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Enzyme Name | UniProtKB | KEGG |
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| P04418 |
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Protein name | Endonuclease V | deoxyribonuclease (pyrimidine dimer)endodeoxyribonuclease (pyrimidine dimer)endodeoxyribonuclease (pyrimidine dimer)bacteriophage T4 endodeoxyribonuclease VT4 endonuclease V |
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Synonyms | EC 3.1.25.1 |
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RefSeq | NP_049733.1 (Protein) NC_000866.4 (DNA/RNA sequence)
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Pfam | PF03013 (Pyr_excise) [Graphical view]
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UniProtKB:Accession Number | P04418 |
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Entry name | END5_BPT4 |
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Activity | Endonucleolytic cleavage near pyrimidine dimers to products with 5''-phosphate. |
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Subunit | Monomer. |
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Subcellular location |
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Cofactor |
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Compound table: links to PDB-related databases & PoSSuM |
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| Substrates | Products |
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KEGG-id | L00011 | C00001 | C00578 | L00013 |
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Compound | cys-syn pyrimidine dimer in DNA | H2O | DNA 5'-phosphate | DNA 3'-trans-alpha,beta unsaturated aldehyde |
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Type | nucleic acids | H2O | nucleic acids,phosphate group/phosphate ion | nucleic acids,carbohydrate |
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ChEBI |
| 15377
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PubChem |
| 22247451 962
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| | | | | | | | | | | |
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1endA |  |  |  |  |  |  |  | Unbound | | Unbound | Unbound |
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1eniA |  |  |  |  |  |  |  | Unbound | | Unbound | Unbound |
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1enjA |  |  |  |  |  |  |  | Unbound | | Unbound | Unbound |
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1enkA |  |  |  |  |  |  |  | Unbound | | Unbound | Unbound |
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1vasA |  |  |  |  |  |  |  | Bound:A-T-C-G-C-G-T-T-G-C-G-C-T(chain B) | | Unbound | Unbound |
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2endA |  |  |  |  |  |  |  | Unbound | | Unbound | Unbound |
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References for Catalytic Mechanism | References | Sections | No. of steps in catalysis |
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[2] | Fig. 1, p.51-54 |
| [6] | Scheme 1, p.17637-17638 |
| [9] | Fig.1 |
| [10] | Fig.1, p.9424 |
| [11] | p.524-525 |
| [12] | Fig.1 |
| [14] | Fig.8, p.182-193 |
| [15] | Fig.1, p.201-205 |
| [17] | Fig.1 |
| [18] | Fig.4, p.778-779 |
| [19] | Fig.1, p.2660-2661 |
| [20] | p.369-371 |
| [21] |
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| [23] | Fig.1, p.32152 |
| [25] | p.258-261 |
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references | [1] |
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PubMed ID | 3172233 |
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Journal | J Mol Biol |
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Year | 1988 |
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Volume | 202 |
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Pages | 683-4 |
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Authors | Morikawa K, Tsujimoto M, Ikehara M, Inaoka T, Ohtsuka E |
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Title | Preliminary crystallographic study of pyrimidine dimer-specific excision-repair enzyme from bacteriophage T4. |
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[2] |
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PubMed ID | 2671706 |
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Journal | Mutat Res |
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Year | 1989 |
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Volume | 218 |
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Pages | 49-65 |
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Authors | Dodson ML, Lloyd RS |
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Title | Structure-function studies of the T4 endonuclease V repair enzyme. |
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[3] |
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PubMed ID | 2695926 |
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Journal | Proteins |
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Year | 1989 |
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Volume | 6 |
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Pages | 128-38 |
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Authors | Lloyd RS, Augustine ML |
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Title | Site-directed mutagenesis of the T4 endonuclease V gene: mutations which enhance enzyme specific activity at low salt concentrations. |
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[4] |
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PubMed ID | 1888726 |
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Journal | Biochemistry |
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Year | 1991 |
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Volume | 30 |
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Pages | 8638-48 |
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Authors | Nickell C, Lloyd RS |
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Title | Mutations in endonuclease V that affect both protein-protein association and target site location. |
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[5] |
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PubMed ID | 2037608 |
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Journal | J Biol Chem |
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Year | 1991 |
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Volume | 266 |
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Pages | 10686-93 |
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Authors | Prince MA, Friedman B, Gruskin EA, Schrock RD 3rd, Lloyd RS |
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Title | Selective metal binding to Cys-78 within endonuclease V causes an inhibition of catalytic activities without altering nontarget and target DNA binding. |
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[6] |
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PubMed ID | 1894643 |
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Journal | J Biol Chem |
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Year | 1991 |
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Volume | 266 |
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Pages | 17631-9 |
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Authors | Schrock RD 3rd, Lloyd RS |
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Title | Reductive methylation of the amino terminus of endonuclease V eradicates catalytic activities. Evidence for an essential role of the amino terminus in the chemical mechanisms of catalysis. |
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[7] |
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PubMed ID | 2067549 |
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Journal | Mutat Res |
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Year | 1991 |
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Volume | 255 |
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Pages | 19-29 |
