3WMR
 
 | | Crystal structure of VinJ | | Descriptor: | 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE, GLYCEROL, Proline iminopeptidase | | Authors: | Shinohara, Y, Miyanaga, A, Kudo, F, Eguchi, T. | | Deposit date: | 2013-11-22 | | Release date: | 2014-02-05 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | The crystal structure of the amidohydrolase VinJ shows a unique hydrophobic tunnel for its interaction with polyketide substrates
Febs Lett., 588, 2014
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1SPA
 | | ROLE OF ASP222 IN THE CATALYTIC MECHANISM OF ESCHERICHIA COLI ASPARTATE AMINOTRANSFERASE: THE AMINO ACID RESIDUE WHICH ENHANCES THE FUNCTION OF THE ENZYME-BOUND COENZYME PYRIDOXAL 5'-PHOSPHATE | | Descriptor: | ASPARTATE AMINOTRANSFERASE, N-METHYL-4-DEOXY-4-AMINO-PYRIDOXAL-5-PHOSPHATE | | Authors: | Hinoue, Y, Yano, T, Metzler, D.E, Miyahara, I, Hirotsu, K, Kagamiyama, H. | | Deposit date: | 1993-01-26 | | Release date: | 1993-10-31 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Role of Asp222 in the catalytic mechanism of Escherichia coli aspartate aminotransferase: the amino acid residue which enhances the function of the enzyme-bound coenzyme pyridoxal 5'-phosphate.
Biochemistry, 31, 1992
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5X17
 | | Crystal structure of murine CK1d in complex with ADP | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, Casein kinase I isoform delta, SULFATE ION | | Authors: | Kikuchi, M, Shinohara, Y, Ueda, H.R, Umehara, T. | | Deposit date: | 2017-01-25 | | Release date: | 2017-10-04 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Temperature-Sensitive Substrate and Product Binding Underlie Temperature-Compensated Phosphorylation in the Clock
Mol. Cell, 67, 2017
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5X18
 | | Crystal structure of Casein kinase I homolog 1 | | Descriptor: | Casein kinase I homolog 1, GLYCEROL, MALONIC ACID | | Authors: | Kikuchi, M, Shinohara, Y, Ueda, H.R, Umehara, T. | | Deposit date: | 2017-01-25 | | Release date: | 2017-10-04 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Temperature-Sensitive Substrate and Product Binding Underlie Temperature-Compensated Phosphorylation in the Clock
Mol. Cell, 67, 2017
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1ZR7
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5CZC
 | | The structure of VinK | | Descriptor: | CALCIUM ION, GLYCEROL, Malonyl-CoA-[acyl-carrier-protein] transacylase | | Authors: | Miyanaga, A, Iwasawa, S, Shinohara, Y, Kudo, F, Eguchi, T. | | Deposit date: | 2015-07-31 | | Release date: | 2016-02-03 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structure-based analysis of the molecular interactions between acyltransferase and acyl carrier protein in vicenistatin biosynthesis.
Proc.Natl.Acad.Sci.USA, 113, 2016
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6Z1H
 | | Ancestral glycosidase (family 1) | | Descriptor: | ANCESTRAL RECONSTRUCTED GLYCOSIDASE, GLYCEROL, ISOPROPYL ALCOHOL, ... | | Authors: | Gavira, J.A, Risso, V.A, Sanchez-Ruiz, J.M, Gamiz-Arco, G, Gutierrez-Rus, L, Ibarra-Molero, B, Hoshino, Y, Petrovic, D, Romero-Rivera, A, Seelig, B, Kamerlin, S.C.L, Gaucher, E.A. | | Deposit date: | 2020-05-13 | | Release date: | 2020-07-22 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase.
Nat Commun, 12, 2021
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6Z1M
 | | Structure of an Ancestral glycosidase (family 1) bound to heme | | Descriptor: | 1,2-ETHANEDIOL, Ancestral reconstructed glycosidase, GLYCEROL, ... | | Authors: | Gavira, J.A, Risso, V.A, Sanchez-Ruiz, J.M, Gamiz-Arco, G, Gutierrez-Rus, L, Ibarra-Molero, B, Oshino, Y, Petrovic, D, Romero-Rivera, A, Seelig, B, Kamerlin, S.C.L, Gaucher, E.A. | | Deposit date: | 2020-05-14 | | Release date: | 2020-07-22 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (2.45 Å) | | Cite: | Heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase.
