Protein Family Models

This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins, including VirB4 components of the Type IV secretory pathway and conjugal transfer protein TrbE. This entry includes the arcaheal Vir4/HerA homologue CedB [2], a membrane-bound protein that is highly induced upon UV treatment and essential for DNA transfer between Sulfolobus cells [2]. [1]. 12533481. The VirB4 family of proposed traffic nucleoside triphosphatases: common motifs in plasmid RP4 TrbE are essential for conjugation and phage adsorption. Rabel C, Grahn AM, Lurz R, Lanka E;. J Bacteriol. 2003;185:1045-1058. [2]. 26884154. The archaeal Ced system imports DNA. van Wolferen M, Wagner A, van der Does C, Albers SV;. Proc Natl Acad Sci U S A. 2016;113:2496-2501. (from Pfam)

Date:

2024-10-16

This family includes both TraG and TraD as well as VirD4 proteins. TraG is essential for DNA transfer in bacterial conjugation. These proteins are thought to mediate interactions between the DNA-processing (Dtr) and the mating pair formation (Mpf) systems [1]. This domain interacts with the relaxosome component TraM via the latter's tetramerisation domain. TraD is a hexameric ring ATPase that forms the cytoplasmic face of the conjugative pore [2]. [1]. 11976307. TraG-like proteins of DNA transfer systems and of the Helicobacter pylori type IV secretion system: inner membrane gate for exported substrates?. Schroder G, Krause S, Zechner EL, Traxler B, Yeo HJ, Lurz R, Waksman G, Lanka E;. J Bacteriol 2002;184:2767-2779. [2]. 18717787. Structural basis of specific TraD-TraM recognition during F plasmid-mediated bacterial conjugation. Lu J, Wong JJ, Edwards RA, Manchak J, Frost LS, Glover JN;. Mol Microbiol. 2008;70:89-99. (from Pfam)

Date:

2024-10-16

The plasmid conjugative coupling protein TrwB forms hexamers from six structurally very similar protomers [1]. This hexamer contains a central channel running from the cytosolic pole (made up by the AADs) to the membrane pole ending at the transmembrane pore shaped by 12 transmembrane helices, rendering an overall mushroom-like structure. The TrwB_AAD (all-alpha domain) domain appears to be the DNA-binding domain of the structure. TrwB, a basic integral inner-membrane nucleoside-triphosphate-binding protein, is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells and export [2]. [1]. 11214325. The bacterial conjugation protein TrwB resembles ring helicases and F1-ATPase. Gomis-Ruth FX, Moncalian G, Perez-Luque R, Gonzalez A, Cabezon E, de la Cruz F, Coll M;. Nature. 2001;409:637-641. [2]. 11748238. Conjugative plasmid protein TrwB, an integral membrane type IV secretion system coupling protein. Detailed structural features and mapping of the active site cleft. Gomis-Ruth FX, Moncalian G, de la Cruz F, Coll M;. J Biol Chem. 2002;277:7556-7566. (from Pfam)

Date:

2024-10-16

These proteins contain a P-loop and walker-B site for nucleotide binding. TraG is essential for DNA transfer in bacterial conjugation. These proteins are thought to mediate interactions between the DNA-processing (Dtr) and the mating pair formation (Mpf) systems [2]. The C-terminus of this domain interacts with the relaxosome component TraM via the latter's tetramerisation domain. TraD is a hexameric ring ATPase that forms the cytoplasmic face of the conjugative pore [3]. The family contains a number of different DNA transfer proteins [4]. [1]. 9767571. Sequence and analysis of the 60 kb conjugative, bacteriocin-producing plasmid pMRC01 from Lactococcus lactis DPC3147. Dougherty BA, Hill C, Weidman JF, Richardson DR, Venter JC, Ross RP;. Mol Microbiol 1998;29:1029-1038. [2]. 11976307. TraG-like proteins of DNA transfer systems and of the Helicobacter pylori type IV secretion system: inner membrane gate for exported substrates?. Schroder G, Krause S, Zechner EL, Traxler B, Yeo HJ, Lurz R, Waksman G, Lanka E;. J Bacteriol 2002;184:2767-2779. [3]. 18717787. Structural basis of specific TraD-TraM recognition during F plasmid-mediated bacterial conjugation. Lu J, Wong JJ, Edwards RA, Manchak J, Frost LS, Glover JN;. Mol Microbiol. 2008;70:89-99. [4]. 17259614. Interaction between the co-inherited TraG coupling protein and the TraJ membrane-associated protein of the H-plasmid conjugative DNA transfer system resembles chromosomal DNA translocases. Gunton JE, Gilmour MW, Baptista KP, Lawley TD, Taylor DE;. Microbiology. 2007;153:428-441. (from Pfam)

Date:

2024-10-16

This entry represents the central domain found in archaeal proteins such as DNA double-strand break repair helicase HerA (EC:3.6.4.12). HerA is a helicase which is able to utilise either 3' or 5' single-stranded DNA extensions for loading and subsequent DNA duplex unwinding [1]. It forms a complex with NurA nuclease, this complex has the 5'-3' DNA end resection activity and is essential for cell viability in the crenarchaeon Sulfolobus islandicus [2]. This domain includes the the central RecA-like catalytic core and a flanking four-helix bundle [3]. The function of this prokaryotic domain is unknown. It contains several conserved aspartates and histidines that could be metal ligands. [1]. 14990749. A bipolar DNA helicase gene, herA, clusters with rad50, mre11 and nurA genes in thermophilic archaea. Constantinesco F, Forterre P, Koonin EV, Aravind L, Elie C;. Nucleic Acids Res. 2004;32:1439-1447. [2]. 25880130. Efficient 5'-3' DNA end resection by HerA and NurA is essential for cell viability in the crenarchaeon Sulfolobus islandicus. Huang Q, Liu L, Liu J, Ni J, She Q, Shen Y;. BMC Mol Biol. 2015;16:2. [3]. 25420454. Structure of the hexameric HerA ATPase reveals a mechanism of translocation-coupled DNA-end processing in archaea. Rzechorzek NJ, Blackwood JK, Bray SM, Maman JD, Pellegrini L, Robinson NP;. Nat Commun. 2014;5:5506. (from Pfam)

Date:

2024-10-16

type IV secretory system conjugative DNA transfer family protein similar to Agrobacterium tumefaciens VirD4

Date:

2024-08-07