Protein Family Models

This is the ssDNA binding domain of anti-restriction factor ArdC deployed by plasmids and phages in polyvalent proteins related to the BHD domains of XPC/Rad4 and the Tc-38 domain found in kinetoplastid minicircle binding proteins [1,2,3]. The structure of this domain is composed of three alpha-helices and a three-stranded beta-sheet that supports a long and protuberant beta-hairpin [3]. This domain is also found in the N-terminal region of the RP4 TraC1 primase [4], together with the Toprim domain (pfam:PF01751, pfam:PF13362 and pfam:PF13662). [1]. 30396152. Unexpected Evolution of Lesion-Recognition Modules in Eukaryotic NER and Kinetoplast DNA Dynamics Proteins from Bacterial Mobile Elements. Krishnan A, Burroughs AM, Iyer LM, Aravind L;. iScience. 2018;9:192-208. [2]. 28559295. Polyvalent Proteins, a Pervasive Theme in the Intergenomic Biological Conflicts of Bacteriophages and Conjugative Elements. Iyer LM, Burroughs AM, Anand S, de Souza RF, Aravind L;. J Bacteriol. 2017; [Epub ahead of print]. [3]. 32348296. ArdC, a ssDNA-binding protein with a metalloprotease domain, overpasses the recipient hsdRMS restriction system broadening conjugation host range. Gonzalez-Montes L, Del Campo I, Garcillan-Barcia MP, de la Cruz F, Moncalian G;. PLoS Genet. 2020;16:e1008750. [4]. 10686096. Antirestriction protein Ard (Type C) encoded by IncW plasmid pSa has a high similarity to the "protein transport" domain of TraC1 primase of promiscuous plasmid RP4. Belogurov AA, Delver EP, Agafonova OV, Belogurova NG, Lee LY, Kado CI;. J Mol Biol. 2000;296:969-977. (from Pfam)

Date:

2024-10-16

This entry includes the catalytic domain of the protein ImmA, which is a metallopeptidase containing an HEXXH zinc-binding motif from peptidase family M78. ImmA is encoded on a conjugative transposon. Conjugating bacteria are able to transfer conjugative transposons that can, for example, confer resistance to antibiotics. The transposon is integrated into the chromosome, but during conjugation excises itself and then moves to the recipient bacterium and re-integrate into its chromosome. Typically a conjugative tranposon encodes only the proteins required for this activity and the proteins that regulate it. During exponential growth, the ICEBs1 transposon of Bacillus subtilis is inactivated by the immunity repressor protein ImmR, which is encoded by the transposon and represses the genes for excision and transfer. Cleavage of ImmR relaxes repression and allows transfer of the transposon. ImmA has been shown to be essential for the cleavage of ImmR [2]. This domain is also found in in metalloprotease IrrE, a central regulator of DNA damage repair in Deinococcaceae [1], HTH-type transcriptional regulators RamB [3] and PrpC [4]. [1]. 19150362. Crystal structure of the IrrE protein, a central regulator of DNA damage repair in deinococcaceae. Vujicic-Zagar A, Dulermo R, Le Gorrec M, Vannier F, Servant P, Sommer S, de Groot A, Serre L;. J Mol Biol. 2009;386:704-716. [2]. 18761623. A conserved anti-repressor controls horizontal gene transfer by proteolysis. Bose B, Auchtung JM, Lee CA, Grossman AD;. Mol Microbiol. 2008;70:570-582. [3]. 15090522. RamB, a novel transcriptional regulator of genes involved in acetate me. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-10-16

These repeats are found in many cyanobacterial proteins. The repeats were first identified in hglK [1]. The function of these repeats is unknown. The structure of this repeat has been predicted to be a beta-helix [2]. The repeat can be approximately described as A(D/N)LXX, where X can be any amino acid. [1]. 7592418. The hglK gene is required for localization of heterocyst-specific glycolipids in the cyanobacterium Anabaena sp. strain PCC 7120. Black K, Buikema WJ, Haselkorn R;. J Bacteriol 1995;177:6440-6448. [2]. 9655353. Structure and distribution of pentapeptide repeats in bacteria. Bateman A, Murzin A, Teichmann SA;. Protein Sci 1998;7:1477-1480. [3]. 9654141. Characterisation of an Arabidopsis cDNA encoding a thylakoid lumen protein related to a novel 'pentapeptide repeat' family of proteins. Kieselbach T, Mant A, Robinson C, Schroder WP;. FEBS Lett 1998;428:241-244. (from Pfam)

Date:

2024-10-16