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1  structure 66  species 0  interactions 68  sequences 1  architecture

Family: REGB_T4 (PF10715)

Summary: Endoribonuclease RegB T4-bacteriophage encoded

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Endoribonuclease RegB T4-bacteriophage encoded Provide feedback

The RegB endoribonuclease encoded by bacteriophage T4 is a unique sequence-specific nuclease that cleaves in the middle of GGAG or, in a few cases, GGAU tetranucleotides, preferentially those found in the Shine-Dalgarno regions of early phage mRNAs. Phage RB49 in addition to RegB utilises Escherichia coli endoribonuclease E for the degradation of its transcripts for gene regB. The deduced primary structure of RegB proteins of 32 phages studied is almost identical to that of T4, while the sequences of RegB encoded by phages RB69, TuIa and RB49 show substantial divergence from their T4 counterpart. Rebuilding from the PDB:2hx6 structure, this family does not fall into the Lysozyme-like family, but rather is a new member of the RelE/YoeB structural and functional family of ribonucleases specialising in mRNA inactivation within the ribosome [2].

Literature references

  1. Piesiniene L, Truncaite L, Zajanckauskaite A, Nivinskas R; , Nucleic Acids Res. 2004;32:5582-5595.: The sequences and activities of RegB endoribonucleases of T4-related bacteriophages. PUBMED:15486207 EPMC:15486207

  2. Odaert B, Saida F, Aliprandi P, Durand S, Crechet JB, Guerois R, Laalami S, Uzan M, Bontems F;, J Biol Chem. 2007;282:2019-2028.: Structural and functional studies of RegB, a new member of a family of sequence-specific ribonucleases involved in mRNA inactivation on the ribosome. PUBMED:17046813 EPMC:17046813


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR019653

The RegB endoribonuclease encoded by Bacteriophage T4 is a unique sequence-specific nuclease that cleaves in the middle of GGAG or, in a few cases, GGAU tetranucleotides, preferentially those found in the Shine-Dalgarno regions of early phage mRNAs. T4 regB expression is regulated autogenously by attacking its own mRNA. The deduced primary structure of RegB proteins in many phages is almost identical to that of T4, while the sequences of RegB encoded by Enterobacteria phage RB69, Enterobacteria phage TuIa and Enterobacteria phage RB49 show substantial divergence from their T4 counterpart [PUBMED:15486207]. In RB49 regB expression is regulated by both RegB and Escherichia coli endoribonuclease E.

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 26 members:

Arc BrnA_antitoxin CcdA CopG_antitoxin DUF1778 DUF2610 HicB HicB-like_2 HicB_lk_antitox MetJ Omega_Repress ParD ParD_antitoxin ParD_like ParG PSK_trans_fac REGB_T4 RelB RepB-RCR_reg RHH_1 RHH_3 RHH_4 RHH_5 RHH_7 TraY VapB_antitoxin

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.

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Full
(68)
Representative proteomes NCBI
(35)
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RP35
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RP55
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RP75
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

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  Seed
(1)
Full
(68)
Representative proteomes NCBI
(35)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
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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
(1)
Full
(68)
Representative proteomes NCBI
(35)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
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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: PRODOM_PD091708, pdb_2hx6
Previous IDs: none
Type: Domain
Author: Mistry J, Coggill P
Number in seed: 1
Number in full: 68
Average length of the domain: 148.10 aa
Average identity of full alignment: 72 %
Average coverage of the sequence by the domain: 97.55 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.1 81.6
Noise cut-off 26.5 19.1
Model length: 150
Family (HMM) version: 5
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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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 REGB_T4 domain has been found. There are 1 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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