Nat Commun, 12, 2021
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1IQP
 | | Crystal Structure of the Clamp Loader Small Subunit from Pyrococcus furiosus | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, RFCS | | Authors: | Oyama, T, Ishino, Y, Cann, I.K.O, Ishino, S, Morikawa, K. | | Deposit date: | 2001-07-24 | | Release date: | 2001-09-19 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Atomic Structure of the Clamp Loader Small Subunit from Pyrococcus furiosus
Mol.Cell, 8, 2001
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1GEF
 | | Crystal structure of the archaeal holliday junction resolvase HJC | | Descriptor: | HOLLIDAY JUNCTION RESOLVASE, SULFATE ION | | Authors: | Nishino, T, Komori, K, Tsuchiya, D, Ishino, Y, Morikawa, K. | | Deposit date: | 2000-11-08 | | Release date: | 2001-03-21 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Crystal structure of the archaeal holliday junction resolvase Hjc and implications for DNA recognition.
Structure, 9, 2001
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1IPI
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1WP9
 | | Crystal structure of Pyrococcus furiosus Hef helicase domain | | Descriptor: | ATP-dependent RNA helicase, putative, PHOSPHATE ION | | Authors: | Nishino, T, Komori, K, Tsuchiya, D, Ishino, Y, Morikawa, K. | | Deposit date: | 2004-08-31 | | Release date: | 2005-02-01 | | Last modified: | 2021-11-10 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Crystal Structure and Functional Implications of Pyrococcus furiosus Hef Helicase Domain Involved in Branched DNA Processing
Structure, 13, 2005
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1J23
 | | Crystal structure of archaeal XPF/Mus81 homolog, Hef from Pyrococcus furiosus, nuclease domain | | Descriptor: | ATP-dependent RNA helicase, putative | | Authors: | Nishino, T, Komori, K, Ishino, Y, Morikawa, K. | | Deposit date: | 2002-12-25 | | Release date: | 2003-04-22 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (1.78 Å) | | Cite: | X-Ray and Biochemical Anatomy of an Archaeal XPF/Rad1/Mus81 Family Nuclease. Similarity between Its Endonuclease Domain and Restriction Enzymes
Structure, 11, 2003
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1IZ4
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1J25
 | | Crystal structure of archaeal XPF/Mus81 homolog, Hef from Pyrococcus furiosus, nuclease domain, Mn cocrystal | | Descriptor: | ATP-dependent RNA helicase, putative, MANGANESE (II) ION | | Authors: | Nishino, T, Komori, K, Ishino, Y, Morikawa, K. | | Deposit date: | 2002-12-25 | | Release date: | 2003-04-22 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (1.78 Å) | | Cite: | X-Ray and Biochemical Anatomy of an Archaeal XPF/Rad1/Mus81 Family Nuclease. Similarity between Its Endonuclease Domain and Restriction Enzymes
Structure, 11, 2003
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1J24
 | | Crystal structure of archaeal XPF/Mus81 homolog, Hef from Pyrococcus furiosus, nuclease domain, Ca cocrystal | | Descriptor: | ATP-dependent RNA helicase, putative, CALCIUM ION | | Authors: | Nishino, T, Komori, K, Ishino, Y, Morikawa, K. | | Deposit date: | 2002-12-25 | | Release date: | 2003-04-22 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (1.78 Å) | | Cite: | X-Ray and Biochemical Anatomy of an Archaeal XPF/Rad1/Mus81 Family Nuclease. Similarity between Its Endonuclease Domain and Restriction Enzymes
Structure, 11, 2003
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1ISQ
 | | Pyrococcus furiosus PCNA complexed with RFCL PIP-box peptide | | Descriptor: | Proliferating Cell Nuclear Antigen, replication factor C large subunit | | Authors: | Matsumiya, S, Ishino, S, Ishino, Y, Morikawa, K. | | Deposit date: | 2001-12-19 | | Release date: | 2002-10-23 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Physical interaction between proliferating cell nuclear antigen and
replication factor C from Pyrococcus furiosus
Genes Cells, 7, 2002
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1IZ5
