8EAC
| Thermus thermophilus methylenetetrahydrofolate reductase | Descriptor: | FLAVIN-ADENINE DINUCLEOTIDE, Methylenetetrahydrofolate reductase | Authors: | Yamada, K, Koutmos, M. | Deposit date: | 2022-08-28 | Release date: | 2023-01-18 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | 5-Formyltetrahydrofolate promotes conformational remodeling in a methylenetetrahydrofolate reductase active site and inhibits its activity. J.Biol.Chem., 299, 2022
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7TH5
| Thermus thermophilus methylenetetrahydrofolate reductase | Descriptor: | FLAVIN-ADENINE DINUCLEOTIDE, Methylenetetrahydrofolate reductase, SODIUM ION | Authors: | Yamada, K, Koutmos, M. | Deposit date: | 2022-01-10 | Release date: | 2023-01-18 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.09 Å) | Cite: | 5-Formyltetrahydrofolate promotes conformational remodeling in a methylenetetrahydrofolate reductase active site and inhibits its activity. J.Biol.Chem., 299, 2022
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7TH4
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5CUZ
| Crystal structure of SeMet-substituted N-terminal truncated human B12-chaperone CblD (108-296) | Descriptor: | Methylmalonic aciduria and homocystinuria type D protein, mitochondrial | Authors: | Yamada, K, Gherasim, C, Banerjee, R, Koutmos, M. | Deposit date: | 2015-07-25 | Release date: | 2015-09-23 | Last modified: | 2015-12-16 | Method: | X-RAY DIFFRACTION (2.31 Å) | Cite: | Structure of Human B12 Trafficking Protein CblD Reveals Molecular Mimicry and Identifies a New Subfamily of Nitro-FMN Reductases. J.Biol.Chem., 290, 2015
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5CV0
| Crystal structure of N-terminal truncated human B12-chaperone CblD (108-296) | Descriptor: | Methylmalonic aciduria and homocystinuria type D protein, mitochondrial | Authors: | Yamada, K, Gherasim, C, Banerjee, R, Koutmos, M. | Deposit date: | 2015-07-24 | Release date: | 2015-09-23 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Structure of Human B12 Trafficking Protein CblD Reveals Molecular Mimicry and Identifies a New Subfamily of Nitro-FMN Reductases. J.Biol.Chem., 290, 2015
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1HQC
| STRUCTURE OF RUVB FROM THERMUS THERMOPHILUS HB8 | Descriptor: | ADENINE, MAGNESIUM ION, RUVB | Authors: | Yamada, K, Kunishima, N, Mayanagi, K, Iwasaki, H, Morikawa, K. | Deposit date: | 2000-12-15 | Release date: | 2001-02-21 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (3.2 Å) | Cite: | Crystal structure of the Holliday junction migration motor protein RuvB from Thermus thermophilus HB8. Proc.Natl.Acad.Sci.USA, 98, 2001
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1IXS
| Structure of RuvB complexed with RuvA domain III | Descriptor: | Holliday junction DNA helicase ruvA, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, RuvB | Authors: | Yamada, K, Miyata, T, Tsuchiya, D, Oyama, T, Fujiwara, Y, Ohnishi, T, Iwasaki, H, Shinagawa, H, Ariyoshi, M, Mayanagi, K, Morikawa, K. | Deposit date: | 2002-07-04 | Release date: | 2002-11-06 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (3.2 Å) | Cite: | Crystal Structure of the RuvA-RuvB Complex: A Structural Basis for the Holliday Junction Migrating Motor Machinery Mol.Cell, 10, 2002
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1IXR
| RuvA-RuvB complex | Descriptor: | Holliday junction DNA helicase ruvA, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, RuvB | Authors: | Yamada, K, Miyata, T, Tsuchiya, D, Oyama, T, Fujiwara, Y, Ohnishi, T, Iwasaki, H, Shinagawa, H, Ariyoshi, M, Mayanagi, K, Morikawa, K. | Deposit date: | 2002-07-04 | Release date: | 2002-11-06 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (3.3 Å) | Cite: | Crystal Structure of the RuvA-RuvB Complex: A Structural Basis for the Holliday Junction Migrating Motor Machinery Mol.Cell, 10, 2002
