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InterPro: IPR006154 Toprim domain, subgroup

Protein matches Help

UniProtKB

Matches:

8675 proteins

Overview:	sorted by AC,	sorted by name,	of known structure,	proteins with splice variants
Detailed:	sorted by AC,	sorted by name,	of known structure	proteins with splice variants
Table:	For all matching proteins,	of known structure
Architectures
Accession List
Matches in BioMart

Accession

IPR006154 Toprim_dom_subgr

Secondary

IPR002936

Type

Domain

Signatures Help

Database	ID	Name	Proteins
SMART	SM00493	TOPRIM	8675
Signatures in BioMart

InterPro Relationships Help

Parent

IPR006171 Toprim domain

Found in

IPR000093 RecR protein
IPR000380 DNA topoisomerase, type IA, core
IPR004466 Primase-related protein
IPR004611 DNA primase-related protein
IPR005733 DNA topoisomerase I, bacterial-type
IPR005736 Reverse gyrase
IPR005738 DNA topoisomerase III, bacterial-type
IPR005739 DNA topoisomerase I, archeal-type
IPR006295 DNA primase, DnaG
IPR014481 Uncharacterised conserved protein, Toprim domain-containing
IPR020607 Uncharacterised protein family UPF0095

GO Term annotation Help

Process

GO:0006259 DNA metabolic process

Function

GO:0003676 nucleic acid binding

InterPro annotation

Entry Details in BioMart

Abstract

The toprim (topoisomerase-primase) domain is a conserved region from DnaG primases, topoisomerases, OLD family nucleases and RecR/M DNA repair proteins. The fold of the TOPRIM domain resembles a Rossman-like nucleotide binding fold, with a central beta-sheet formed by 4 parallel beta-strands flanked by 3 alpha-helices. Only 5 residues are conserved across all TOPRIM domain, 2 of these are glycines which may play a structural role, the other 3 are acidic residues that are present in 2 conserved sequence motifs. These may have a metal binding function [1]

The TOPRIM domain may form a shallow groove on these molecules and play a role in the binding of double-helical DNA/RNA hybrids.

Structural links Help

PDB - click here

SCOP: c.136.1.1 , e.10.1.1 , e.13.1.1 , e.13.1.2 , e.49.1.1

CATH: 3.40.1360.10 , 3.40.50.140

Database links Help

Blocks: IPB006154

Taxonomic coverage Help

Overlapping InterPro entries Help

IPR006154

Numbers of overlapping proteins

Average numbers of overlapping amino acids

Example proteins Help

O61660 DNA topoisomerase 3

O70157 DNA topoisomerase 3-alpha

O95985 DNA topoisomerase 3-beta-1

O96651 DNA topoisomerase 3-beta

P13099 DNA topoisomerase 3

More proteins

Example Proteins Key

InterPro entry accession number/name and structure databases		Colour code
IPR006154	Toprim domain, subgroup
IPR000380	DNA topoisomerase, type IA, core
IPR013826	DNA topoisomerase, type IA, central region, subdomain 3
IPR003601	DNA topoisomerase, type IA, domain 2
IPR013824	DNA topoisomerase, type IA, central region, subdomain 1
IPR001878	Zinc finger, CCHC-type
IPR013498	DNA topoisomerase, type IA, zn finger
IPR003602	DNA topoisomerase, type IA, DNA-binding
IPR006171	Toprim domain
IPR013497	DNA topoisomerase, type IA, central
	SWISS-MODEL
	ModBase

Publications Open in usermanual
1.	Podobnik M, McInerney P, O'Donnell M, Kuriyan J. A TOPRIM domain in the crystal structure of the catalytic core of Escherichia coli primase confirms a structural link to DNA topoisomerases. J. Mol. Biol. 300 353-62 2000 [PubMed: 10873470] http://dx.doi.org/10.1006/jmbi.2000.3844

Additional Reading Open in usermanual
	Corn JE, Pelton JG, Berger JM. Identification of a DNA primase template tracking site redefines the geometry of primer synthesis. Nat. Struct. Mol. Biol. 15 2008 163-9 [PubMed: 18193061] http://dx.doi.org/10.1038/nsmb.1373
	Rezacova P, Borek D, Moy SF, Joachimiak A, Otwinowski Z. Crystal structure and putative function of small Toprim domain-containing protein from Bacillus stearothermophilus. Proteins 70 2008 311-9 [PubMed: 17705269] http://dx.doi.org/10.1002/prot.21511
	Timmins J, Leiros I, McSweeney S. Crystal structure and mutational study of RecOR provide insight into its mode of DNA binding. EMBO J. 26 2007 3260-71 [PubMed: 17581636] http://dx.doi.org/10.1038/sj.emboj.7601760
	Lee BI, Kim KH, Park SJ, Eom SH, Song HK, Suh SW. Ring-shaped architecture of RecR: implications for its role in homologous recombinational DNA repair. EMBO J. 23 2004 2029-38 [PubMed: 15116069] http://dx.doi.org/10.1038/sj.emboj.7600222
	Kato M, Ito T, Wagner G, Richardson CC, Ellenberger T. Modular architecture of the bacteriophage T7 primase couples RNA primer synthesis to DNA synthesis. Mol. Cell 11 2003 1349-60 [PubMed: 12769857] http://dx.doi.org/10.1016/S1097-2765(03)00195-3

InterPro 24.0