 | | Pyrococcus furiosus PCNA mutant (Met73Leu, Asp143Ala, Asp147Ala): orthorhombic form | | Descriptor: | Proliferating cell nuclear antigen | | Authors: | Matsumiya, S, Ishino, S, Ishino, Y, Morikawa, K. | | Deposit date: | 2002-09-23 | | Release date: | 2003-04-01 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Intermolecular ion pairs maintain the toroidal structure of Pyrococcus furiosus PCNA
PROTEIN SCI., 12, 2003
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1X2I
 | | Crystal Structure Of Archaeal Xpf/Mus81 Homolog, Hef From Pyrococcus Furiosus, Helix-hairpin-helix Domain | | Descriptor: | Hef helicase/nuclease | | Authors: | Nishino, T, Komori, K, Ishino, Y, Morikawa, K. | | Deposit date: | 2005-04-24 | | Release date: | 2005-09-13 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | Structural and Functional Analyses of an Archaeal XPF/Rad1/Mus81 Nuclease: Asymmetric DNA Binding and Cleavage Mechanisms
STRUCTURE, 13, 2005
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1J22
 | | Crystal structure of archaeal XPF/Mus81 homolog, Hef from Pyrococcus furiosus, nuclease domain, selenomet derivative | | Descriptor: | ATP-dependent RNA helicase, putative | | Authors: | Nishino, T, Komori, K, Ishino, Y, Morikawa, K. | | Deposit date: | 2002-12-25 | | Release date: | 2003-04-22 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | X-Ray and Biochemical Anatomy of an Archaeal XPF/Rad1/Mus81 Family Nuclease. Similarity between Its Endonuclease Domain and Restriction Enzymes
Structure, 11, 2003
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5GKI
 | | Structure of EndoMS-dsDNA3 complex | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, DNA (5'-D(*GP*CP*CP*TP*AP*GP*GP*TP*CP*CP*CP*GP*TP*CP*C)-3'), DNA (5'-D(*GP*GP*AP*CP*GP*GP*GP*GP*CP*CP*TP*AP*GP*GP*C)-3'), ... | | Authors: | Nakae, S, Hijikata, A, Tsuji, T, Yonezawa, K, Kouyama, K, Mayanagi, K, Ishino, S, Ishino, Y, Shirai, T. | | Deposit date: | 2016-07-04 | | Release date: | 2016-11-02 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease
Structure, 24, 2016
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5GKG
 | | Structure of EndoMS-dsDNA1'' complex | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, DNA (5'-D(*CP*GP*CP*TP*AP*CP*AP*GP*GP*TP*CP*GP*TP*CP*C)-3'), DNA (5'-D(*GP*GP*AP*CP*GP*AP*CP*GP*TP*GP*TP*AP*GP*CP*G)-3'), ... | | Authors: | Nakae, S, Hijikata, A, Tsuji, T, Yonezawa, K, Kouyama, K, Mayanagi, K, Ishino, S, Ishino, Y, Shirai, T. | | Deposit date: | 2016-07-04 | | Release date: | 2016-11-02 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease
Structure, 24, 2016
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5GKJ
 | | Structure of EndoMS in apo form | | Descriptor: | Endonuclease EndoMS | | Authors: | Nakae, S, Hijikata, A, Tsuji, T, Yonezawa, K, Kouyama, K, Mayanagi, K, Ishino, S, Ishino, Y, Shirai, T. | | Deposit date: | 2016-07-04 | | Release date: | 2016-11-02 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.2 Å) | | Cite: | Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease
Structure, 24, 2016
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5GKF
 | | Structure of EndoMS-dsDNA1' complex | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, DNA (5'-D(*CP*GP*CP*TP*AP*CP*AP*TP*GP*TP*CP*GP*TP*CP*C)-3'), DNA (5'-D(*GP*GP*AP*CP*GP*AP*CP*TP*TP*GP*TP*AP*GP*CP*G)-3'), ... | | Authors: | Nakae, S, Hijikata, A, Tsuji, T, Yonezawa, K, Kouyama, K, Mayanagi, K, Ishino, S, Ishino, Y, Shirai, T. | | Deposit date: | 2016-07-04 | | Release date: | 2016-11-02 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease
Structure, 24, 2016
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5GKH
 | | Structure of EndoMS-dsDNA2 complex | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, DNA (5'-D(*AP*CP*GP*GP*CP*AP*CP*TP*TP*GP*GP*CP*AP*CP*G)-3'), DNA (5'-D(*CP*GP*TP*GP*CP*CP*AP*GP*GP*TP*GP*CP*CP*GP*T)-3'), ... | | Authors: | Nakae, S, Hijikata, A, Tsuji, T, Yonezawa, K, Kouyama, K, Mayanagi, K, Ishino, S, Ishino, Y, Shirai, T. | | Deposit date: | 2016-07-04 | | Release date: | 2016-11-02 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease
Structure, 24, 2016
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