3WGT
 
 | | Crystal structure of D-amino acid oxidase mutant | | Descriptor: | (1R)-1-phenylethanamine, D-amino-acid oxidase, FLAVIN-ADENINE DINUCLEOTIDE, ... | | Authors: | Yasukawa, K, Nakano, S, Asano, Y. | | Deposit date: | 2013-08-09 | | Release date: | 2014-04-02 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.88 Å) | | Cite: | Tailoring D-amino acid oxidase from the pig kidney to R-stereoselective amine oxidase and its use in the deracemization of alpha-methylbenzylamine.
Angew.Chem.Int.Ed.Engl., 53, 2014
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5WX2
 | | Crystal structure of porcine kidney D-amino acid oxidase mutant (I230A/R283G) | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, D-amino-acid oxidase, FLAVIN-ADENINE DINUCLEOTIDE, ... | | Authors: | Motojima, F, Yasukawa, K, Ohno, A, Asano, Y. | | Deposit date: | 2017-01-06 | | Release date: | 2018-01-17 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Tailoring D-amino acid oxidase from the pid kidney to R-stereoselective amine oxidase and its use in the deracemization of 4-chlorobenzhydrylamine
To Be Published
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5WWV
 | | Crystal structure of porcine kidney D-amino acid oxidase mutant (I230A/R283G) | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, (S)-(4-chlorophenyl)-phenyl-methanamine, D-amino-acid oxidase, ... | | Authors: | Motojima, F, Yasukawa, K, Ohno, A, Asano, Y. | | Deposit date: | 2017-01-05 | | Release date: | 2018-01-17 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (3.2 Å) | | Cite: | Tailoring D-amino acid oxidase from the pid kidney to R-stereoselective amine oxidase and its use in the deracemization of 4-chlorobenzhydrylamine
To Be Published
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8Y1M
 | | Xylanase R from Bacillus sp. TAR-1 complexed with xylobiose. | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ACETATE ION, ... | | Authors: | Nakamura, T, Kuwata, K, Takita, T, Mizutani, K, Mikami, B, Nakamura, S, Yasukawa, K. | | Deposit date: | 2024-01-25 | | Release date: | 2024-05-22 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Activity-stability trade-off observed in variants at position 315 of the GH10 xylanase XynR.
Sci Rep, 14, 2024
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8XY0
 | | Activity-stability trade-off observed in variants at position 315 of the GH10 xylanase XynR | | Descriptor: | CALCIUM ION, DI(HYDROXYETHYL)ETHER, Endo-1,4-beta-xylanase A | | Authors: | Nakamura, T, Takita, T, Mizutani, K, Mikami, B, Nakamura, S, Yasukawa, K. | | Deposit date: | 2024-01-19 | | Release date: | 2024-05-22 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Activity-stability trade-off observed in variants at position 315 of the GH10 xylanase XynR.
Sci Rep, 14, 2024
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3A74
 | | Lysyl-tRNA synthetase from Bacillus stearothermophilus complexed with Diadenosine Tetraphosphate (AP4A) | | Descriptor: | 2,6-DIAMINO-HEXANOIC ACID AMIDE, BIS(ADENOSINE)-5'-TETRAPHOSPHATE, Lysyl-tRNA synthetase, ... | | Authors: | Sakurama, H, Takita, T, Mikami, B, Itoh, T, Yasukawa, K, Inouye, K. | | Deposit date: | 2009-09-13 | | Release date: | 2010-09-22 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal Structure of Lysyl-tRNA Synthetase from Bacillus stearothermophilus in Complex with Diadenosine Tetraphosphate (AP4A): Insights into AP4A Synthesis Mechanisms and Implication for Recognition of Discriminator Base of tRNA^Lys
To be Published
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6KJL
 | | Xylanase J from Bacillus sp. strain 41M-1 | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, CALCIUM ION, ... | | Authors: | Manami, S, Teisuke, T, Nakatani, K, Katano, K, Kojima, K, Saka, N, Mikami, B, Yatsunami, R, Nakamura, S, Yasukawa, K. | | Deposit date: | 2019-07-22 | | Release date: | 2019-09-04 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.45 Å) | | Cite: | Increase in the thermostability of GH11 xylanase XynJ from Bacillus sp. strain 41M-1 using site saturation mutagenesis.
Enzyme.Microb.Technol., 130, 2019
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9JER
 | | Arginine decarboxylase in Aspergillus oryzae, ligand-free form | | Descriptor: | 1,2-ETHANEDIOL, DI(HYDROXYETHYL)ETHER, L-tryptophan decarboxylase PsiD-like domain-containing protein | | Authors: | Mikami, B, Yasukawa, K, Fujiwara, S, Takita, T, Mizutani, K, Odagaki, Y, Murakami, Y. | | Deposit date: | 2024-09-03 | | Release date: | 2024-10-09 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Unveiling the reaction mechanism of arginine decarboxylase in Aspergillus oryzae: Insights from crystal structure analysis.
