PROSITE documentation PDOC50880
Toprim domain profile


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 β-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 α/β 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].

Last update:

November 2012 / First entry.


Technical section

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

TOPRIM, PS50880; Toprim domain profile  (MATRIX)


1AuthorsAravind L. Leipe D.D. Koonin E.V.
TitleToprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins.
SourceNucleic Acids Res. 26:4205-4213(1998).
PubMed ID9722641

2AuthorsAllemand F. Mathy N. Brechemier-Baey D. Condon C.
TitleThe 5S rRNA maturase, ribonuclease M5, is a Toprim domain family member.
SourceNucleic Acids Res. 33:4368-4376(2005).
PubMed ID16077031

3AuthorsFu G. Wu J. Liu W. Zhu D. Hu Y. Deng J. Zhang X.-E. Bi L.
TitleWang D.-C. Crystal structure of DNA gyrase B' domain sheds lights on the mechanism for T-segment navigation.
SourceNucleic Acids Res. 37:5908-5916(2009).
PubMed ID19596812

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