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Authors | Dodson ML, Prince MA, Anderson WF, Lloyd RS |
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Title | Site-directed deletion mutagenesis within the T4 endonuclease V gene: dispensable sequences within putative loop regions. |
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[8] |
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PubMed ID | 1841278 |
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Journal | Nucleic Acids Symp Ser |
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Year | 1991 |
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Volume | 4 |
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Pages | 181-4 |
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Authors | Morikawa K, Matsumoto O, Tsujimoto M, Katayanagi K, Doi T, Ariyoshi M, Ikehara M, Inaoka T, Ohtsuka E |
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Title | Atomic structure of a pyrimidine-dimer specific excision-repair enzyme from bacteriophage T4. |
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[9] |
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PubMed ID | 1357629 |
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Journal | Nucleic Acids Res |
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Year | 1992 |
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Volume | 20 |
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Pages | 4761-4 |
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Authors | Hori N, Doi T, Karaki Y, Kikuchi M, Ikehara M, Ohtsuka E |
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Title | Participation of glutamic acid 23 of T4 endonuclease V in the beta-elimination reaction of an abasic site in a synthetic duplex DNA. |
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[10] |
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PubMed ID | 1409651 |
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Journal | Proc Natl Acad Sci U S A |
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Year | 1992 |
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Volume | 89 |
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Pages | 9420-4 |
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Authors | Doi T, Recktenwald A, Karaki Y, Kikuchi M, Morikawa K, Ikehara M, Inaoka T, Hori N, Ohtsuka E |
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Title | Role of the basic amino acid cluster and Glu-23 in pyrimidine dimer glycosylase activity of T4 endonuclease V. |
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[11] |
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Comments | X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS). |
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PubMed ID | 1575827 |
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Journal | Science |
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Year | 1992 |
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Volume | 256 |
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Pages | 523-6 |
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Authors | Morikawa K, Matsumoto O, Tsujimoto M, Katayanagi K, Ariyoshi M, Doi T, Ikehara M, Inaoka T, Ohtsuka E |
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Title | X-ray structure of T4 endonuclease V: an excision repair enzyme specific for a pyrimidine dimer. |
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Related UniProtKB | P04418 |
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[12] |
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PubMed ID | 8347626 |
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Journal | Biochemistry |
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Year | 1993 |
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Volume | 32 |
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Pages | 8284-90 |
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Authors | Dodson ML, Schrock RD 3rd, Lloyd RS |
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Title | Evidence for an imino intermediate in the T4 endonuclease V reaction. |
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[13] |
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PubMed ID | 8441681 |
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Journal | Nucleic Acids Res |
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Year | 1993 |
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Volume | 21 |
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Pages | 727-32 |
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Authors | Green AP, deRiel JK, Henderson EE |
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Title | Structure/function analysis of the Ala116-->Lys121 region of endonuclease V by random targeted mutagenesis. |
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[14] |
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PubMed ID | 7916555 |
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Journal | Ann N Y Acad Sci |
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Year | 1994 |
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Volume | 26 |
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Pages | 181-96 |
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Authors | Latham KA, Lloyd RS |
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Title | T4 endonuclease V. Perspectives on catalysis. |
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[15] |
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PubMed ID | 8092676 |
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Journal | Ann N Y Acad Sci |
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Year | 1994 |
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Volume | 26 |
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Pages | 198-207 |
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Authors | Morikawa K, Ariyoshi M, Vassylyev D, Katayanagi K, Nakamura H, Doi T, Hori N, Ohtsuka E |
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Title | Crystal structure of T4 endonuclease V. An excision repair enzyme for a pyrimidine dimer. |
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[16] |
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PubMed ID | 8286363 |
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Journal | Biochemistry |
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Year | 1994 |
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Volume | 33 |
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Pages | 57-64 |
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Authors | Lee BJ, Sakashita H, Ohkubo T, Ikehara M, Doi T, Morikawa K, Kyogoku Y, Osafune T, Iwai S, Ohtsuka E |
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Title | Nuclear magnetic resonance study of the interaction of T4 endonuclease V with DNA. |
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[17] |
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PubMed ID | 7718562 |
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Journal | Biochemistry |
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Year | 1995 |
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Volume | 34 |
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Pages | 4601-9 |
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Authors | Iwai S, Maeda M, Shirai M, Shimada Y, Osafune T, Murata T, Ohtsuka E |
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Title | Reaction mechanism of T4 endonuclease V determined by analysis using modified oligonucleotide duplexes. |
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[18] |
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Comments | X-ray crystallography |
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PubMed ID | 8521494 |
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Journal | Cell |
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Year | 1995 |
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Volume | 83 |
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Pages | 773-82 |