Biochem.Biophys.Res.Commun., 733, 2024
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9JF5
 | | Arginine decarboxylase in Aspergillus oryzae complexed with arginine | | Descriptor: | 1,2-ETHANEDIOL, AGMATINE, DI(HYDROXYETHYL)ETHER, ... | | Authors: | Mikami, B, Yasukawa, K, Fujiwara, S, Takita, T, Mizutani, K, Odagaki, Y, Murakami, Y. | | Deposit date: | 2024-09-04 | | Release date: | 2024-10-09 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Unveiling the reaction mechanism of arginine decarboxylase in Aspergillus oryzae: Insights from crystal structure analysis.
Biochem.Biophys.Res.Commun., 733, 2024
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9JFN
 | | Arginine decarboxylase in Aspergillus oryzae complexed with agmatine | | Descriptor: | 1,2-ETHANEDIOL, AGMATINE, DI(HYDROXYETHYL)ETHER, ... | | Authors: | Mikami, B, Yasukawa, K, Fujiwara, S, Takita, T, Mizutani, K, Odagaki, Y, Murakami, Y. | | Deposit date: | 2024-09-05 | | Release date: | 2024-10-09 | | Method: | X-RAY DIFFRACTION (2.15 Å) | | Cite: | Unveiling the reaction mechanism of arginine decarboxylase in Aspergillus oryzae: Insights from crystal structure analysis.
Biochem.Biophys.Res.Commun., 733, 2024
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7WSS
 | | Collagenase from Grimontia (Vibrio) hollisae 1706B | | Descriptor: | 1,2-ETHANEDIOL, CALCIUM ION, DI(HYDROXYETHYL)ETHER, ... | | Authors: | Ikeuchi, T, Yasumoto, M, Takita, T, Mizutani, K, Mikami, B, Tanaka, K, Hattori, S, Yasukawa, K. | | Deposit date: | 2022-02-01 | | Release date: | 2022-06-29 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (2.19 Å) | | Cite: | Crystal structure of Grimontia hollisae collagenase provides insights into its novel substrate specificity toward collagen.
J.Biol.Chem., 298, 2022
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7XEB
 | | Collagenase from Grimontia (Vibrio) hollisae 1706B complexed with Gly-Pro-Hyp | | Descriptor: | 1,2-ETHANEDIOL, CALCIUM ION, GLY-PRO-HYP peptide, ... | | Authors: | Ikeuchi, T, Yasumoto, M, Takita, T, Mizutani, K, Mikami, B, Tanaka, K, Hattori, S, Yasukawa, K. | | Deposit date: | 2022-03-30 | | Release date: | 2022-06-29 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.39 Å) | | Cite: | Crystal structure of Grimontia hollisae collagenase provides insights into its novel substrate specificity toward collagen.
J.Biol.Chem., 298, 2022
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3E9I
 | | Lysyl-tRNA synthetase from Bacillus stearothermophilus complexed with L-Lysine hydroxamate-AMP | | Descriptor: | 5'-O-{(R)-hydroxy[(L-lysylamino)oxy]phosphoryl}adenosine, Lysyl-tRNA synthetase, MAGNESIUM ION, ... | | Authors: | Sakurama, H, Takita, T, Mikami, B, Itoh, T, Yasukawa, K, Inouye, K. | | Deposit date: | 2008-08-22 | | Release date: | 2009-07-14 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Two crystal structures of lysyl-tRNA synthetase from Bacillus stearothermophilus in complex with lysyladenylate-like compounds: insights into the irreversible formation of the enzyme-bound adenylate of L-lysine hydroxamate
J.Biochem., 145, 2009
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3E9H
 | | Lysyl-tRNA synthetase from Bacillus stearothermophilus complexed with L-Lysylsulfamoyl adenosine | | Descriptor: | 5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE, Lysyl-tRNA synthetase, MAGNESIUM ION | | Authors: | Sakurama, H, Takita, T, Mikami, B, Itoh, T, Yasukawa, K, Inouye, K. | | Deposit date: | 2008-08-22 | | Release date: | 2009-07-14 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Two crystal structures of lysyl-tRNA synthetase from Bacillus stearothermophilus in complex with lysyladenylate-like compounds: insights into the irreversible formation of the enzyme-bound adenylate of L-lysine hydroxamate
J.Biochem., 145, 2009
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7CPK
 | | Xylanase R from Bacillus sp. TAR-1 | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, CALCIUM ION, Endo-1,4-beta-xylanase A, ... | | Authors: | Kuwata, K, Suzuki, M, Takita, T, Nakatani, K, Li, T, Katano, Y, Kojima, K, Mizutani, K, Mikami, B, Yatsunami, R, Nakamura, S, Yasukawa, K. | | Deposit date: | 2020-08-07 | | Release date: | 2020-09-02 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Insight into the mechanism of thermostabilization of GH10 xylanase from Bacillus sp. strain TAR-1 by the mutation of S92 to E.
