Summary: T4-page Endoribonuclease RegB
T4-page Endoribonuclease RegB 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 .
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
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
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.
It's worth noting that 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 [PUBMED:17046813].
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Loading domain graphics...
The families in this clan are plasmid encoded anti-toxins involved in plasmid maintenance. The plasmid encodes both a toxin and an antitoxin. Upon loss of the plasmid the antitoxin is inactivated more rapidly than the toxin. This allows the toxin to interact with its target thus killing the cell or impeding growth.
The clan contains the following 12 members:BrnT_toxin Gp49 HigB-like_toxin MqsR_toxin ParE-like_toxin ParE_toxin PHD_like PhdYeFM_antitox REGB_T4 RelE YafQ_toxin YoeB_toxin
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
If you find these logos useful in your own work, please consider citing the following article:
Note: You can also download the data file for the tree.
Curation and family details
|Seed source:||PRODOM_PD091708, pdb_2hx6|
|Author:||Mistry J, Coggill P|
|Number in seed:||1|
|Number in full:||1|
|Average length of the domain:||150.00 aa|
|Average identity of full alignment:||100 %|
|Average coverage of the sequence by the domain:||98.04 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||8|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
How the sunburst is generated
Colouring and labels
Anomalies in the taxonomy tree
Missing taxonomic levels
Unmapped species names
Too many species/sequences
The tree shows the occurrence of this domain across different species. More...
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
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.
Loading structure mapping...