{PDOC51027}
{PS51027; INTEGRASE_DBD}
{BEGIN}
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* Integrase DNA binding domain profile *
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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 beta-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.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: October 2004 / First entry.

[ 1] Frankel A.D., Young J.A.
     HIV-1: fifteen proteins and an RNA."
     "Annu. Rev. Biochem. 67:1-25(1998).
     PubMed=9759480; DOI=10.1146/annurev.biochem.67.1.1
[ 2] Esposito D., Craigie R.
     "HIV integrase structure and function."
     Adv. Virus. Res. 52:319-333(1999).
     PubMed=10384240
[ 3] Van Gent D.C., Elgersma Y., Bolk M.W., Vink C., Plasterk R.H.
     Nucleic Acids Res. 19:3821-3827(1991).
[ 4] Chen J.C., Krucinski J., Miercke L.J., Finer-Moore J.S., Tang A.H.,
     Leavitt A.D., Stroud R.M.
     "Crystal structure of the HIV-1 integrase catalytic core and
     C-terminal domains: a model for viral DNA binding."
     Proc. Natl. Acad. Sci. U.S.A. 97:8233-8238(2000).
     PubMed=10890912; DOI=10.1073/pnas.150220297

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