PROSITE documentation PDOC51900
Core-binding (CB) domain profile


Tyrosine-type site-specific recombinases mediate a wide range of important genetic rearrangement reactions. They catalyze functionally diverse processes, including integration and excision of phages from their host chromosomes, conjugative transposition, partioning of phage, bacterial and plasmid genomes during cell division, antigenic phase variation, dissemination of antibiotic- and antiseptic-resistance gene cassettes, and relaxation of DNA supercoils. Tyrosine recombinases have two or three domains, depending upon whether the system includes regulated integration and excision reactions. The C-terminal catalytic domain contains six active site amino acids, RK(H/K)R(H/W)Y, required for catalysis (see <PDOC51898>). The core-binding (CB) domain, which interacts primarily with the major groove on the attachment site and facilitates binding to the core DNA sequence, is widely conserved among viral, eubacterial and archaeal recombinases. It is also involved in protein-protein interactions. Some recombinases, like lambda Int and IntDOT, have an additional amino-terminal domain that recognizes sites, called arm-type sites, that flank the crossover region and gives directionality to the recombination reaction [1,2,3].

The CB domain contains four major α-helices, arranged in an orthogonally crossed conformation (see <PDB:2A3V>) [1,2].

The profile we developed covers the entire CB domain.

Last update:

July 2019 / First entry.


Technical section

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

CB, PS51900; Core-binding (CB) domain profile  (MATRIX)


1AuthorsSwalla B.M. Gumport R.I. Gardner J.F.
TitleConservation of structure and function among tyrosine recombinases: homology-based modeling of the lambda integrase core-binding domain.
SourceNucleic. Acids. Res. 31:805-818(2003).
PubMed ID12560475

2AuthorsMalanowska K. Cioni J. Swalla B.M. Salyers A. Gardner J.F.
TitleMutational analysis and homology-based modeling of the IntDOT core-binding domain.
SourceJ. Bacteriol. 191:2330-2339(2009).
PubMed ID19168607

3AuthorsKim S. Swalla B.M. Gardner J.F.
TitleStructure-function analysis of IntDOT.
SourceJ. Bacteriol. 192:575-586(2010).
PubMed ID19915028

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