1OCZ
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1J1G
| Crystal structure of the RNase MC1 mutant N71S in complex with 5'-GMP | Descriptor: | GUANOSINE-5'-MONOPHOSPHATE, Ribonuclease MC1 | Authors: | Numata, T, Suzuki, A, Kakuta, Y, Kimura, K, Yao, M, Tanaka, I, Yoshida, Y, Ueda, T, Kimura, M. | Deposit date: | 2002-12-04 | Release date: | 2003-05-20 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | Crystal Structures of the Ribonuclease MC1 Mutants N71T and N71S in Complex with 5'-GMP: Structural Basis for Alterations in Substrate Specificity Biochemistry, 42, 2003
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4WLC
| Structure of dextran glucosidase with glucose | Descriptor: | CALCIUM ION, GLYCEROL, Glucan 1,6-alpha-glucosidase, ... | Authors: | Kobayashi, M, Kato, K, Yao, M. | Deposit date: | 2014-10-07 | Release date: | 2015-08-26 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.402 Å) | Cite: | Structural insights into the catalytic reaction that is involved in the reorientation of Trp238 at the substrate-binding site in GH13 dextran glucosidase Febs Lett., 589, 2015
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5E1Q
| Mutant (D415G) GH97 alpha-galactosidase in complex with Gal-Lac | Descriptor: | CALCIUM ION, GLYCEROL, Retaining alpha-galactosidase, ... | Authors: | Matsunaga, K, Yamashita, K, Tagami, T, Yao, M, Okuyama, M, Kimura, A. | Deposit date: | 2015-09-30 | Release date: | 2016-10-05 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.943 Å) | Cite: | Efficient synthesis of alpha-galactosyl oligosaccharides using a mutant Bacteroides thetaiotaomicron retaining alpha-galactosidase (BtGH97b). FEBS J., 284, 2017
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4XB3
| Structure of dextran glucosidase | Descriptor: | CALCIUM ION, Glucan 1,6-alpha-glucosidase, HEXAETHYLENE GLYCOL | Authors: | Kobayashi, M, Kato, K, Yao, M. | Deposit date: | 2014-12-16 | Release date: | 2015-08-26 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.093 Å) | Cite: | Structural insights into the catalytic reaction that is involved in the reorientation of Trp238 at the substrate-binding site in GH13 dextran glucosidase Febs Lett., 589, 2015
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4Y7E
| Crystal structure of beta-mannanase from Streptomyces thermolilacinus with mannohexaose | Descriptor: | CALCIUM ION, Endoglucanase, GLYCEROL, ... | Authors: | Kumagai, Y, Yamashita, K, Okuyama, M, Hatanaka, T, Yao, M, Kimura, A. | Deposit date: | 2015-02-14 | Release date: | 2015-09-23 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.5 Å) | Cite: | The loop structure of Actinomycete glycoside hydrolase family 5 mannanases governs substrate recognition Febs J., 282, 2015
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1GD6
| STRUCTURE OF THE BOMBYX MORI LYSOZYME | Descriptor: | LYSOZYME | Authors: | Matsuura, A, Aizawa, T, Yao, M, Kawano, K, Tanaka, I, Nitta, K. | Deposit date: | 2000-09-19 | Release date: | 2001-03-21 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Structural analysis of an insect lysozyme exhibiting catalytic efficiency at low temperatures. Biochemistry, 41, 2002
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3IS1
| Crystal structure of functional region of UafA from Staphylococcus saprophyticus in C2 form at 2.45 angstrom resolution | Descriptor: | GLYCEROL, Uro-adherence factor A | Authors: | Tanaka, Y, Matsuoka, E, Shouji, Y, Kuroda, M, Tanaka, I, Yao, M. | Deposit date: | 2009-08-24 | Release date: | 2010-09-08 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.45 Å) | Cite: | Crystal structure of the functional region of Uro-adherence factor A from Staphylococcus saprophyticus reveals participation of the B domain in ligand binding Protein Sci., 20, 2011
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3IS0
| Crystal structure of functional region of UafA from Staphylococcus saprophyticus in the presence of cholesterol | Descriptor: | GLYCEROL, Uro-adherence factor A | Authors: | Tanaka, Y, Shouji, Y, Matsuoka, E, Kuroda, M, Tanaka, I, Yao, M. | Deposit date: | 2009-08-24 | Release date: | 2010-09-08 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.75 Å) | Cite: | Crystal Structure of Functional Region of UafA from Staphylococcus saprophyticus To be Published
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3IRP
