sequence-Based Design Method with or without Phylogenetic Data.
Biochemistry, 57, 2018
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4UBS
 | | The crystal structure of cytochrome P450 105D7 from Streptomyces avermitilis in complex with Diclofenac | | Descriptor: | 2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID, DI(HYDROXYETHYL)ETHER, PHOSPHATE ION, ... | | Authors: | Xu, L.H, Ikeda, H, Arakawa, T, Wakagi, T, Shoun, H, Fushinobu, S. | | Deposit date: | 2014-08-13 | | Release date: | 2014-11-05 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Structural basis for the 4'-hydroxylation of diclofenac by a microbial cytochrome P450 monooxygenase.
Appl.Microbiol.Biotechnol., 99, 2015
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5Z75
 | | Artificial L-threonine 3-dehydrogenase designed by ancestral sequence reconstruction. | | Descriptor: | Artificial L-threonine 3-dehydrogenase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, NONAETHYLENE GLYCOL, ... | | Authors: | Nakano, S, Motoyama, T, Miyashita, Y, Ishizuka, Y, Matsuo, N, Tokiwa, H, Shinoda, S, Asano, Y, Ito, S. | | Deposit date: | 2018-01-27 | | Release date: | 2018-08-22 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Benchmark Analysis of Native and Artificial NAD+-Dependent Enzymes Generated by a Sequence-Based Design Method with or without Phylogenetic Data.
Biochemistry, 57, 2018
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1IQP
 | | Crystal Structure of the Clamp Loader Small Subunit from Pyrococcus furiosus | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, RFCS | | Authors: | Oyama, T, Ishino, Y, Cann, I.K.O, Ishino, S, Morikawa, K. | | Deposit date: | 2001-07-24 | | Release date: | 2001-09-19 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Atomic Structure of the Clamp Loader Small Subunit from Pyrococcus furiosus
Mol.Cell, 8, 2001
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5GQG
 | | Crystal structure of lacto-N-biosidase LnbX from Bifidobacterium longum subsp. longum, galacto-N-biose complex | | Descriptor: | CALCIUM ION, Lacto-N-biosidase, beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose | | Authors: | Yamada, C, Arakawa, T, Katayama, T, Fushinobu, S. | | Deposit date: | 2016-08-07 | | Release date: | 2017-04-19 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Molecular Insight into Evolution of Symbiosis between Breast-Fed Infants and a Member of the Human Gut Microbiome Bifidobacterium longum
Cell Chem Biol, 24, 2017
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5GQF
 | | Crystal structure of lacto-N-biosidase LnbX from Bifidobacterium longum subsp. longum, lacto-N-biose complex | | Descriptor: | CALCIUM ION, Lacto-N-biosidase, beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose | | Authors: | Yamada, C, Arakawa, T, Katayama, T, Fushinobu, S. | | Deposit date: | 2016-08-07 | | Release date: | 2017-04-19 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.82 Å) | | Cite: | Molecular Insight into Evolution of Symbiosis between Breast-Fed Infants and a Member of the Human Gut Microbiome Bifidobacterium longum
Cell Chem Biol, 24, 2017
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8K2K
 | | Crystal structure of Group 3 Oligosaccharide/Monosaccharide-releasing beta-N-acetylgalactosaminidase NgaDssm in complex with GalNAc-thiazoline | | Descriptor: | (3aR,5R,6R,7R,7aR)-5-(hydroxymethyl)-2-methyl-5,6,7,7a-tetrahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol, CHLORIDE ION, GLYCEROL, ... | | Authors: | Sumida, T, Fushinobu, S. | | Deposit date: | 2023-07-12 | | Release date: | 2024-04-24 | | Last modified: | 2024-05-22 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | Genetic and functional diversity of beta-N-acetylgalactosamine-targeting glycosidases expanded by deep-sea metagenome analysis.
Nat Commun, 15, 2024
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8K2L
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8K2J
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8K2H
 | | Crystal structure of Group 2Oligosaccharide/Monosaccharide-releasing beta-N-acetylhexosaminidase NgaAt from Arabidopsis thaliana in complex with GalNAc-thiazoline | | Descriptor: | (3aR,5R,6R,7R,7aR)-5-(hydroxymethyl)-2-methyl-5,6,7,7a-tetrahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol, CHLORIDE ION, DI(HYDROXYETHYL)ETHER, ... | | Authors: | Sumida, T, Fushinobu, S. | | Deposit date: | 2023-07-12 | | Release date: | 2024-04-24 | | Last modified: | 2024-05-22 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Genetic and functional diversity of beta-N-acetylgalactosamine-targeting glycosidases expanded by deep-sea metagenome analysis.
Nat Commun, 15, 2024
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8K2G
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8K2I
 | | Crystal structure of Group 2 Oligosaccharide/Monosaccharide-releasing beta-N-acetylhexosaminidase NgaAt from Arabidopsis thaliana in complex with GlcNAc-thiazoline | | Descriptor: | 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL, CHLORIDE ION, DI(HYDROXYETHYL)ETHER, ... | | Authors: | Sumida, T, Fushinobu, S. | | Deposit date: | 2023-07-12 | | Release date: | 2024-04-24 | | Last modified: | 2024-05-22 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Genetic and functional diversity of beta-N-acetylgalactosamine-targeting glycosidases expanded by deep-sea metagenome analysis.
Nat Commun, 15, 2024
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8K2M
 | | Crystal structure of Group 4 Monosaccharide-releasing beta-N-acetylgalactosaminidase NgaP2 from Paenibacillus sp. TS12 in complex with GalNAc-thiazoline | | Descriptor: | (3aR,5R,6R,7R,7aR)-5-(hydroxymethyl)-2-methyl-5,6,7,7a-tetrahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol, BROMIDE ION, Monosaccharide-releasing beta-N-acetylgalactosaminidase | | Authors: | Sumida, T, Fushinobu, S. | | Deposit date: | 2023-07-12 | | Release date: | 2024-04-24 | | Last modified: | 2024-05-22 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Genetic and functional diversity of beta-N-acetylgalactosamine-targeting glycosidases expanded by deep-sea metagenome analysis.
Nat Commun, 15, 2024
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8K2N
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