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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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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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: | 2024-10-23 | | 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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8UY1
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8UY2
 | | Methylenetetrahydrofolate reductase from Chaetomium thermophilum DSM 1495, AdoMet-bound, Inhibited (T) State | | Descriptor: | ACETATE ION, FLAVIN-ADENINE DINUCLEOTIDE, GLYCEROL, ... | | Authors: | Yamada, K, Mendoza, J, Koutmos, M. | | Deposit date: | 2023-11-12 | | Release date: | 2024-06-19 | | Last modified: | 2024-07-03 | | Method: | X-RAY DIFFRACTION (2.83 Å) | | Cite: | Structural basis of S-adenosylmethionine-dependent allosteric transition from active to inactive states in methylenetetrahydrofolate reductase.
Nat Commun, 15, 2024
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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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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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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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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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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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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: | 2024-05-08 | | 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: | 2024-05-08 | | Method: | X-RAY DIFFRACTION (3.601 Å) | | Cite: | Structure and Mechanism of the Chromatin Remodelling Factor Isw1A
Nature, 472, 2011
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8SSC
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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: | 2024-05-01 | | 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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8SSD
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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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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: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (3.2 Å) | | Cite: | Artificial Blood for Dogs
Sci Rep, 6, 2016
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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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