7WW5
 
 | | Crystal structure of MutT-8-oxo-dGTP complex | | Descriptor: | 7,8-dihydro-8-oxoguanine-triphosphatase, 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, SODIUM ION, ... | | Authors: | Nakamura, T, Yamagata, Y. | | Deposit date: | 2022-02-12 | | Release date: | 2022-06-01 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.57 Å) | | Cite: | Visualization of mutagenic nucleotide processing by Escherichia coli MutT, a Nudix hydrolase.
Proc.Natl.Acad.Sci.USA, 119, 2022
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7X9N
 | | Crystal structure of MutT-8-oxo-dGTP complex with three Mg2+ ions: Reaction using Mg2+ | | Descriptor: | 7,8-dihydro-8-oxoguanine-triphosphatase, 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE, 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, ... | | Authors: | Nakamura, T, Yamagata, Y. | | Deposit date: | 2022-03-15 | | Release date: | 2022-06-01 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Visualization of mutagenic nucleotide processing by Escherichia coli MutT, a Nudix hydrolase.
Proc.Natl.Acad.Sci.USA, 119, 2022
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3A6V
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3A6T
 | | Crystal structure of MutT-8-OXO-DGMP complex | | Descriptor: | 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE, Mutator mutT protein, SODIUM ION, ... | | Authors: | Nakamura, T, Yamagata, Y. | | Deposit date: | 2009-09-09 | | Release date: | 2009-10-27 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.96 Å) | | Cite: | Structural and dynamic features of the MutT protein in the recognition of nucleotides with the mutagenic 8-oxoguanine base
J.Biol.Chem., 285, 2010
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3A6U
 | | Crystal structure of MutT-8-OXO-dGMP-MN(II) complex | | Descriptor: | 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE, MANGANESE (II) ION, Mutator mutT protein, ... | | Authors: | Nakamura, T, Yamagata, Y. | | Deposit date: | 2009-09-09 | | Release date: | 2009-10-27 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.56 Å) | | Cite: | Structural and dynamic features of the MutT protein in the recognition of nucleotides with the mutagenic 8-oxoguanine base
J.Biol.Chem., 285, 2010
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3A6S
 | | Crystal structure of the MutT protein | | Descriptor: | L(+)-TARTARIC ACID, Mutator mutT protein, SODIUM ION | | Authors: | Nakamura, T, Yamagata, Y. | | Deposit date: | 2009-09-09 | | Release date: | 2009-10-27 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structural and dynamic features of the MutT protein in the recognition of nucleotides with the mutagenic 8-oxoguanine base
J.Biol.Chem., 285, 2010
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3A2W
 | | Peroxiredoxin (C50S) from Aeropytum pernix K1 (peroxide-bound form) | | Descriptor: | GLYCEROL, PEROXIDE ION, Probable peroxiredoxin | | Authors: | Nakamura, T, Kado, Y, Yamaguchi, F, Matsumura, H, Ishikawa, K, Inoue, T. | | Deposit date: | 2009-06-04 | | Release date: | 2009-10-27 | | Last modified: | 2021-11-10 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Crystal structure of peroxiredoxin from Aeropyrum pernix K1 complexed with its substrate, hydrogen peroxide
J.Biochem., 147, 2010
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3A2V
 | | Peroxiredoxin (C207S) from Aeropyrum pernix K1 complexed with hydrogen peroxide | | Descriptor: | PEROXIDE ION, Probable peroxiredoxin | | Authors: | Nakamura, T, Kado, Y, Yamaguchi, F, Ishikawa, K, Matsumura, H, Inoue, T. | | Deposit date: | 2009-06-04 | | Release date: | 2009-10-27 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Crystal structure of peroxiredoxin from Aeropyrum pernix K1 complexed with its substrate, hydrogen peroxide
J.Biochem., 147, 2010
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3A5W
 | | Peroxiredoxin (wild type) from Aeropyrum pernix K1 (reduced form) | | Descriptor: | Probable peroxiredoxin | | Authors: | Nakamura, T, Kado, Y, Yamaguchi, T, Matsumura, H, Ishikawa, K, Inoue, T. | | Deposit date: | 2009-08-12 | | Release date: | 2009-10-27 | | Last modified: | 2014-01-22 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Crystal structure of peroxiredoxin from Aeropyrum pernix K1 complexed with its substrate, hydrogen peroxide
J.Biochem., 147, 2010
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3A2X
 | | Peroxiredoxin (C50S) from Aeropyrum pernix K1 (acetate-bound form) | | Descriptor: | ACETATE ION, Probable peroxiredoxin | | Authors: | Nakamura, T, Kado, Y, Yamaguchi, F, Matsumura, H, Ishikawa, K, Inoue, T. | | Deposit date: | 2009-06-04 | | Release date: | 2009-10-27 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Crystal structure of peroxiredoxin from Aeropyrum pernix K1 complexed with its substrate, hydrogen peroxide
J.Biochem., 147, 2010
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3VOV
 | | Crystal Structure of ROK Hexokinase from Thermus thermophilus | | Descriptor: | GLYCEROL, Glucokinase, ZINC ION | | Authors: | Nakamura, T, Kashima, Y, Mine, S, Oku, T, Uegaki, K. | | Deposit date: | 2012-02-21 | | Release date: | 2012-06-27 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.02 Å) | | Cite: | Characterization and crystal structure of the thermophilic ROK hexokinase from Thermus thermophilus
J.Biosci.Bioeng., 2012
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7EF9
 | | Crystal structure of mouse MUTYH in complex with DNA containing AP site analogue:8-oxoG (Form II) | | Descriptor: | Adenine DNA glycosylase, DNA (5'-D(*AP*TP*GP*AP*GP*AP*CP*(8OG)P*GP*GP*GP*AP*CP*T)-3'), DNA (5'-D(*TP*AP*GP*TP*CP*CP*CP*(3DR)P*GP*TP*CP*TP*C)-3'), ... | | Authors: | Nakamura, T, Nakabeppu, Y, Yamagata, Y. | | Deposit date: | 2021-03-21 | | Release date: | 2021-06-23 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (1.97 Å) | | Cite: | Structure of the mammalian adenine DNA glycosylase MUTYH: insights into the base excision repair pathway and cancer.