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Authors | Vassylyev DG, Kashiwagi T, Mikami Y, Ariyoshi M, Iwai S, Ohtsuka E, Morikawa K |
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Title | Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition. |
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Related PDB | 1vas |
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[19] |
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PubMed ID | 7852333 |
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Journal | J Biol Chem |
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Year | 1995 |
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Volume | 270 |
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Pages | 2652-61 |
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Authors | Manuel RC, Latham KA, Dodson ML, Lloyd RS |
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Title | Involvement of glutamic acid 23 in the catalytic mechanism of T4 endonuclease V. |
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[20] |
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Comments | X-ray crystallography |
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PubMed ID | 7783199 |
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Journal | J Mol Biol |
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Year | 1995 |
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Volume | 249 |
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Pages | 360-75 |
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Authors | Morikawa K, Ariyoshi M, Vassylyev DG, Matsumoto O, Katayanagi K, Ohtsuka E |
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Title | Crystal structure of a pyrimidine dimer-specific excision repair enzyme from bacteriophage T4: refinement at 1.45 A and X-ray analysis of the three active site mutants. |
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Related PDB | 1end,1eni,1enj,1enk,2end |
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[21] |
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PubMed ID | 8943268 |
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Journal | J Biol Chem |
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Year | 1996 |
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Volume | 271 |
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Pages | 32147-52 |
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Authors | McCullough AK, Scharer O, Verdine GL, Lloyd RS |
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Title | Structural determinants for specific recognition by T4 endonuclease V. |
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[22] |
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PubMed ID | 9100001 |
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Journal | Biochemistry |
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Year | 1997 |
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Volume | 36 |
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Pages | 4080-8 |
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Authors | Nyaga SG, Dodson ML, Lloyd RS |
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Title | Role of specific amino acid residues in T4 endonuclease V that alter nontarget DNA binding. |
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[23] |
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PubMed ID | 9341165 |
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Journal | J Biol Chem |
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Year | 1997 |
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Volume | 272 |
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Pages | 27210-7 |
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Authors | McCullough AK, Dodson ML, Scharer OD, Lloyd RS |
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Title | The role of base flipping in damage recognition and catalysis by T4 endonuclease V. |
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[24] |
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PubMed ID | 9582353 |
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Journal | J Biol Chem |
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Year | 1998 |
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Volume | 273 |
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Pages | 13136-42 |
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Authors | McCullough AK, Romberg MT, Nyaga S, Wei Y, Wood TG, Taylor JS, Van Etten JL, Dodson ML, Lloyd RS |
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Title | Characterization of a novel cis-syn and trans-syn-II pyrimidine dimer glycosylase/AP lyase from a eukaryotic algal virus, Paramecium bursaria chlorella virus-1. |
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[25] |
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PubMed ID | 10946233 |
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Journal | Mutat Res |
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Year | 2000 |
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Volume | 460 |
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Pages | 257-75 |
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Authors | Morikawa K, Shirakawa M |
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Title | Three-dimensional structural views of damaged-DNA recognition: T4 endonuclease V, E. coli Vsr protein, and human nucleotide excision repair factor XPA. |
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[26] |
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PubMed ID | 11265291 |
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Journal | Methods Mol Biol |
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Year | 2001 |
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Volume | 60 |
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Pages | 3-14 |
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Authors | Lloyd RS |
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Title | Processivity of DNA repair enzymes. |
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[27] |
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PubMed ID | 12783877 |
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Journal | J Biol Chem |
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Year | 2003 |
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Volume | 278 |
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Pages | 30985-92 |
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Authors | Ahn HC, Ohkubo T, Iwai S, Morikawa K, Lee BJ |
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Title | Interaction of T4 endonuclease V with DNA: importance of the flexible loop regions in protein-DNA interaction. |
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comments | Although this enzyme classified into hydrolase (E.C. 3.-.-.-), it does not catalyzes hydrolysis. According to the literature [18], [19], [20], [23] & [25], this enzyme catalyzes the following reactions succesively, although the detailed mechanism has not been elucidated. (I) glycosylase reaction to form Schiff-base intermediate. (A) Transfer of deoxyribose group from pyrimidine dimer to the N-terminal alpha-amino group. (B) Eliminative double-bond formation; Ring opening of deoxyribose, forming Schiff-base intermediate. (II) AP lyase reaction. (C) Isomerization; Shift of double-bond from Schiff-base to adjacent bond. (D) Eliminative double-bond formation; beta-elimination of 3'-phosphate from the opened deoxyribose group. (E) Exchange of double-bonded atoms; Schiff-base deformation (hydration) #### The N-terminal alpha-amino group of Thr2 forms Schiff-base with C1' atom of the deoxyribose. Glu23 seems to be required for both reactions, (I) & (II).
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created | updated |
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2004-03-19 | 2009-02-26 |
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