{PDOC50880}
{PS50880; TOPRIM}
{BEGIN}
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* Toprim domain profile *
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The Toprim  (topoisomerase-primase)  domain is a structurally conserved domain
of ~100  amino  acids  that  is  found  in bacterial DnaG-type primases, small
primase-like proteins   from  bacteria  and  archaea,  type  IA  and  type  II
topoisomerases, bacterial  and  archaeal  nucleases  of  the  OLD  family  and
bacterial DNA  repair  proteins of the RecR/M family. The Toprim domain can be
found alone  or  in  combination  with  several other domains, such as the ASM
domain, the  superfamily 2 helicase domain, the superfamily 3 helicase domain,
the DnaB  interaction  domain,  the  C4  'little finger' domain, the CHC2 zinc
finger, the  ATPase  domain  of the HSP90-gyrase-histidine kinase superfamily,
the S5  domain,  the  SET  domain,  the  helix-hairpin-helix (HhH) DNA-binding
domain, the  mobilization  (MOB)  domain  or  the  ATPase  domain  of  the ABC
transporter/SMC superfamily.  The Toprim domain is a catalytic domain involved
in DNA strand breakage and rejoining [1].

The Toprim  domain  has  two  conserved  motifs,  one  of  which  centers at a
conserved glutamate  and the other one at two conserved aspartates (DxD). Both
motifs are  preceded  by conserved hydrophobic regions predicted to form beta-
strands. The  glutamate residue is probably involved in catalysis, whereas the
DxD motif is involved in the co-ordination of Mg(2++) that is required for the
activity of  all  Toprim-containing  enzymes.  The Toprim domain has a compact
alpha/beta fold,   with   four   conserved  strands  and  three  helices  (see
<PDB:1CY7>); with  the  exception  of  the  second  helix  and  the C-terminal
strands, each  of these elements contains positions that are highly conserved.
The Toprim  domain  contains three regions that can accommodate variable sized
inserts, which are particularly prominent in the topoisomerases [1,2,3].

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: November 2012 / First entry.

[ 1] Aravind L., Leipe D.D., Koonin E.V.
     "Toprim--a conserved catalytic domain in type IA and II
     topoisomerases, DnaG-type  primases, OLD family nucleases and RecR
     proteins."
     Nucleic Acids Res. 26:4205-4213(1998).
     PubMed=9722641
[ 2] Allemand F., Mathy N., Brechemier-Baey D., Condon C.
     "The 5S rRNA maturase, ribonuclease M5, is a Toprim domain family
     member."
     Nucleic Acids Res. 33:4368-4376(2005).
     PubMed=16077031; DOI=10.1093/nar/gki752
[ 3] Fu G., Wu J., Liu W., Zhu D., Hu Y., Deng J., Zhang X.-E., Bi L.,
     Wang D.-C.
     "Crystal structure of DNA gyrase B' domain sheds lights on the
     mechanism for T-segment navigation."
     Nucleic Acids Res. 37:5908-5916(2009).
     PubMed=19596812; DOI=10.1093/nar/gkp586

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