4H04
 
 | | Lacto-N-biosidase from Bifidobacterium bifidum | | Descriptor: | Lacto-N-biosidase, SULFATE ION, beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose | | Authors: | Ito, T, Katayama, T, Wada, J, Suzuki, R, Ashida, H, Wakagi, T, Yamamoto, K, Fushinobu, S. | | Deposit date: | 2012-09-07 | | Release date: | 2013-03-20 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal structures of a glycoside hydrolase family 20 lacto-N-biosidase from Bifidobacterium bifidum
J.Biol.Chem., 288, 2013
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4JAW
 | | Crystal Structure of Lacto-N-Biosidase from Bifidobacterium bifidum complexed with LNB-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, Lacto-N-biosidase, SULFATE ION, ... | | Authors: | Ito, T, Katayama, T, Stubbs, K.A, Fushinobu, S. | | Deposit date: | 2013-02-19 | | Release date: | 2013-03-20 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal structures of a glycoside hydrolase family 20 lacto-N-biosidase from Bifidobacterium bifidum
J.Biol.Chem., 288, 2013
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8W7P
 | | Extracellular domain of a sensor histidine kinase | | Descriptor: | Extracellular domain of a sensor histidine kinase NagS, GLYCEROL | | Authors: | Itoh, T, Ogawa, T, Hibi, T, Kimoto, H. | | Deposit date: | 2023-08-31 | | Release date: | 2024-01-10 | | Last modified: | 2024-03-06 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Characterization of the extracellular domain of sensor histidine kinase NagS from Paenibacillus sp. str. FPU-7: nagS interacts with oligosaccharide binding protein NagB1 in complexes with N, N'-diacetylchitobiose.
Biosci.Biotechnol.Biochem., 88, 2024
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4YVG
 | | Crystal Structure of H. influenzae TrmD in complex with AdoMet | | Descriptor: | S-ADENOSYLMETHIONINE, tRNA (guanine-N(1)-)-methyltransferase | | Authors: | Ito, T, Yokoyama, S. | | Deposit date: | 2015-03-20 | | Release date: | 2015-07-15 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.549 Å) | | Cite: | Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
Proc.Natl.Acad.Sci.USA, 112, 2015
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2EVX
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1Q8K
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3WKX
 | | Crystal structure of GH127 beta-L-arabinofuranosidase HypBA1 from Bifidobacterium longum arabinose complex form | | Descriptor: | Non-reducing end beta-L-arabinofuranosidase, ZINC ION, beta-L-arabinofuranose | | Authors: | Ito, T, Saikawa, K, Arakawa, T, Wakagi, T, Fujita, K. | | Deposit date: | 2013-11-01 | | Release date: | 2014-04-30 | | Last modified: | 2022-08-24 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Crystal structure of glycoside hydrolase family 127 beta-l-arabinofuranosidase from Bifidobacterium longum.
Biochem.Biophys.Res.Commun., 447, 2014
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1U2F
 | | SOLUTION STRUCTURE OF THE FIRST RNA-BINDING DOMAIN OF HU2AF65 | | Descriptor: | PROTEIN (SPLICING FACTOR U2AF 65 KD SUBUNIT) | | Authors: | Ito, T, Muto, Y, Green, M.R, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 1999-05-26 | | Release date: | 1999-08-20 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | Solution structures of the first and second RNA-binding domains of human U2 small nuclear ribonucleoprotein particle auxiliary factor (U2AF(65)).
EMBO J., 18, 1999
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3WKW
 | | Crystal structure of GH127 beta-L-arabinofuranosidase HypBA1 from Bifidobacterium longum ligand free form | | Descriptor: | Non-reducing end beta-L-arabinofuranosidase | | Authors: | Ito, T, Saikawa, K, Arakawa, T, Wakagi, T, Fujita, K. | | Deposit date: | 2013-11-01 | | Release date: | 2014-04-30 | | Last modified: | 2022-08-24 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Crystal structure of glycoside hydrolase family 127 beta-l-arabinofuranosidase from Bifidobacterium longum.
Biochem.Biophys.Res.Commun., 447, 2014
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2U2F
 | | SOLUTION STRUCTURE OF THE SECOND RNA-BINDING DOMAIN OF HU2AF65 | | Descriptor: | PROTEIN (SPLICING FACTOR U2AF 65 KD SUBUNIT) | | Authors: | Ito, T, Muto, Y, Green, M.R, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 1999-05-26 | | Release date: | 1999-08-20 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | Solution structures of the first and second RNA-binding domains of human U2 small nuclear ribonucleoprotein particle auxiliary factor (U2AF(65)).
