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8  structures 3434  species 0  interactions 5120  sequences 20  architectures

Family: RadC (PF04002)

Summary: RadC-like JAB domain

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RadC-like JAB domain Provide feedback

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].

Literature references

  1. Saveson CJ, Lovett ST; , Genetics 1999;152:5-13.: Tandem repeat recombination induced by replication fork defects in Escherichia coli requires a novel factor, RadC. PUBMED:10224240 EPMC:10224240

  2. Lombardo MJ, Rosenberg SM; , J Bacteriol. 2000;182:6287-6291.: radC102 of Escherichia coli is an allele of recG. PUBMED:11053371 EPMC:11053371

  3. Iyer LM, Zhang D, Rogozin IB, Aravind L;, Nucleic Acids Res. 2011; [Epub ahead of print]: Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. PUBMED:21890906 EPMC:21890906


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR025657

This domain is found in a family of proteins present widely across bacteria. This family was named initially with reference to the Escherichia coli radC102 mutation which suggested that RadC was involved in repair of DNA lesions [PUBMED:10224240]. However, the relevant mutation has subsequently been shown to be in recG, where radC is in fact an allele of recG [PUBMED:11053371]. In addition, all attempts to characterise a radiation-related function for RadC in Streptococcus pneumoniae failed, suggesting that it is not involved in repair of DNA lesions, in recombination during transformation, in gene conversion, nor in mismatch repair [PUBMED:18556794].

The RadC-like domain belongs to the JAB superfamily of metalloproteins [PUBMED:21890906]. 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 [PUBMED:21890906].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan JAB (CL0366), which has the following description:

This superfamily includes a number of proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits, regulators of transcription factors and ubiquitination-assisting protein families. In eukaryotes and in prokaryotic cognates of the ubiquitin-based modification pathway, they function as ubiquitin isopeptidases/ deubiquitinases. JAB domains are also found in diverse metabolic pathways in prokaryotes such as siderophore and cysteine biosynthesis. Other distinct versions of the JAB domain, such as RadC are predicted to function as nucleases. Structurally, the JAB domain is related to the nucleotide deaminase and binds a Zinc ion in a similar structural location.

The clan contains the following 6 members:

JAB NPL4 Prok-JAB RadC Toxin-JAB1 UPF0172

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(107)
Full
(5120)
Representative proteomes NCBI
(3486)
Meta
(385)
RP15
(330)
RP35
(632)
RP55
(813)
RP75
(980)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(107)
Full
(5120)
Representative proteomes NCBI
(3486)
Meta
(385)
RP15
(330)
RP35
(632)
RP55
(813)
RP75
(980)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(107)
Full
(5120)
Representative proteomes NCBI
(3486)
Meta
(385)
RP15
(330)
RP35
(632)
RP55
(813)
RP75
(980)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: COG2003
Previous IDs: RadC; DUF2466;
Type: Family
Author: Kerrison ND, Finn RD, Iyer LM, Zhang D, Aravind L
Number in seed: 107
Number in full: 5120
Average length of the domain: 118.30 aa
Average identity of full alignment: 39 %
Average coverage of the sequence by the domain: 57.04 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.6 20.6
Trusted cut-off 20.6 20.6
Noise cut-off 20.5 20.3
Model length: 123
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the RadC domain has been found. There are 8 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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