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1WCZ
| Crystal structure of an alkaline form of v8 protease from Staphylococcus aureus | Descriptor: | Glutamyl endopeptidase, ZINC ION | Authors: | Yamada, K, Ohta, M, Hasegawa, T, Torii, K, Murakami, M, Kouyama, K. | Deposit date: | 2004-05-10 | Release date: | 2004-06-01 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Crystal structure of an alkaline form of v8 protease from Staphylococcus aureus To be Published
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5VON
| Methionine synthase folate-binding domain from Thermus thermophilus HB8 | Descriptor: | 5-methyltetrahydrofolate homocysteine S-methyltransferase, GLYCEROL | Authors: | Yamada, K, Koutmos, M. | Deposit date: | 2017-05-03 | Release date: | 2018-01-17 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | The folate-binding module of Thermus thermophilus cobalamin-dependent methionine synthase displays a distinct variation of the classical TIM barrel: a TIM barrel with a `twist'. Acta Crystallogr D Struct Biol, 74, 2018
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1UHR
| Solution structure of the SWIB domain of mouse BRG1-associated factor 60a | Descriptor: | SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily D member 1 | Authors: | Yamada, K, Saito, K, Nameki, N, Inoue, M, Koshiba, S, Shirouzu, M, Terada, T, Yabuki, T, Aoki, M, Matsuda, T, Seki, E, Hirota, H, Yoshida, M, Tanaka, A, Osanai, T, Arakawa, T, Carninci, P, Kawai, J, Hayashizaki, Y, Kigawa, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2003-07-09 | Release date: | 2004-08-24 | Last modified: | 2023-12-27 | Method: | SOLUTION NMR | Cite: | Solution structure of the SWIB domain of mouse BRG1-associated factor 60a To be Published
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1V6B
| Solution structure of the third PDZ domain of mouse harmonin | Descriptor: | harmonin isoform a1 | Authors: | Yamada, K, Nameki, N, Saito, K, Koshiba, S, Inoue, M, Kigawa, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2003-11-28 | Release date: | 2004-05-28 | Last modified: | 2023-12-27 | Method: | SOLUTION NMR | Cite: | Solution structure of the third PDZ domain of mouse harmonin To be Published
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2Y9Y
| Chromatin Remodeling Factor ISW1a(del_ATPase) | Descriptor: | IMITATION SWITCH PROTEIN 1 (DEL_ATPASE), ISWI ONE COMPLEX PROTEIN 3 | Authors: | Yamada, K, Frouws, T.D, Angst, B, Fitzgerald, D.J, DeLuca, C, Schimmele, K, Sargent, D.F, Richmond, T.J. | Deposit date: | 2011-02-17 | Release date: | 2011-04-20 | Last modified: | 2012-03-28 | Method: | X-RAY DIFFRACTION (3.25 Å) | Cite: | Structure and Mechanism of the Chromatin Remodelling Factor Isw1A. Nature, 472, 2011
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2Y9Z
| Chromatin Remodeling Factor ISW1a(del_ATPase) in DNA complex | Descriptor: | I-DNA/E-DNA, IMITATION SWITCH PROTEIN 1 (DEL_ATPASE), ISWI ONE COMPLEX PROTEIN 3 | Authors: | Yamada, K, Frouws, T.D, Angst, B, Fitzgerald, D.J, DeLuca, C, Schimmele, K, Sargent, D.F, Richmond, T.J. | Deposit date: | 2011-02-17 | Release date: | 2011-04-20 | Last modified: | 2012-03-28 | Method: | X-RAY DIFFRACTION (3.601 Å) | Cite: | Structure and Mechanism of the Chromatin Remodelling Factor Isw1A Nature, 472, 2011
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8SSD
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8SSE
| Methionine synthase, C-terminal fragment, Cobalamin and Reactivation Domains from Thermus thermophilus HB8 | Descriptor: | COBALAMIN, Methionine synthase | Authors: | Yamada, K, Mendoza, J, Koutmos, M. | Deposit date: | 2023-05-08 | Release date: | 2023-10-11 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (3.15 Å) | Cite: | Structure of full-length cobalamin-dependent methionine synthase and cofactor loading captured in crystallo Nat Commun, 14, 2023
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8SSC
