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CATH domain | Related DB codes (homologues) |
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2.30.30.10 : SH3 type barrels. | M00206,M00135 | 3.10.10.10 : HIV Type 1 Reverse Transcriptase; Chain A, domain 1 | M00206,M00135,M00166 | 3.30.420.10 : Nucleotidyltransferase; domain 5 | M00206,T00252,M00019,M00020,M00055,M00135,M00166,M00173,M00175,M00186 | 3.30.70.270 : Alpha-Beta Plaits | M00206,M00019,M00135,M00166,M00209 |
UniProtKB:Accession Number | P03354 |
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Entry name | POL_RSVP |
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Activity | Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).,Endonucleolytic cleavage to 5''- phosphomonoester. |
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Subunit | The integrase forms a homotetramer. Reverse transcriptase is a heterodimer of alpha and beta subunits. |
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Subcellular location |
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Cofactor | Binds 8 manganese or magnesium ions per integrase homotetramer (By similarity). |
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Compound table: links to PDB-related databases & PoSSuM |
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| Cofactors | Substrates | Products |
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KEGG-id | C00034 | C00677 | C00039 | C00046 | C00001 | C00013 | C00039 | C00960 |
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E.C. |
| 2.7.7.49,2.7.7.7 | 2.7.7.49,2.7.7.7 | 3.1.26.4 | 3.1.26.4 | 2.7.7.49,2.7.7.7 | 2.7.7.49,2.7.7.7 | 3.1.26.4 |
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Compound | Manganese | Deoxynucleoside triphosphate | DNA(n) | RNA | H2O | Pyrophosphate | DNA(n+1) | RNA 5'-phosphate |
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Type | heavy metal | nucleotide | nucleic acids | nucleic acids | H2O | phosphate group/phosphate ion | nucleic acids | nucleic acids,phosphate group/phosphate ion |
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ChEBI | 18291 35154
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| 15377
| 29888
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PubChem | 23930
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| 22247451 962
| 1023 21961011
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| | | | | | | | | | | | | | | |
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1c0mA01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound |
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1c0mB01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound |
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1c0mC01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound |
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1c0mD01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound |
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1c1aA01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound |
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1c1aB01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound |
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1a5vA |  |  |  |  |  |  |  | Bound:_MN | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound |
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1a5wA |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound |
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1a5xA |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound |
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1asuA |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound |
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1asvA |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound |
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1aswA |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound |
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1cxqA |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound |
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1cxuA |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound |
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1cz9A |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | | Analogue:SO4 | Unbound | Unbound |
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1czbA |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound |
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1vsdA |  |  |  |  |  |  |  | Analogue:_MG | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound |
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1vseA |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound |
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1vsfA |  |  |  |  |  |  |  | Bound:_MN | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound |
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1vshA |  |  |  |  |  |  |  | Analogue:2x_ZN | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound |
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1vsiA |  |  |  |  |  |  |  | Analogue:_CA | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound |
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1vskA |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound |
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1vslA |  |  |  |  |  |  |  | Analogue:_ZN | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound |
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1vsmA |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound |
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1c0mA02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound |
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1c0mB02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound |
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1c0mC02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound |
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1c0mD02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound |
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1c1aA02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound |
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1c1aB02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound |
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References for Catalytic Mechanism | References | Sections | No. of steps in catalysis |
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[1] | p.339 |
| [2] | Fig.3 |
| [3] |
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| [14] | Fig.9, p.12097-12098 | 3 |
references | [1] |
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PubMed ID | 7563093 |
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Journal | J Mol Biol |
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Year | 1995 |
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Volume | 253 |
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Pages | 333-46 |
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Authors | Bujacz G, Jaskolski M, Alexandratos J, Wlodawer A, Merkel G, Katz RA, Skalka AM |
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Title | High-resolution structure of the catalytic domain of avian sarcoma virus integrase. |
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Related PDB | 1asu,1asv,1asw |
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[2] |
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PubMed ID | 8805516 |
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Journal | Structure |
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Year | 1996 |
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Volume | 4 |
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Pages | 89-96 |
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Authors | Bujacz G, Jaskolski M, Alexandratos J, Wlodawer A, Merkel G, Katz RA, Skalka AM |
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Title | The catalytic domain of avian sarcoma virus integrase: conformation of the active-site residues in the presence of divalent cations. |
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Related PDB | 1vsd,1vse,1vsf |
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[3] |
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PubMed ID | 9218451 |
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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 | 18161-8 |
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Authors | Bujacz G, Alexandratos J, Wlodawer A, Merkel G, Andrake M, Katz RA, Skalka AM |
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Title | Binding of different divalent cations to the active site of avian sarcoma virus integrase and their effects on enzymatic activity. |
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Related PDB | 1vsh,1vsi,1vsj |
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[4] |
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PubMed ID | 9295344 |
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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 | 23938-45 |
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Authors | Vora AC, Chiu R, McCord M, Goodarzi G, Stahl SJ, Mueser TC, Hyde CC, Grandgenett DP |
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Title | Avian retrovirus U3 and U5 DNA inverted repeats. Role Of nonsymmetrical nucleotides in promoting full-site integration by purified virion and bacterial recombinant integrases. |
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[5] |
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PubMed ID | 9560188 |
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Journal | Proc Natl Acad Sci U S A |
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Year | 1998 |
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Volume | 95 |
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Pages | 4831-6 |