EMBO J., 18, 1999
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5ZEQ
 | | Carboxypeptidase B in complex with DD28 | | Descriptor: | (2~{S})-2-[(6-azanyl-5-chloranyl-pyridin-3-yl)methyl]-3-selanyl-propanoic acid, CACODYLATE ION, Carboxypeptidase B, ... | | Authors: | Itoh, T, Yoshimoto, N, Yamamoto, K. | | Deposit date: | 2018-02-27 | | Release date: | 2018-06-20 | | Last modified: | 2018-07-04 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Structural basis for the selective inhibition of activated thrombin-activatable fibrinolysis inhibitor (TAFIa) by a selenium-containing inhibitor with chloro-aminopyridine as a basic group
Bioorg. Med. Chem. Lett., 28, 2018
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3AFH
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3AL0
 | | Crystal structure of the glutamine transamidosome from Thermotoga maritima in the glutamylation state. | | Descriptor: | Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B, Glutamyl-tRNA(Gln) amidotransferase subunit A, Glutamyl-tRNA(Gln) amidotransferase subunit C,Linker,Glutamate--tRNA ligase 2, ... | | Authors: | Ito, T, Yokoyama, S. | | Deposit date: | 2010-07-19 | | Release date: | 2010-09-29 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (3.368 Å) | | Cite: | Two enzymes bound to one transfer RNA assume alternative conformations for consecutive reactions.
Nature, 467, 2010
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3AKZ
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1VD5
 | | Crystal Structure of Unsaturated Glucuronyl Hydrolase, Responsible for the Degradation of Glycosaminoglycan, from Bacillus sp. GL1 at 1.8 A Resolution | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 2,3-DIHYDROXY-1,4-DITHIOBUTANE, GLYCINE, ... | | Authors: | Itoh, T, Akao, S, Hashimoto, W, Mikami, B, Murata, K. | | Deposit date: | 2004-03-18 | | Release date: | 2004-07-13 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal Structure of Unsaturated Glucuronyl Hydrolase, Responsible for the Degradation of Glycosaminoglycan, from Bacillus sp. GL1 at 1.8 A Resolution
J.Biol.Chem., 279, 2004
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5GZT
 | | Crystal Structure of Chitinase ChiW from Paenibacillus sp. str. FPU-7 Reveals a Novel Type of Bacterial Cell-Surface-Expressed Multi-Modular Enzyme Machinery | | Descriptor: | Chitinase, FORMIC ACID, PHOSPHATE ION, ... | | Authors: | Itoh, T, Hibi, T, Suzuki, F, Sugimoto, I, Fujiwara, A, Inaka, K, Tanaka, H, Ohta, K, Fujii, Y, Taketo, A, Kimoto, H. | | Deposit date: | 2016-10-01 | | Release date: | 2016-12-28 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Crystal Structure of Chitinase ChiW from Paenibacillus sp. str. FPU-7 Reveals a Novel Type of Bacterial Cell-Surface-Expressed Multi-Modular Enzyme Machinery
PLoS ONE, 11, 2016
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5GZV
 | | Crystal Structure of Chitinase ChiW from Paenibacillus sp. str. FPU-7 Reveals a Novel Type of Bacterial Cell-Surface-Expressed Multi-Modular Enzyme Machinery | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Chitinase, PHOSPHATE ION | | Authors: | Itoh, T, Hibi, T, Suzuki, F, Sugimoto, I, Fujiwara, A, Inaka, K, Tanaka, H, Ohta, K, Fujii, Y, Taketo, A, Kimoto, H. | | Deposit date: | 2016-10-01 | | Release date: | 2016-12-28 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.61 Å) | | Cite: | Crystal Structure of Chitinase ChiW from Paenibacillus sp. str. FPU-7 Reveals a Novel Type of Bacterial Cell-Surface-Expressed Multi-Modular Enzyme Machinery
PLoS ONE, 11, 2016
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5GZU
 | | Crystal Structure of Chitinase ChiW from Paenibacillus sp. str. FPU-7 Reveals a Novel Type of Bacterial Cell-Surface-Expressed Multi-Modular Enzyme Machinery | | Descriptor: | Chitinase, PHOSPHATE ION | | Authors: | Itoh, T, Hibi, T, Suzuki, F, Sugimoto, I, Fujiwara, A, Inaka, K, Tanaka, H, Ohta, K, Fujii, Y, Taketo, A, Kimoto, H. | | Deposit date: | 2016-10-01 | | Release date: | 2016-12-28 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.03 Å) | | Cite: | Crystal Structure of Chitinase ChiW from Paenibacillus sp. str. FPU-7 Reveals a Novel Type of Bacterial Cell-Surface-Expressed Multi-Modular Enzyme Machinery
PLoS ONE, 11, 2016
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5I05
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6K5J
 | | Structure of a glycoside hydrolase family 3 beta-N-acetylglucosaminidase from Paenibacillus sp. str. FPU-7 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, GH3 beta-N-acetylglucosaminidase, GLYCEROL | | Authors: | Itoh, T, Araki, T, Nishiyama, T, Hibi, T, Kimoto, H. | | Deposit date: | 2019-05-29 | | Release date: | 2019-09-25 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.903 Å) | | Cite: | Structural and functional characterization of a glycoside hydrolase family 3 beta-N-acetylglucosaminidase from Paenibacillus sp. str. FPU-7.
