InterPro : IPR006171

Name  Toprim domain Short Name  Toprim_domain
Type  Domain Description  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 mobilisation (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 [].The Toprim domain has two conserved motifs, one of which centres 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; 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 [, , ].

Sequence Features

GO Displayer


InterPro protein domain ID --> Contigs



0 Child Features

1 Contains

Id Name Short Name Type
IPR018522 DNA topoisomerase, type IIA, conserved site TopoIIA_CS Conserved_site

8 Found In

Id Name Short Name Type
IPR000380 DNA topoisomerase, type IA Topo_IA Family
IPR013760 DNA topoisomerase, type IIA-like domain Topo_IIA_like_dom Domain
IPR013759 DNA topoisomerase, type IIA, central domain Topo_IIA_cen_dom Domain
IPR000093 DNA recombination protein RecR DNA_Rcmb_RecR Family
IPR005740 DNA topoisomerase 4 subunit B, Gram-positive ParE Family
IPR011557 DNA gyrase, subunit B GyrB Family
IPR000565 DNA topoisomerase, type IIA, subunit B Topo_IIA_B Family
IPR020607 Uncharacterised protein family UPF0095 UPF0095 Family

0 Parent Features

3 Publications

First Author Title Year Journal Volume Pages
Aravind L Toprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins. 1998 Nucleic Acids Res 26 4205-13
Fu G Crystal structure of DNA gyrase B' domain sheds lights on the mechanism for T-segment navigation. 2009 Nucleic Acids Res 37 5908-16
Allemand F The 5S rRNA maturase, ribonuclease M5, is a Toprim domain family member. 2005 Nucleic Acids Res 33 4368-76

To cite PlanMine, please refer to the following publication:

Rozanski, A., Moon, H., Brandl, H., Martín-Durán, J. M., Grohme, M., Hüttner, K., Bartscherer, K., Henry, I., & Rink, J. C.
PlanMine 3.0—improvements to a mineable resource of flatworm biology and biodiversity
Nucleic Acids Research, gky1070. doi:10.1093/nar/gky1070 (2018)