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InterPro: IPR006171 Toprim domain

Protein matches Help

UniProtKB

Matches:

11403 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

IPR006171 Toprim_domain

Secondary

IPR002936

Type

Domain

Signatures Help

Database	ID	Name	Proteins
Pfam	PF01751	Toprim	11403
Signatures in BioMart

InterPro Relationships Help

Children

IPR006154 Toprim domain, subgroup

Found in

IPR000093 RecR protein
IPR000565 DNA topoisomerase, type IIA, subunit B
IPR005740 DNA topoisomerase IV, subunit B, Gram-positive
IPR011557 DNA gyrase, subunit B
IPR013759 DNA topoisomerase, type IIA, subunit B or N-terminal, alpha-beta
IPR013760 DNA topoisomerase, type IIA, central
IPR020607 Uncharacterised protein family UPF0095

Contains

IPR018522 DNA topoisomerase, type IIA, conserved site

InterPro annotation

Entry Details in BioMart

Abstract

This is a conserved region from DNA primase. This corresponds to the Toprim (topoisomerase-primase) domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR/M DNA repair proteins [1]. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division [2]. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases [3]. Type II DNA topoisomerases catalyse the relaxation of DNA supercoiling by causing transient double strand breaks.

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

PANDIT: PF01751

Taxonomic coverage Help

Overlapping InterPro entries Help

IPR006171

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
IPR000380	DNA topoisomerase, type IA, core
IPR013826	DNA topoisomerase, type IA, central region, subdomain 3
IPR013824	DNA topoisomerase, type IA, central region, subdomain 1
IPR003602	DNA topoisomerase, type IA, DNA-binding
IPR006154	Toprim domain, subgroup
IPR003601	DNA topoisomerase, type IA, domain 2
IPR010666	Zinc finger, GRF-type
IPR001878	Zinc finger, CCHC-type
IPR006171	Toprim domain
IPR013498	DNA topoisomerase, type IA, zn finger
IPR013497	DNA topoisomerase, type IA, central
	ModBase
	SWISS-MODEL

Publications Open in usermanual
1.	Bergerat A, de Massy B, Gadelle D, Varoutas PC, Nicolas A, Forterre P. An atypical topoisomerase II from Archaea with implications for meiotic recombination. Nature 386 414-7 1997 [PubMed: 9121560] http://dx.doi.org/10.1038/386414a0
2.	Versalovic J, Lupski JR. The Haemophilus influenzae dnaG sequence and conserved bacterial primase motifs. Gene 136 281-6 1993 [PubMed: 8294018] http://dx.doi.org/10.1016/0378-1119(93)90480-Q
3.	Aravind L, Leipe DD, Koonin EV. Toprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins. Nucleic Acids Res. 26 4205-13 1998 [PubMed: 9722641] http://dx.doi.org/10.1093/nar/26.18.4205

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
	Szafranski P, Smith CL, Cantor CR. Cloning and analysis of the dnaG gene encoding Pseudomonas putida DNA primase. Biochim. Biophys. Acta 1352 1997 243-8 [PubMed: 9224947] http://dx.doi.org/10.1016/S0167-4781(97)00059-6

InterPro 23.1