Integration of provirus

Lewinski MK, Bushman FD. Retroviral DNA integration--mechanism and consequences. Adv Genet. 2005;55():147–81. doi: 10.1016/s0065-2660(05)55005-3. PMID: 16291214.; Gao K, Wong S, Bushman F. Metal Binding by the D,DX 35 E Motif of Human Immunodeficiency Virus Type 1 Integrase: Selective Rescue of Cys Substitutions by Mn 2+ In Vitro. J Virol. 2004 Jul;78(13):6715–22. doi: 10.1128/jvi.78.13.6715-6722.2004.; Hansen MS, Carteau S, Hoffmann C, Li L, Bushman F. Retroviral cDNA integration: mechanism, applications and inhibition. Genet Eng (N Y). 1998;20():41–61. doi: 10.1007/978-1-4899-1739-3_3. PMID: 9666555.; Miller MD, Farnet CM, Bushman FD. Human immunodeficiency virus type 1 preintegration complexes: studies of organization and composition. J Virol. 1997 Jul;71(7):5382–90. doi: 10.1128/jvi.71.7.5382-5390.1997.; Balakrishnan M, Jonsson CB. Functional identification of nucleotides conferring substrate specificity to retroviral integrase reactions. 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J Virol. 1992 Apr;66(4):2359–68. doi: 10.1128/jvi.66.4.2359-2368.1992.; Engelman A, Mizuuchi K, Craigie R. HIV-1 DNA integration: mechanism of viral DNA cleavage and DNA strand transfer. Cell. 1991 Dec 20;67(6):1211–21. doi: 10.1016/0092-8674(91)90297-c. PMID: 1760846.; Farnet CM, Haseltine WA. Determination of viral proteins present in the human immunodeficiency virus type 1 preintegration complex. J Virol. 1991 Apr;65(4):1910–5. doi: 10.1128/jvi.65.4.1910-1915.1991.; Bushman FD, Craigie R. Activities of human immunodeficiency virus (HIV) integration protein in vitro: specific cleavage and integration of HIV DNA. Proc. Natl. Acad. Sci. U.S.A. 1991 Feb 15;88(4):1339–43. doi: 10.1073/pnas.88.4.1339.; Bushman FD, Craigie R. Sequence requirements for integration of Moloney murine leukemia virus DNA in vitro. J Virol. 1990 Nov;64(11):5645–8. doi: 10.1128/jvi.64.11.5645-5648.1990.; Vincent KA, York-Higgins D, Quiroga M, Brown PO. Host sequences flanking the HIV provirus. Nucleic Acids Res. 1990 Oct 25;18(20):6045–7. PMID: 2235486; PMCID: PMC332403.; Katz RA, Merkel G, Kulkosky J, Leis J, Skalka AM. The avian retroviral IN protein is both necessary and sufficient for integrative recombination in vitro. Cell. 1990 Oct 05;63(1):87–95. doi: 10.1016/0092-8674(90)90290-u. PMID: 2170022.; Bushman FD, Fujiwara T, Craigie R. Retroviral DNA integration directed by HIV integration protein in vitro. Science. 1990 Sep 28;249(4976):1555–8. doi: 10.1126/science.2171144. PMID: 2171144.; Craigie R, Fujiwara T, Bushman F. The IN protein of Moloney murine leukemia virus processes the viral DNA ends and accomplishes their integration in vitro. Cell. 1990 Aug 24;62(4):829–37. doi: 10.1016/0092-8674(90)90126-y. PMID: 2167180.; Sherman PA, Fyfe JA. Human immunodeficiency virus integration protein expressed in Escherichia coli possesses selective DNA cleaving activity. Proc. Natl. Acad. Sci. U.S.A. 1990 Jul;87(13):5119–23. doi: 10.1073/pnas.87.13.5119.; Ellison V, Abrams H, Roe T, Lifson J, Brown P. Human immunodeficiency virus integration in a cell-free system. J Virol. 1990 Jun;64(6):2711–5. doi: 10.1128/jvi.64.6.2711-2715.1990.; Farnet CM, Haseltine WA. Integration of human immunodeficiency virus type 1 DNA in vitro. Proc. Natl. Acad. Sci. U.S.A. 1990 Jun;87(11):4164–8. doi: 10.1073/pnas.87.11.4164.; Katzman M, Katz RA, Skalka AM, Leis J. The avian retroviral integration protein cleaves the terminal sequences of linear viral DNA at the in vivo sites of integration. J Virol. 