Summary: RF-1 domain
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RF-1 domain Provide feedback
This domain is found in peptide chain release factors such as RF-1 (P07011) and RF-2 (P07012), and a number of smaller proteins of unknown function such as P40711. This domain contains the peptidyl-tRNA hydrolase activity. The domain contains a highly conserved motif GGQ, where the glutamine is thought to coordinate the water that mediates the hydrolysis.
Song H, Mugnier P, Das AK, Webb HM, Evans DR, Tuite MF, Hemmings BA, Barford D; , Cell 2000;100:311-321.: The crystal structure of human eukaryotic release factor eRF1--mechanism of stop codon recognition and peptidyl-tRNA hydrolysis. PUBMED:10676813 EPMC:10676813
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000352Peptide chain release factors (RFs) are required for the termination of protein biosynthesis [PUBMED:8821264]. At present two classes of RFs can be distinguished. Class I RFs bind to ribosomes that have encountered a stop codon at their decoding site and induce release of the nascent polypeptide. Class II RFs are GTP-binding proteins that interact with class I RFs and enhance class I RF activity. In prokaryotes there are two class I RFs that act in a codon specific manner [PUBMED:2215213]: RF-1 (gene prfA) mediates UAA and UAG-dependent termination while RF-2 (gene prfB) mediates UAA and UGA-dependent termination. RF-1 and RF-2 are structurally and evolutionary related proteins which have been shown to be part of a larger family [PUBMED:1408743].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||translation release factor activity (GO:0003747)|
|Biological process||translational termination (GO:0006415)|
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Curation and family details
|Author:||Bateman A, Finn RD|
|Number in seed:||100|
|Number in full:||11930|
|Average length of the domain:||115.70 aa|
|Average identity of full alignment:||40 %|
|Average coverage of the sequence by the domain:||37.79 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||15|
|Download:||download the raw HMM for this family|
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There are 3 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 RF-1 domain has been found. There are 19 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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