PROSITE documentation PDOC00607

Prokaryotic-type class I peptide chain release factors signature

Peptide chain release factors (RFs) are required for the termination of protein biosynthesis [1]. 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 [2]: 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 [3] to make up a family that also contains the following proteins:

• Fungal MRF1, a mitochondrial RF (m-RF) which recognizes the UAA and UAG codons.
• Escherichia coli RF-H, a protein of unknown function.
• Escherichia coli hypothetical protein yaeJ and a close Pseudomonas putida homolog.

We use as a signature pattern a highly conserved region located in the central part of the 40 to 45 Kd RF-1/2 and m-RF and in the N-terminal of the 15 to 16 Kd RF-H and yaeJ.