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22  structures 1255  species 0  interactions 2296  sequences 13  architectures

Family: RelB (PF04221)

Summary: RelB antitoxin

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RelB antitoxin Provide feedback

RelE and RelB form a toxin-antitoxin system. RelE represses translation, probably through binding ribosomes ([1] [2]). RelB stably binds RelE, presumably deactivating it.

Literature references

  1. Galvani C, Terry J, Ishiguro EE; , J Bacteriol 2001;183:2700-2703.: Purification of the RelB and RelE proteins of Escherichia coli: RelE binds to RelB and to ribosomes. PUBMED:11274135 EPMC:11274135

  2. Pedersen K, Christensen SK, Gerdes K; , Mol Microbiol 2002;45:501-510.: Rapid induction and reversal of a bacteriostatic condition by controlled expression of toxins and antitoxins. PUBMED:12123459 EPMC:12123459

This tab holds annotation information from the InterPro database.

InterPro entry IPR007337

Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. Several toxin/antitoxin pairs may occur in a single species. RelE and RelB form a toxin-antitoxin system; RelE cleaves mRNA during translation on the ribosome [ PUBMED:11274135 , PUBMED:12123459 , PUBMED:22981948 ]. RelB binds and inhibits RelE and it regulates transcription by operator binding and conditional cooperativity controlled by RelE. RelE and RelB form a V-shaped heterotetrameric complex which has a ribbon-helix-helix (RHH) dimerization domain at the apex. [ PUBMED:22981948 ].

DinJ is an antitoxin component of a toxin-antitoxin (TA) module. It is a labile antitoxin that counteracts the effect of the YafQ toxin [ PUBMED:24923448 ]. It forms a heterotetrameric complex with YafQ and the structure of this complex revealed that the N-terminal region of DinJ folds into a ribbon-helix-helix motif that dimerises for DNA recognition, and the C-terminal portion of each DinJ wraps around a YafQ molecule [ PUBMED:24923448 ]. Together, they they bind their own promoter, and by analogy to other TA modules probably repress its expression. Cell death governed by the mazEF and dinJ-yafQ TA modules seems to play a role in biofilm formation [ PUBMED:17263853 , PUBMED:19210620 , PUBMED:19707553 ].

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 Met_repress (CL0057), which has the following description:

This superfamily contains many antitoxin families, all of which carry a ribbon-helix-helix DNA-binding motif with the beta-ribbon located in and recognising the major groove of operator DNA [1].

The clan contains the following 43 members:

Arc BrnA_antitoxin CcdA CopG_antitoxin DndE DUF1778 DUF1902 DUF2540 DUF2610 DUF6290 DUF6364 HicB HicB-like_2 HicB_lk_antitox MatP_C MetJ MobC MobC_2 Omega_Repress ParB_C ParD ParD_antitoxin ParD_like ParG Plasmid_stab_B PSK_trans_fac RelB RepB-RCR_reg Repressor_Mnt RHH_1 RHH_3 RHH_4 RHH_5 RHH_6 RHH_7 RHH_8 RHH_9 SeqA_N TraY VAPB_antitox VapB_antitoxin VirC2 VirD1


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

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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.

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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: COG3077
Previous IDs: DUF415;
Type: Domain
Sequence Ontology: SO:0000417
Author: Mifsud W
Number in seed: 5
Number in full: 2296
Average length of the domain: 79.70 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 85.16 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.4 22.4
Trusted cut-off 22.4 22.4
Noise cut-off 22.3 22.3
Model length: 83
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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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 RelB domain has been found. There are 22 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 sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
P0C079 View 3D Structure Click here
Q47150 View 3D Structure Click here