Biosci.Biotechnol.Biochem., 85, 2021
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7CPL
 | | Xylanase R from Bacillus sp. TAR-1 | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, CALCIUM ION, Endo-1,4-beta-xylanase A, ... | | Authors: | Kuwata, K, Suzuki, M, Takita, T, Nakatani, K, Li, T, Katano, Y, Kojima, K, Mizutani, K, Mikami, B, Yatsunami, R, Nakamura, S, Yasukawa, K. | | Deposit date: | 2020-08-07 | | Release date: | 2020-09-02 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.52 Å) | | Cite: | Insight into the mechanism of thermostabilization of GH10 xylanase from Bacillus sp. strain TAR-1 by the mutation of S92 to E.
Biosci.Biotechnol.Biochem., 85, 2021
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4YJF
 | | Crystal structure of DAAO(Y228L/R283G) variant (S-methylbenzylamine binding form) | | Descriptor: | (1S)-1-phenylethanamine, D-amino-acid oxidase, FLAVIN-ADENINE DINUCLEOTIDE, ... | | Authors: | Nakano, S, Yasukawa, K, Kawahara, N, Ishitsubo, E, Tokiwa, H, Asano, Y. | | Deposit date: | 2015-03-03 | | Release date: | 2016-04-06 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Crystal structure of DAAO variant
To Be Published
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4YJG
 | | Crystal structure of DAAO(Y228L/R283G) variant (R-3-amino 1-phenylbutane binding form) | | Descriptor: | (2R)-4-phenylbutan-2-amine, D-amino-acid oxidase, FLAVIN-ADENINE DINUCLEOTIDE, ... | | Authors: | Nakano, S, Yasukawa, K, Kawahara, N, Ishitsubo, E, Tokiwa, H, Asano, Y. | | Deposit date: | 2015-03-03 | | Release date: | 2016-04-06 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Crystal structure of DAAO variant
To Be Published
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4YJH
 | | Crystal structure of DAAO(Y228L/R283G) variant (R-2-phenylpyrrolidine binding form) | | Descriptor: | (2R)-2-phenylpyrrolidine, D-amino-acid oxidase, FLAVIN-ADENINE DINUCLEOTIDE, ... | | Authors: | Nakano, S, Yasukawa, K, Kawahara, N, Ishitsubo, E, Tokiwa, H, Asano, Y. | | Deposit date: | 2015-03-03 | | Release date: | 2016-04-06 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Crystal structure of DAAO variant
To Be Published
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4YJD
 | | Crystal structure of DAAO(Y228L/R283G) variant (apo form) | | Descriptor: | D-amino-acid oxidase, FLAVIN-ADENINE DINUCLEOTIDE, SULFATE ION | | Authors: | Nakano, S, Yasukawa, K, Kawahara, N, Ishitsubo, E, Tokiwa, H, Asano, Y. | | Deposit date: | 2015-03-03 | | Release date: | 2016-04-06 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Crystal structure of DAAO variant
To Be Published
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5X7E
 | | Crystal structure of vitamin D hydroxylase cytochrome P450 105A1 (R84A mutant) in complex with 1,25-dihydroxyvitamin D2 | | Descriptor: | (1R,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(E,2R,5S)-5,6-dimethyl-6-oxidanyl-hept-3-en-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydr o-1H-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol, PROTOPORPHYRIN IX CONTAINING FE, Vitamin D3 dihydroxylase | | Authors: | Hayashi, K, Yasuda, K, Shiro, Y, Sugimoto, H, Sakaki, T. | | Deposit date: | 2017-02-25 | | Release date: | 2017-05-10 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Production of an active form of vitamin D2 by genetically engineered CYP105A1
Biochem. Biophys. Res. Commun., 486, 2017
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6KKA
 | | Xylanase J mutant from Bacillus sp. 41M-1 | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, CALCIUM ION, ... | | Authors: | Suzuki, M, Takita, T, Nakatani, K. | | Deposit date: | 2019-07-24 | | Release date: | 2019-09-04 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.36 Å) | | Cite: | Increase in the thermostability of GH11 xylanase XynJ from Bacillus sp. strain 41M-1 using site saturation mutagenesis.
Enzyme.Microb.Technol., 130, 2019
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8JT1
 | | COLLAGENASE FROM GRIMONTIA (VIBRIO) HOLLISAE 1706B COMPLEXED WITH GLY-PRO-HYP-GLY-PRO-HYP | | Descriptor: | 1,2-ETHANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 6-mer peptide, ... | | Authors: | Ueshima, S, Yaskawa, K, Takita, T, Mikami, B. | | Deposit date: | 2023-06-21 | | Release date: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Insights into the catalytic mechanism of Grimontia hollisae collagenase through structural and mutational analyses.
Febs Lett., 597, 2023
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7C9J
 | | Transglutaminase from Geobacillus stearothermophilus (without C-terminal extension) | | Descriptor: | 1,2-ETHANEDIOL, CITRIC ACID, Protein-glutamine gamma-glutamyltransferase | | Authors: | Takita, T, Mikami, B, Lei, Y, Jing, Y, Yamada, A, Yasukawa, K. | | Deposit date: | 2020-06-06 | | Release date: | 2021-06-09 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Transglutaminase from Geobacillus stearothermophilus (without C-terminal extension)
To be published
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