| Crystal structure of functional region of UafA from Staphylococcus saprophyticus at 1.50 angstrom resolution | Descriptor: | GLYCEROL, POTASSIUM ION, Uro-adherence factor A | Authors: | Tanaka, Y, Shouji, Y, Matsuoka, E, Kuroda, M, Tanaka, I, Yao, M. | Deposit date: | 2009-08-24 | Release date: | 2010-09-08 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.5 Å) | Cite: | Crystal structure of the functional region of Uro-adherence factor A from Staphylococcus saprophyticus reveals participation of the B domain in ligand binding Protein Sci., 20, 2011
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3IRZ
| Crystal structure of functional region of UafA from Staphylococcus saprophyticus in P212121 form | Descriptor: | GLYCEROL, Uro-adherence factor A | Authors: | Tanaka, Y, Shouji, Y, Matsuoka, E, Kuroda, M, Tanaka, I, Yao, M. | Deposit date: | 2009-08-24 | Release date: | 2010-09-08 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Crystal structure of the functional region of Uro-adherence factor A from Staphylococcus saprophyticus reveals participation of the B domain in ligand binding Protein Sci., 20, 2011
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5DCV
| Crystal structure of PhoRpp38-SL12M complex | Descriptor: | 50S ribosomal protein L7Ae, RNA (47-MER) | Authors: | Oshima, K, Tanaka, Y, Yao, M. | Deposit date: | 2015-08-24 | Release date: | 2016-07-06 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (3.401 Å) | Cite: | Structural basis for recognition of a kink-turn motif by an archaeal homologue of human RNase P protein Rpp38 Biochem.Biophys.Res.Commun., 474, 2016
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1MJI
| DETAILED ANALYSIS OF RNA-PROTEIN INTERACTIONS WITHIN THE BACTERIAL RIBOSOMAL PROTEIN L5/5S RRNA COMPLEX | Descriptor: | 50S ribosomal protein L5, 5S rRNA fragment, MAGNESIUM ION, ... | Authors: | Perederina, A, Nevskaya, N, Nikonov, O, Nikulin, A, Dumas, P, Yao, M, Tanaka, I, Garber, M, Gongadze, G, Nikonov, S. | Deposit date: | 2002-08-28 | Release date: | 2003-01-21 | Last modified: | 2011-07-13 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Detailed analysis of RNA-protein interactions within the bacterial ribosomal
protein L5/5S rRNA complex RNA, 8, 2002
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1J1W
| Crystal Structure Of The Monomeric Isocitrate Dehydrogenase In Complex With NADP+ | Descriptor: | Isocitrate Dehydrogenase, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE | Authors: | Yasutake, Y, Watanabe, S, Yao, M, Takada, Y, Fukunaga, N, Tanaka, I. | Deposit date: | 2002-12-19 | Release date: | 2003-09-23 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (3.2 Å) | Cite: | Crystal Structure of the Monomeric Isocitrate Dehydrogenase in the Presence of NADP+ J.Biol.Chem., 278, 2003
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8JHH
| Glycoside hydrolase family 55 endo-beta-1,3-glucanase from Microdochium nivale | Descriptor: | GLYCEROL, MnLam55A | Authors: | Ota, T, Saburi, W, Yamashita, K, Tagami, T, Yu, J, Komba, S, Jewell, L.E, Hsiang, T, Imai, R, Yao, M, Mori, H. | Deposit date: | 2023-05-23 | Release date: | 2024-04-03 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Molecular mechanism for endo-type action of glycoside hydrolase family 55 endo-beta-1,3-glucanase on beta 1-3/1-6-glucan. J.Biol.Chem., 299, 2023
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1UCG
| Crystal structure of Ribonuclease MC1 N71T mutant | Descriptor: | MANGANESE (II) ION, Ribonuclease MC | Authors: | Suzuki, A, Numata, T, Yao, M, Tanaka, I, Kimura, M. | Deposit date: | 2003-04-14 | Release date: | 2003-04-29 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | Crystal structures of the ribonuclease MC1 mutants N71T and N71S in complex with 5'-GMP: structural basis for alterations in substrate specificity Biochemistry, 42, 2003
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1J0D
| ACC deaminase mutant complexed with ACC | Descriptor: | 1-aminocyclopropane-1-carboxylate deaminase, N-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-Y-LMETHYL]-1-AMINO-CYCLOPROPANECARBOXYLIC ACID | Authors: | Ose, T, Fujino, A, Yao, M, Honma, M, Tanaka, I. | Deposit date: | 2002-11-12 | Release date: | 2003-05-12 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Reaction intermediate structures of 1-aminocyclopropane-1-carboxylate deaminase: insight into PLP-dependent cyclopropane ring-opening reaction J.BIOL.CHEM., 278, 2003