Nucleic Acids Res., 49, 2021
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7EF8
 | | Crystal structure of mouse MUTYH in complex with DNA containing AP site analogue:8-oxoG (Form I) | | Descriptor: | Adenine DNA glycosylase, DNA (5'-D(*TP*AP*GP*TP*CP*CP*CP*(3DR)P*GP*TP*CP*TP*C)-3'), DNA (5'-D(*TP*GP*AP*GP*AP*CP*(8OG)P*GP*GP*GP*AP*CP*T)-3'), ... | | Authors: | Nakamura, T, Nakabeppu, Y, Yamagata, Y. | | Deposit date: | 2021-03-21 | | Release date: | 2021-06-23 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.45 Å) | | Cite: | Structure of the mammalian adenine DNA glycosylase MUTYH: insights into the base excision repair pathway and cancer.
Nucleic Acids Res., 49, 2021
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7EFA
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3W6G
 | | Structure of peroxiredoxin from anaerobic hyperthermophilic archaeon Pyrococcus horikoshii | | Descriptor: | CITRATE ANION, Probable peroxiredoxin | | Authors: | Nakamura, T, Mori, A, Niiyama, M, Matsumura, H, Tokuyama, C, Morita, J, Uegaki, K, Inoue, T. | | Deposit date: | 2013-02-14 | | Release date: | 2013-07-10 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.25 Å) | | Cite: | Structure of peroxiredoxin from the anaerobic hyperthermophilic archaeon Pyrococcus horikoshii
Acta Crystallogr.,Sect.F, 69, 2013
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3AK1
 | | Superoxide dismutase from Aeropyrum pernix K1, apo-form | | Descriptor: | 1,2-ETHANEDIOL, Superoxide dismutase [Mn/Fe] | | Authors: | Nakamura, T, Uegaki, K. | | Deposit date: | 2010-06-30 | | Release date: | 2011-02-02 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.57 Å) | | Cite: | Crystal structure of the cambialistic superoxide dismutase from Aeropyrum pernix K1 - insights into the enzyme mechanism and stability
Febs J., 278, 2011
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3AK3
 | | Superoxide dismutase from Aeropyrum pernix K1, Fe-bound form | | Descriptor: | 1,2-ETHANEDIOL, FE (III) ION, Superoxide dismutase [Mn/Fe] | | Authors: | Nakamura, T, Uegaki, K. | | Deposit date: | 2010-06-30 | | Release date: | 2011-02-02 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.48 Å) | | Cite: | Crystal structure of the cambialistic superoxide dismutase from Aeropyrum pernix K1 - insights into the enzyme mechanism and stability
Febs J., 278, 2011
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3VSA
 | | Crystal Structure of O-phosphoserine sulfhydrylase without acetate | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, PYRIDOXAL-5'-PHOSPHATE, Protein CysO | | Authors: | Nakamura, T, Kawai, Y, Kataoka, M, Ishikawa, K. | | Deposit date: | 2012-04-24 | | Release date: | 2012-05-16 | | Last modified: | 2017-11-22 | | Method: | X-RAY DIFFRACTION (2.07 Å) | | Cite: | Structural analysis of the substrate recognition mechanism in O-phosphoserine sulfhydrylase from the hyperthermophilic archaeon Aeropyrum pernix K1
J.Mol.Biol., 422, 2012
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3VSC
 | | Crystal Structure of the K127A Mutant of O-Phosphoserine Sulfhydrylase Complexed with External Schiff Base of Pyridoxal 5'-Phosphate with O-Phospho-L-Serine | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, PHOSPHOSERINE, PYRIDOXAL-5'-PHOSPHATE, ... | | Authors: | Nakamura, T, Kawai, Y, Kataoka, M, Ishikawa, K. | | Deposit date: | 2012-04-24 | | Release date: | 2012-05-16 | | Last modified: | 2017-11-22 | | Method: | X-RAY DIFFRACTION (2.07 Å) | | Cite: | Structural analysis of the substrate recognition mechanism in O-phosphoserine sulfhydrylase from the hyperthermophilic archaeon Aeropyrum pernix K1
J.Mol.Biol., 422, 2012
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3VSD