1989 Dec;63(12):5319–27. doi: 10.1128/jvi.63.12.5319-5327.1989.; Roth MJ, Schwartzberg PL, Goff SP. Structure of the termini of DNA intermediates in the integration of retroviral DNA: dependence on IN function and terminal DNA sequence. Cell. 1989 Jul 14;58(1):47–54. doi: 10.1016/0092-8674(89)90401-7. PMID: 2546673.; Bowerman B, Brown PO, Bishop JM, Varmus HE. A nucleoprotein complex mediates the integration of retroviral DNA. Genes Dev. 1989 Apr;3(4):469–78. doi: 10.1101/gad.3.4.469. PMID: 2721960.; Brown PO, Bowerman B, Varmus HE, Bishop JM. Retroviral integration: structure of the initial covalent product and its precursor, and a role for the viral IN protein. Proc. Natl. Acad. Sci. U.S.A. 1989 Apr;86(8):2525–9. doi: 10.1073/pnas.86.8.2525.; Donehower LA. Analysis of mutant Moloney murine leukemia viruses containing linker insertion mutations in the 3' region of pol. J Virol. 1988 Nov;62(11):3958–64. doi: 10.1128/jvi.62.11.3958-3964.1988.; Fujiwara T, Mizuuchi K. Retroviral DNA integration: structure of an integration intermediate. Cell. 1988 Aug 12;54(4):497–504. doi: 10.1016/0092-8674(88)90071-2. PMID: 3401925.; Quinn TP, Grandgenett DP. Genetic evidence that the avian retrovirus DNA endonuclease domain of pol is necessary for viral integration. J Virol. 1988 Jul;62(7):2307–12. doi: 10.1128/jvi.62.7.2307-2312.1988.; Colicelli J, Goff SP. Sequence and spacing requirements of a retrovirus integration site. Journal of Molecular Biology. 1988 Jan;199(1):47–59. doi: 10.1016/0022-2836(88)90378-6.; Brown PO, Bowerman B, Varmus HE, Bishop JM. Correct integration of retroviral DNA in vitro. Cell. 1987 May 08;49(3):347–56. doi: 10.1016/0092-8674(87)90287-x. PMID: 3032450.; Colicelli J, Goff SP. Mutants and pseudorevertants of Moloney murine leukemia virus with alterations at the integration site. Cell. 1985 Sep;42(2):573–80. doi: 10.1016/0092-8674(85)90114-x. PMID: 4028161.; Panganiban AT, Temin HM. The retrovirus pol gene encodes a product required for DNA integration: identification of a retrovirus int locus. Proc. Natl. Acad. Sci. U.S.A. 1984 Dec;81(24):7885–9. doi: 10.1073/pnas.81.24.7885.; Donehower LA, Varmus HE. A mutant murine leukemia virus with a single missense codon in pol is defective in a function affecting integration. Proc. Natl. Acad. Sci. U.S.A. 1984 Oct;81(20):6461–5. doi: 10.1073/pnas.81.20.6461.; Schwartzberg P, Colicelli J, Goff SP. Construction and analysis of deletion mutations in the pol gene of Moloney murine leukemia virus: a new viral function required for productive infection. Cell. 1984 Jul;37(3):1043–52. doi: 10.1016/0092-8674(84)90439-2. PMID: 6204767.; Panganiban AT, Temin HM. The terminal nucleotides of retrovirus DNA are required for integration but not virus production. Nature. 1983 Nov;306(5939):155–60. doi: 10.1038/306155a0. PMID: 6316141.; Hughes SH, Mutschler A, Bishop JM, Varmus HE. A Rous sarcoma virus provirus is flanked by short direct repeats of a cellular DNA sequence present in only one copy prior to integration. Proc. Natl. Acad. Sci. U.S.A. 1981 Jul;78(7):4299–303. doi: 10.1073/pnas.78.7.4299.; Dhar R, McClements WL, Enquist LW, Vande Woude GF. Nucleotide sequences of integrated Moloney sarcoma provirus long terminal repeats and their host and viral junctions. Proc. Natl. Acad. Sci. U.S.A. 1980 Jul;77(7):3937–41. doi: 10.1073/pnas.77.7.3937.; Hughes SH, Shank PR, Spector DH, Kung HJ, Bishop JM, Varmus HE, Vogt PK, Breitman ML. Proviruses of avian sarcoma virus are terminally redundant, co-extensive with unintegrated linear DNA and integrated at many sites. Cell. 1978 Dec;15(4):1397–410. doi: 10.1016/0092-8674(78)90064-8. PMID: 215325.

Metabolites



Enzyme

EC Number name full name note
2.7.7.-
2.7.7.49 RNA-directed DNA polymerase deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (RNA-directed)
2.7.7.7 DNA-directed DNA polymerase deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (DNA-directed)
3.1.13.2 exoribonuclease H
3.1.26.13 retroviral ribonuclease H
3.4.23.16 HIV-1 retropepsin
4.2.99.18 DNA-(apurinic or apyrimidinic site) lyase DNA-(apurinic or apyrimidinic site) 5'-phosphomonoester-lyase
5.2.1.8 peptidylprolyl isomerase Peptidylproline cis-trans-isomerase
5.6.2.4 DNA 3'-5' helicase DNA 3'-5' helicase (ATP-hydrolysing)
6.5.1.1 DNA ligase (ATP) poly(deoxyribonucleotide)-3'-hydroxyl:5'-phospho-poly(deoxyribonucleotide) ligase (ATP)


Proteins

Protein ID name full name