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5GHK
| Crystal Structure Analysis of Canine serum albumin | Descriptor: | Serum albumin | Authors: | Kihira, K, Yamada, K, Kureishi, M, Yokomaku, K, Shinohara, R, Akiyama, M, Komatsu, T. | Deposit date: | 2016-06-20 | Release date: | 2016-11-23 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (3.2 Å) | Cite: | Artificial Blood for Dogs Sci Rep, 6, 2016
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5VOO
| Methionine synthase folate-binding domain with methyltetrahydrofolate from Thermus thermophilus HB8 | Descriptor: | 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID, 5-methyltetrahydrofolate homocysteine S-methyltransferase, CHLORIDE ION, ... | Authors: | Koutmos, M, Yamada, K. | Deposit date: | 2017-05-03 | Release date: | 2018-01-17 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | The folate-binding module of Thermus thermophilus cobalamin-dependent methionine synthase displays a distinct variation of the classical TIM barrel: a TIM barrel with a `twist'. Acta Crystallogr D Struct Biol, 74, 2018
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5VOP
| Methionine synthase folate-binding domain from Thermus thermophilus HB8 native | Descriptor: | 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID, 5-methyltetrahydrofolate homocysteine S-methyltransferase, CITRATE ANION, ... | Authors: | Koutmos, M, Yamada, K. | Deposit date: | 2017-05-03 | Release date: | 2018-01-17 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | The folate-binding module of Thermus thermophilus cobalamin-dependent methionine synthase displays a distinct variation of the classical TIM barrel: a TIM barrel with a `twist'. Acta Crystallogr D Struct Biol, 74, 2018
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3APT
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3APY
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4M3P
| Betaine-Homocysteine S-Methyltransferase from Homo sapiens complexed with Homocysteine | Descriptor: | 2-AMINO-4-MERCAPTO-BUTYRIC ACID, Betaine--homocysteine S-methyltransferase 1, POTASSIUM ION, ... | Authors: | Koutmos, M, Yamada, K, Mladkova, J, Paterova, J, Diamond, C.E, Tryon, K, Jungwirth, P, Garrow, T.A, Jiracek, J. | Deposit date: | 2013-08-06 | Release date: | 2014-06-18 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (1.895 Å) | Cite: | Specific potassium ion interactions facilitate homocysteine binding to betaine-homocysteine S-methyltransferase. Proteins, 82, 2014
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4JGT
| Structure and kinetic analysis of H2S production by human Mercaptopyruvate Sulfurtransferase | Descriptor: | 3-mercaptopyruvate sulfurtransferase, GLYCEROL, PYRUVIC ACID, ... | Authors: | Koutmos, M, Yamada, K, Yadav, P.K, Chiku, T, Banerjee, R. | Deposit date: | 2013-03-03 | Release date: | 2013-05-29 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.161 Å) | Cite: | Structure and Kinetic Analysis of H2S Production by Human Mercaptopyruvate Sulfurtransferase. J.Biol.Chem., 288, 2013
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1WUA
| The structure of Aplyronine A-actin complex | Descriptor: | (8R,9R,10R,11R,14S,18S,20S,24S)-24-{(1R,2S,3R,6R,7R,8R,9S,10E)-8-(ACETYLOXY)-6-[(N,N-DIMETHYLALANYL)OXY]-11-[FORMYL(MET HYL)AMINO]-2-HYDROXY-1,3,7,9-TETRAMETHYLUNDEC-10-ENYL}-10-HYDROXY-14,20-DIMETHOXY-9,11,15,18-TETRAMETHYL-2-OXOOXACYCLOTE TRACOSA-3,5,15,21-TETRAEN-8-YL N,N,O-TRIMETHYLSERINATE, ADENOSINE-5'-TRIPHOSPHATE, Actin, ... | Authors: | Hirata, K, Muraoka, S, Suenaga, K, Kuroda, T, Kato, K, Tanaka, H, Yamamoto, M, Takata, M, Yamada, K, Kigoshi, H. | Deposit date: | 2004-12-03 | Release date: | 2006-02-14 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.45 Å) | Cite: | Structure basis for antitumor effect of aplyronine a J.Mol.Biol., 356, 2006
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