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Authors | Lubkowski J, Yang F, Alexandratos J, Wlodawer A, Zhao H, Burke TR Jr, Neamati N, Pommier Y, Merkel G, Skalka AM |
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Title | Structure of the catalytic domain of avian sarcoma virus integrase with a bound HIV-1 integrase-targeted inhibitor. |
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Related PDB | 1a5v,1a5w,1a5x |
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[6] |
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PubMed ID | 9830010 |
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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 | 32685-9 |
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Authors | Lubkowski J, Yang F, Alexandratos J, Merkel G, Katz RA, Gravuer K, Skalka AM, Wlodawer A |
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Title | Structural basis for inactivating mutations and pH-dependent activity of avian sarcoma virus integrase. |
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Related PDB | 1vsk,1vsl,1vsm |
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[7] |
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PubMed ID | 10521258 |
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Journal | Biochemistry |
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Year | 1999 |
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Volume | 38 |
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Pages | 13512-22 |
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Authors | Lubkowski J, Dauter Z, Yang F, Alexandratos J, Merkel G, Skalka AM, Wlodawer A |
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Title | Atomic resolution structures of the core domain of avian sarcoma virus integrase and its D64N mutant. |
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Related PDB | 1cxq,1cxu,1cxu,1cz9,1czb |
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[8] |
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PubMed ID | 10384241 |
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Journal | Adv Virus Res |
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Year | 1999 |
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Volume | 52 |
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Pages | 335-50 |
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Authors | Wlodawer A |
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Title | Crystal structures of catalytic core domains of retroviral integrases and role of divalent cations in enzymatic activity. |
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[9] |
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Comments | X-ray crystallography |
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PubMed ID | 10669607 |
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Journal | J Mol Biol |
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Year | 2000 |
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Volume | 296 |
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Pages | 535-48 |
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Authors | Yang ZN, Mueser TC, Bushman FD, Hyde CC |
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Title | Crystal structure of an active two-domain derivative of Rous sarcoma virus integrase. |
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Related PDB | 1c0m,1c1a |
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[10] |
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PubMed ID | 10685051 |
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Journal | Biopolymers |
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Year | 2000 |
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Volume | 53 |
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Pages | 308-15 |
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Authors | Lins RD, Straatsma TP, Briggs JM |
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Title | Similarities in the HIV-1 and ASV integrase active sites upon metal cofactor binding. |
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[11] |
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PubMed ID | 10961674 |
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Journal | Acta Biochim Pol |
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Year | 2000 |
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Volume | 47 |
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Pages | 11-22 |
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Authors | Ouali M, Laboulais C, Leh H, Gill D, Xhuvani E, Zouhiri F, Desmaele D, d'Angelo J, Auclair C, Mouscadet JF, Le Bret M |
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Title | Tautomers of styrylquinoline derivatives containing a methoxy substituent: computation of their population in aqueous solution and their interaction with RSV integrase catalytic core. |
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[12] |
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PubMed ID | 11441016 |
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Journal | J Biol Chem |
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Year | 2001 |
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Volume | 276 |
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Pages | 34213-20 |
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Authors | Katz RA, DiCandeloro P, Kukolj G, Skalka AM |
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Title | Role of DNA end distortion in catalysis by avian sarcoma virus integrase. |
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[13] |
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PubMed ID | 11024025 |
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Journal | J Biol Chem |
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Year | 2001 |
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Volume | 276 |
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Pages | 114-24 |
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Authors | Skinner LM, Sudol M, Harper AL, Katzman M |
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Title | Nucleophile selection for the endonuclease activities of human, ovine, and avian retroviral integrases. |
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[14] |
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PubMed ID | 11821409 |
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Journal | J Biol Chem |
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Year | 2002 |
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Volume | 277 |
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Pages | 12089-98 |
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Authors | Bao KK, Skalka AM, Wong I |
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Title | Presteady-state analysis of avian sarcoma virus integrase. I. A splicing activity and structure-function implications for cognate site recognition. |
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[15] |
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PubMed ID | 11821408 |
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Journal | J Biol Chem |
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Year | 2002 |
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Volume | 277 |
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Pages | 12099-108 |
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Authors | Bao KK, Skalka AM, Wong I |
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Title | Presteady-state analysis of avian sarcoma virus integrase. II. Reverse-polarity substrates identify preferential processing of the U3-U5 pair. |
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[16] |
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PubMed ID | 12610159 |
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Journal | J Virol |
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Year | 2003 |
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Volume | 77 |
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Pages | 3838-45 |
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Authors | Harper AL, Sudol M, Katzman M |
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Title | An amino acid in the central catalytic domain of three retroviral integrases that affects target site selection in nonviral DNA. |
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[17] |
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PubMed ID | 12446721 |
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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 | 1323-7 |
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Authors | Bao KK, Wang H, Miller JK, Erie DA, Skalka AM, Wong I |
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Title | Functional oligomeric state of avian sarcoma virus integrase. |
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comments | The tertiary structure of the N-terminal domains of this enzyme has not been determined yet. Only the catalytic domain of integrase has been solved so far. However, this enzyme seems to be homologous to the structures of its homologue, Pol polyprotein from Moloney murine leukemia virus (M00135 in EzCatDB), except for its N-terminal protease domain. This enzyme catalyzes two successive reactions, hydrolysis (called processing) and transfer (called joining) (see [3]). Although manganese is annotated as the cofactor, other divalent metal such as magnesium, cadmium and zinc can act as the cofactor (see [2] & [3]). However, in the presence of zinc ions, the polynucleotidyl transfer reaction can be inhibited, whilst the endonucleolytic reaction (hydrolysis) can be catalyzed (see [3]).
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created | updated |
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2002-07-31 | 2009-03-16 |
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