PROSITE documentation PDOC51027Integrase 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.
-------------------------------------------------------------------------------
PROSITE method (with tools and information) covered by this documentation:
| 1 | Authors | Frankel A.D. Young J.A. |
| Title | HIV-1: fifteen proteins and an RNA. | |
| Source | Annu. Rev. Biochem. 67:1-25(1998). | |
| PubMed ID | 9759480 | |
| DOI | 10.1146/annurev.biochem.67.1.1 |
| 2 | Authors | Esposito D. Craigie R. |
| Title | HIV integrase structure and function. | |
| Source | Adv. Virus. Res. 52:319-333(1999). | |
| PubMed ID | 10384240 |
| 3 | Authors | Van Gent D.C. Elgersma Y. Bolk M.W. Vink C. Plasterk R.H. |
| Source | Nucleic Acids Res. 19:3821-3827(1991). |
| 4 | Authors | Chen J.C. Krucinski J. Miercke L.J. Finer-Moore J.S. Tang A.H. Leavitt A.D. Stroud R.M. |
| Title | Crystal structure of the HIV-1 integrase catalytic core and C-terminal domains: a model for viral DNA binding. | |
| Source | Proc. Natl. Acad. Sci. U.S.A. 97:8233-8238(2000). | |
| PubMed ID | 10890912 | |
| DOI | 10.1073/pnas.150220297 |
PROSITE is copyrighted by the SIB Swiss Institute of Bioinformatics and distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives (CC BY-NC-ND 4.0) License, see prosite_license.html.
View entry in original PROSITE document format
View entry in raw text format (no links)