Protein Family Models

Bacteriophage T7 DNA helicase/primase (also known as Gp4) is an ATP-dependent DNA helicase and primase that is essential for viral DNA replication and recombination [1-4]. Primase activity synthesises short RNA primers at the sequence 5'-GTC-3' on the lagging strand that the polymerase elongates using dNTPs and providing the primase is still present. It consists of an N-terminal zinc ribbon (Pfam:PF08273) followed by a RNA Polymerase Domain that can be subdivided in an N-terminal alpha+beta structure, represented in this entry and a C-terminal TOPRIM fold (Pfam:PF13155) [1]. At the C-terminal end of the protein there is a DNA helicase domain (Pfam:PF03796). Paper describing PDB structure 1nui. [1]. 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. Paper describing PDB structure 1q57. [2]. 14636571. The crystal structure of the bifunctional primase-helicase of bacteriophage T7. Toth EA, Li Y, Sawaya MR, Cheng Y, Ellenberger T;. Mol Cell. 2003;12:1113-1123. Paper describing PDB structure 5ikn. [3]. 28052235. Hybrid Methods Reveal Multiple Flexibly Linked DNA Polymerases within the Bacteriophage T7 Replisome. Wallen JR, Zhang H, Weis C, Cui W, Foster BM, Ho CMW, Hammel M, Tainer JA, Gross ML, Ellenberger T;. Structure. 2017;25:157-166. Paper describing PDB structure 6n7i. [4]. 30679383. Structures and operating principles of the replisome. Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou ZH, Yang W;. Science. 2019; [Epub ahead of print] (from Pfam)

Date:

2024-10-16

This AAA domain is found in a wide variety of presumed DNA repair proteins. (from Pfam)

Date:

2024-08-14

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

The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerisation of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. (from Pfam)

Date:

2024-08-14

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