PROSITE documentation PDOC51027
Integrase DNA binding domain profile


The retroviral integrase is the enzyme responsible for the insertion of a DNA copy of the viral genome into host DNA, an essential step in the replication cycle of viruses [1]. Integrases comprise three functional and structural domains: the central core domain, which contains the catalytic residues (see <PDOC50994>), an N-terminal zinc finger (see <PDOC50876>) and a C-terminal DNA binding domain [2]. The DNA binding domain displays the same DNA binding characteristic and affinity for viral and nonspecific double-stranded DNA as the intact integrase protein [3].

The structure of the DNA binding domain of HIV-1 integrase has been determined (see <PDB:1IHV>). The domain dimerizes in solution, and each subunit is composed of a five-stranded β-barrel with a topology very similar to that of the SH3 domain. Dimerization form a large central saddle-shaped groove. This cleft contains a number of positively charged residues, and its dimensions are appropriate for accommodating a double-stranded DNA helix [4].

The profile we developed covers the whole integrase DNA binding domain.

Last update:

October 2004 / First entry.


Technical section

PROSITE method (with tools and information) covered by this documentation:

INTEGRASE_DBD, PS51027; Integrase DNA binding domain profile  (MATRIX)


1AuthorsFrankel A.D. Young J.A.
TitleHIV-1: fifteen proteins and an RNA.
SourceAnnu. Rev. Biochem. 67:1-25(1998).
PubMed ID9759480

2AuthorsEsposito D. Craigie R.
TitleHIV integrase structure and function.
SourceAdv. Virus. Res. 52:319-333(1999).
PubMed ID10384240

3AuthorsVan Gent D.C. Elgersma Y. Bolk M.W. Vink C. Plasterk R.H.
SourceNucleic Acids Res. 19:3821-3827(1991).

4AuthorsChen J.C. Krucinski J. Miercke L.J. Finer-Moore J.S. Tang A.H. Leavitt A.D. Stroud R.M.
TitleCrystal structure of the HIV-1 integrase catalytic core and C-terminal domains: a model for viral DNA binding.
SourceProc. Natl. Acad. Sci. U.S.A. 97:8233-8238(2000).
PubMed ID10890912

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