{PDOC51900}
{PS51900; CB}
{BEGIN}
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* Core-binding (CB) domain profile *
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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 alpha-helices, arranged in an orthogonally
crossed conformation (see <PDB:2A3V>) [1,2].

The profile we developed covers the entire CB domain.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: July 2019 / First entry.

[ 1] Swalla B.M., Gumport R.I., Gardner J.F.
     "Conservation of structure and function among tyrosine recombinases:
     homology-based modeling of the lambda integrase core-binding domain."
     Nucleic. Acids. Res. 31:805-818(2003).
     PubMed=12560475; DOI=10.1093/nar/gkg142
[ 2] Malanowska K., Cioni J., Swalla B.M., Salyers A., Gardner J.F.
     "Mutational analysis and homology-based modeling of the IntDOT
     core-binding domain."
     J. Bacteriol. 191:2330-2339(2009).
     PubMed=19168607; DOI=10.1128/JB.01280-08
[ 3] Kim S., Swalla B.M., Gardner J.F.
     "Structure-function analysis of IntDOT."
     J. Bacteriol. 192:575-586(2010).
     PubMed=19915028; DOI=10.1128/JB.01052-09

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