Protein Family Models

This domain is functionally uncharacterised, found at the N-terminal of the uncharacterised UPF0758 proteins from bacteria and archaea, and is approximately 90 amino acids in length. UPF0758 was previously known as the radC family, a name that was assigned according to the radC102 mutant of E. coli which was later demonstrated to be an allele of the transcription-repair-coupling factor recG [1, 2]. UPF0758 has been described as a putative JAMM-family deubiquitinating enzyme, but its function remains to be determined [3]. Structure prediction using Colab notebook from AlphaFold DB suggests that it has an alpha bundle fold. It may contain two helix-hairpin-helix (HhH) motifs. This domain is found in association with Pfam:PF04002 [4]. [1]. 11053371. radC102 of Escherichia coli is an allele of recG. Lombardo MJ, Rosenberg SM;. J Bacteriol. 2000;182:6287-6291. [2]. 18556794. RadC, a misleading name?. Attaiech L, Granadel C, Claverys JP, Martin B;. J Bacteriol. 2008;190:5729-5732. [3]. 14737182. JAMM: a metalloprotease-like zinc site in the proteasome and signalosome. Ambroggio XI, Rees DC, Deshaies RJ;. PLoS Biol. 2004;2:E2. [4]. 21890906. Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. Iyer LM, Zhang D, Rogozin IB, Aravind L;. Nucleic Acids Res. 2011; [Epub ahead of print] (from Pfam)

Date:

2024-10-16

These are metalloenzymes that function as the ubiquitin isopeptidase/ deubiquitinase in the ubiquitin-based signaling and protein turnover pathways in eukaryotes [1]. Prokaryotic JAB domains are predicted to have a similar role in their cognates of the ubiquitin modification pathway [2]. The domain is widely found in bacteria, archaea and phages where they are present in several gene contexts in addition to those that correspond to the prokaryotic cognates of the eukaryotic Ub pathway. Other contexts in which JAB domains are present include gene neighbor associations with ubiquitin fold domains in cysteine and siderophore biosynthesis, and phage tail morphogenesis, where they are shown or predicted to process the associated ubiquitin [2,3]. A distinct family, the RadC-like JAB domains are widespread in bacteria and are predicted to function as nucleases [4]. In halophilic archaea the JAB domain shows strong gene-neighborhood associations with a nucleotidyltransferase suggesting a role in nucleotide metabolism [4]. [1]. 12183636. Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome. Verma R, Aravind L, Oania R, McDonald WH, Yates JR 3rd, Koonin EV, Deshaies RJ;. Science. 2002;298:611-615. [2]. 16859499. The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains. Iyer LM, Burroughs AM, Aravind L;. Genome Biol. 2006;7:R60. [3]. 16104727. Reconstitution of a new cysteine biosynthetic pathway in Mycobacterium tuberculosis. Burns KE, Baumgart S, Dorrestein PC, Zhai H, McLafferty FW, Begley TP;. J Am Chem Soc. 2005;127:11602. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-10-16

A family of proteins present widely across the bacteria. This family was named initially with reference to the E. coli radC102 mutation which suggested that RadC was involved in repair of DNA lesions [1]. However the relevant mutation has subsequently been shown to be in recG, where radC is in fact an allele of recG [2]. In addition, a personal communication from Claverys, J-P, et al, indicates a total failure of all attempts to characterise a radiation-related function for RadC in Streptococcus pneumoniae, suggesting that it is not involved in repair of DNA lesions, in recombination during transformation, in gene conversion, nor in mismatch repair. Computational analysis, however, provides a possible function. The RadC-like family belong to the JAB superfamily of metalloproteins [3]. The domain shows fusions to an N-terminal Helix-hairpin-Helix (HhH) domain in most instances. Other domain combinations include fusions to the anti-restriction module ArdC, the DinG/RAD3-like superfamily II helicases and the DNAG-like primase. In some bacteria, closely related DinG/Rad3- like superfamily II helicases are fused to a 3'-5' exonuclease in the same position as the RadC-like JAB domain. These conserved domain associations lead to the hypothesis that the RadC-like JAB domains might function as a nuclease [3]. [1]. 10224240. Tandem repeat recombination induced by replication fork defects in Escherichia coli requires a novel factor, RadC. Saveson CJ, Lovett ST;. Genetics 1999;152:5-13. [2]. 11053371. radC102 of Escherichia coli is an allele of recG. Lombardo MJ, Rosenberg SM;. J Bacteriol. 2000;182:6287-6291. [3]. 21890906. Evolu. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-10-16

JAB or Mpr1p, Pad1p N-terminal (MPN) domain-containing protein contains the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, which is involved in zinc ion coordination; a function as a nuclease has been suggested

Date:

2023-03-08

RadC was at one time ascribed a role in determining sensitivity to DNA damaging agents such as UV irradiation. Subsequent work casts doubt on that assertion. Three of four members of this family in Escherichia coli K-12, namely YfjY, YkfG, and YeeS, are found in prophage regions.

Gene:

radC

Date:

2024-12-11

Gene:

radC

Date:

2024-12-11