Protein Family Models

This is a family or Toprim-like proteins. (from Pfam)

Date:

2024-08-14

The toprim domain is found in a wide variety of enzymes involved in nucleic acid manipulation [1]. [1]. 9722641. Toprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins. Aravind L, Leipe DD, Koonin EV;. Nucleic Acids Res 1998;26:4205-4213. (from Pfam)

Date:

2024-10-16

This domain is the C-terminal region three-helical domain of primase [1]. Primases synthesise short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. Primases are recruited to single-stranded DNA by helicases, and this domain is the region of the primase which binds DnaB-helicase [2]. It is associated with the Toprim domain (Pfam:PF01751) which is the central catalytic core. [1]. 10741967. Structure of the RNA polymerase domain of E. coli primase. Keck JL, Roche DD, Lynch AS, Berger JM;. Science. 2000;287:2482-2486. [2]. 10873470. A TOPRIM domain in the crystal structure of the catalytic core of Escherichia coli primase confirms a structural link to DNA topoisomerases. Podobnik M, McInerney P, O'Donnell M, Kuriyan J;. J Mol Biol. 2000;300:353-362. (from Pfam)

Date:

2024-10-16

DNA primase (DNAG) is a a nucleotidyltransferase which synthesises the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork. It can also prime the leading strand and has been implicated in cell division [1]. Primases comprise three domains: a zinc-binding domain at the N-terminal (Pfam:PF01807), a polymerase domain (catalytic core), and a domain that interacts with the replicative helicase (Pfam:PF01807). The catalytic core consists of an alpha+beta domain at the N-terminal (this entry) and a TOPRIM domain at the C-terminal (Pfam:PF13155) [1,2]. [1]. 8294018. The Haemophilus influenzae dnaG sequence and conserved bacterial primase motifs. Versalovic J, Lupski JR;. Gene 1993;136:281-286. [2]. 12769857. Modular architecture of the bacteriophage T7 primase couples RNA primer synthesis to DNA synthesis. Kato M, Ito T, Wagner G, Richardson CC, Ellenberger T;. Mol Cell 2003;11:1349-1360. (from Pfam)

Date:

2024-10-16

This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR 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 [1]. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesises 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 [4]. Type II DNA topoisomerases catalyse the relaxation of DNA supercoiling by causing transient double strand breaks. [1]. 9722641. Toprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins. Aravind L, Leipe DD, Koonin EV;. Nucleic Acids Res 1998;26:4205-4213. [2]. 9224947. Cloning and analysis of the dnaG gene encoding Pseudomonas putida DNA primase. Szafranski P, Smith CL, Cantor CR;. Biochim Biophys Acta 1997;1352:243-248. [3]. 8294018. The Haemophilus influenzae dnaG sequence and conserved bacterial primase motifs. Versalovic J, Lupski JR;. Gene 1993;136:281-286. [4]. 9121560. An atypical topoisomerase II from Archaea with implications for meiotic recombination. Bergerat A, de Massy B, Gadelle D, Varoutas PC, Nicolas A, Forterre P;. Nature 1997;386:414-417. (from Pfam)

Date:

2024-10-16

This domain is principally involved in DNA binding in DNA primases. [1]. 10745010. Structure of the zinc-binding domain of Bacillus stearothermophilus DNA primase. Pan H, Wigley DB;. Structure Fold Des 2000;8:231-239. (from Pfam)

Date:

2024-10-16

DNA primase is a DNA-dependent RNA polymerase that synthesizes short RNA primers for DNA polymerase during DNA replication

Date:

2022-09-27

Members of this family are DNA primase, a ubiquitous bacteria protein. Most members of this family contain nearly two hundred additional residues C-terminal to the region represented here, but conservation between species is poor and the C-terminal region was not included in the seed alignment. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).

Gene:

dnaG

Date:

2021-04-27