J.Biochem., 166, 2019
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6K0M
 | | Catalytic domain of GH87 alpha-1,3-glucanase from Paenibacillus glycanilyticus FH11 | | Descriptor: | Alpha-1,3-glucanase, CALCIUM ION, GLYCEROL, ... | | Authors: | Itoh, T, Intuy, R, Suyotha, W, Hayashi, J, Yano, S, Makabe, K, Wakayama, M, Hibi, T. | | Deposit date: | 2019-05-07 | | Release date: | 2019-12-25 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Structural insights into substrate recognition and catalysis by glycoside hydrolase family 87 alpha-1,3-glucanase from Paenibacillus glycanilyticus FH11.
Febs J., 287, 2020
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6K0U
 | | Catalytic domain of GH87 alpha-1,3-glucanase D1068A in complex with tetrasaccharides | | Descriptor: | Alpha-1,3-glucanase, CALCIUM ION, SULFATE ION, ... | | Authors: | Itoh, T, Intuy, R, Suyotha, W, Hayashi, J, Yano, S, Makabe, K, Wakayama, M, Hibi, T. | | Deposit date: | 2019-05-07 | | Release date: | 2019-12-25 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Structural insights into substrate recognition and catalysis by glycoside hydrolase family 87 alpha-1,3-glucanase from Paenibacillus glycanilyticus FH11.
Febs J., 287, 2020
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6K0Q
 | | Catalytic domain of GH87 alpha-1,3-glucanase D1068A in complex with nigerose | | Descriptor: | ACETIC ACID, Alpha-1,3-glucanase, CALCIUM ION, ... | | Authors: | Itoh, T, Intuy, R, Suyotha, W, Hayashi, J, Yano, S, Makabe, K, Wakayama, M, Hibi, T. | | Deposit date: | 2019-05-07 | | Release date: | 2019-12-25 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.564 Å) | | Cite: | Structural insights into substrate recognition and catalysis by glycoside hydrolase family 87 alpha-1,3-glucanase from Paenibacillus glycanilyticus FH11.
Febs J., 287, 2020
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6K0N
 | | Catalytic domain of GH87 alpha-1,3-glucanase in complex with nigerose | | Descriptor: | ACETIC ACID, Alpha-1,3-glucanase, CALCIUM ION, ... | | Authors: | Itoh, T, Intuy, R, Suyotha, W, Hayashi, J, Yano, S, Makabe, K, Wakayama, M, Hibi, T. | | Deposit date: | 2019-05-07 | | Release date: | 2019-12-25 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Structural insights into substrate recognition and catalysis by glycoside hydrolase family 87 alpha-1,3-glucanase from Paenibacillus glycanilyticus FH11.
Febs J., 287, 2020
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6K0P
 | | Catalytic domain of GH87 alpha-1,3-glucanase D1045A in complex with nigerose | | Descriptor: | ACETIC ACID, Alpha-1,3-glucanase, CALCIUM ION, ... | | Authors: | Itoh, T, Intuy, R, Suyotha, W, Hayashi, J, Yano, S, Makabe, K, Wakayama, M, Hibi, T. | | Deposit date: | 2019-05-07 | | Release date: | 2019-12-25 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.424 Å) | | Cite: | Structural insights into substrate recognition and catalysis by glycoside hydrolase family 87 alpha-1,3-glucanase from Paenibacillus glycanilyticus FH11.
Febs J., 287, 2020
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