 | | Crystal Structure of the K127A Mutant of O-Phosphoserine Sulfhydrylase Complexed with External Schiff Base of Pyridoxal 5'-Phosphate with O-Acetyl-L-Serine | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, O-ACETYLSERINE, PYRIDOXAL-5'-PHOSPHATE, ... | | Authors: | Nakamura, T, Kawai, Y, Kataoka, M, Ishikawa, K. | | Deposit date: | 2012-04-24 | | Release date: | 2012-05-16 | | Last modified: | 2017-11-22 | | Method: | X-RAY DIFFRACTION (2.09 Å) | | Cite: | Structural analysis of the substrate recognition mechanism in O-phosphoserine sulfhydrylase from the hyperthermophilic archaeon Aeropyrum pernix K1
J.Mol.Biol., 422, 2012
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6LCS
 | | Crystal structure of 73MuL9 Fv-clasp fragment in complex with GA-pyridine analogue | | Descriptor: | (2~{S})-6-[4-(hydroxymethyl)-3-oxidanyl-pyridin-1-ium-1-yl]-2-(phenylmethoxycarbonylamino)hexanoic acid, PHOSPHATE ION, VH-SARAH, ... | | Authors: | Nakamura, T, Takagi, J, Yamagata, Y, Morioka, H. | | Deposit date: | 2019-11-19 | | Release date: | 2020-11-25 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Molecular recognition of a single-chain Fv antibody specific for GA-pyridine, an advanced glycation end-product (AGE), elucidated using biophysical techniques and synthetic antigen analogues.
J.Biochem., 170, 2021
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5B36
 | | Crystal Structure of the O-Phosphoserine Sulfhydrylase from Aeropyrum pernix Complexed with Cysteine | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, CYSTEINE, PYRIDOXAL-5'-PHOSPHATE, ... | | Authors: | Nakamura, T, Takeda, E, Kawai, Y, Kataoka, M, Ishikawa, K. | | Deposit date: | 2016-02-10 | | Release date: | 2016-03-16 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.15 Å) | | Cite: | Role of F225 in O-phosphoserine sulfhydrylase from Aeropyrum pernix K1
Extremophiles, 20, 2016
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5B3A
 | | Crystal Structure of O-Phoshoserine Sulfhydrylase from Aeropyrum pernix in Complexed with the alpha-Aminoacrylate Intermediate | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid, Protein CysO | | Authors: | Nakamura, T, Takeda, E, Kawai, Y, Kataoka, M, Ishikawa, K. | | Deposit date: | 2016-02-12 | | Release date: | 2016-03-16 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.14 Å) | | Cite: | Role of F225 in O-phosphoserine sulfhydrylase from Aeropyrum pernix K1
Extremophiles, 20, 2016
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5WS7
 | | Crystal structure of human MTH1(G2K/C87A/C104S mutant) in complex with 2-oxo-dATP | | Descriptor: | 7,8-dihydro-8-oxoguanine triphosphatase, SODIUM ION, [[(2R,3S,5R)-5-(6-azanyl-2-oxidanylidene-1H-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate | | Authors: | Nakamura, T, Waz, S, Hirata, K, Nakabeppu, Y, Yamagata, Y. | | Deposit date: | 2016-12-05 | | Release date: | 2017-01-04 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1 Å) | | Cite: | Structural and Kinetic Studies of the Human Nudix Hydrolase MTH1 Reveal the Mechanism for Its Broad Substrate Specificity
J. Biol. Chem., 292, 2017
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5GHJ
 | | Crystal structure of human MTH1(G2K mutant) in complex with 2-oxo-dATP | | Descriptor: | 7,8-dihydro-8-oxoguanine triphosphatase, SODIUM ION, [[(2R,3S,5R)-5-(6-azanyl-2-oxidanylidene-1H-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate | | Authors: | Nakamura, T, Waz, S, Hirata, K, Nakabeppu, Y, Yamagata, Y. | | Deposit date: | 2016-06-20 | | Release date: | 2017-01-04 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.2 Å) | | Cite: | Structural and Kinetic Studies of the Human Nudix Hydrolase MTH1 Reveal the Mechanism for Its Broad Substrate Specificity
J. Biol. Chem., 292, 2017
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