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1J0E
| ACC deaminase mutant reacton intermediate | Descriptor: | 1-AMINOCYCLOPROPANECARBOXYLIC ACID, 1-aminocyclopropane-1-carboxylate deaminase, PYRIDOXAL-5'-PHOSPHATE | Authors: | Ose, T, Fujino, A, Yao, M, Honma, M, Tanaka, I. | Deposit date: | 2002-11-12 | Release date: | 2003-05-12 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.45 Å) | Cite: | Reaction intermediate structures of 1-aminocyclopropane-1-carboxylate deaminase: insight into PLP-dependent cyclopropane ring-opening reaction J.BIOL.CHEM., 278, 2003
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4P1Y
| Crystal structure of staphylococcal gamma-hemolysin prepore | Descriptor: | Gamma-hemolysin component A, Gamma-hemolysin component B | Authors: | Yamashita, D, Tanaka, Y, Tanaka, I, Yao, M. | Deposit date: | 2014-02-28 | Release date: | 2014-10-01 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.992 Å) | Cite: | Molecular basis of transmembrane beta-barrel formation of staphylococcal pore-forming toxins. Nat Commun, 5, 2014
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3AZV
| Crystal structure of the receptor binding domain | Descriptor: | D/C mosaic neurotoxin, SULFATE ION | Authors: | Nuemket, N, Tanaka, Y, Tsukamoto, K, Tsuji, T, Nakamura, K, Kozaki, S, Yao, M, Tanaka, I. | Deposit date: | 2011-06-02 | Release date: | 2011-12-28 | Last modified: | 2017-10-11 | Method: | X-RAY DIFFRACTION (3.1 Å) | Cite: | Structural and mutational analyses of the receptor binding domain of botulinum D/C mosaic neurotoxin: insight into the ganglioside binding mechanism Biochem.Biophys.Res.Commun., 411, 2011
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3AZW
| Crystal structure of the receptor binding domain | Descriptor: | D/C mosaic neurotoxin, SULFATE ION | Authors: | Nuemket, N, Tanaka, Y, Tsukamoto, K, Tsuji, T, Nakamura, K, Kozaki, S, Yao, M, Tanaka, I. | Deposit date: | 2011-06-02 | Release date: | 2011-12-28 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.99 Å) | Cite: | Structural and mutational analyses of the receptor binding domain of botulinum D/C mosaic neurotoxin: insight into the ganglioside binding mechanism Biochem.Biophys.Res.Commun., 411, 2011
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4P1X
| Crystal structure of staphylococcal LUK prepore | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, Gamma-hemolysin component B, Gamma-hemolysin component C | Authors: | Yamashita, D, Tanaka, Y, Tanaka, I, Yao, M. | Deposit date: | 2014-02-28 | Release date: | 2014-10-01 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Molecular basis of transmembrane beta-barrel formation of staphylococcal pore-forming toxins. Nat Commun, 5, 2014
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3B0P
| tRNA-dihydrouridine synthase from Thermus thermophilus | Descriptor: | FLAVIN MONONUCLEOTIDE, tRNA-dihydrouridine synthase | Authors: | Yu, F, Tanaka, Y, Yamashita, K, Nakamura, A, Yao, M, Tanaka, I. | Deposit date: | 2011-06-12 | Release date: | 2011-12-14 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Molecular basis of dihydrouridine formation on tRNA Proc.Natl.Acad.Sci.USA, 108, 2011
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4DWQ
| RNA ligase RtcB-GMP/Mn(2+) complex | Descriptor: | GLYCEROL, GUANOSINE-5'-MONOPHOSPHATE, MALONATE ION, ... | Authors: | Okada, C, Xia, S, Englert, M, Yao, M, Soll, D, Wang, J. | Deposit date: | 2012-02-26 | Release date: | 2012-09-05 | Last modified: | 2017-08-02 | Method: | X-RAY DIFFRACTION (2.25 Å) | Cite: | Structural and mechanistic insights into guanylylation of RNA-splicing ligase RtcB joining RNA between 3'-terminal phosphate and 5'-OH. Proc.Natl.Acad.Sci.USA, 109, 2012
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1WE5
| Crystal Structure of Alpha-Xylosidase from Escherichia coli | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, Putative family 31 glucosidase yicI | Authors: | Ose, T, Kitamura, M, Okuyama, M, Mori, H, Kimura, A, Watanabe, N, Yao, M, Tanaka, I. | Deposit date: | 2004-05-24 | Release date: | 2005-02-15 | Last modified: | 2017-10-11 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Crystal Structure of Alpha-Xylosidase from Escherichia coli TO BE PUBLISHED
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