PROSITE documentation PDOC52044

Vms1-like release factor 1 (VLRF1) domain profile

Stalling of ribosomes engaged in protein synthesis can lead to significant defects in the function of newly synthesized proteins and thereby impair protein homeostasis. Ribosomal surveillance pathways scan for ribosomes that are transiently paused or terminally stalled owing to structural elements in mRNAs or nascent chain sequences. Ribosome-associated quality control (RQC) provides a rescue pathway for eukaryotic cells to process faulty proteins after translational stalling of cytoplasmic ribosomes. The general mechanisms and factors acting at different stages of RQC, from recognizing aberrant translation to degradation, have been shown to be highly conserved in eukaryotes. Stalled ribosomes are recognized by specific factors that trigger the separation of large ribosomal subunits (LSUs) and small ribosomal subunits (SSUs). Ribosome splitting recycles the SSU, but the LSU remains associated with a tRNA attached to an incomplete nascent polypeptide chain. Such LSU-nascent chain complexes undergo processing by an addition of Ala (in mammals and bacteria) or Ala/Thr (in yeast) C-terminal tails ("CAT tails") to nascent peptides. Tailing serves as a signal for the recruitment of specific factors that mark the nascent chains by ubiquitination for subsequent degradation. However, to be degraded, nascent chains first have to be released from the tRNA. In eukaryotes, this is accomplished by a specific nuclease that cleaves off the peptidyl-tRNA CCA end. An endonuclease, the ankyrin repeat (see <PDOC50088>) and zinc finger (see <PDOC00028>) domain-containing protein 1 (ANKZF1; S. cerevisiae Vms1), selectively cleaves off the 3'-CCA nucleotides of the peptidyl-tRNA on LSU RQC complexes and is responsible for the release of the ubiquitinated polypeptide from the tRNA in the LSU. Because the 3'-CCA is invariant on all tRNAs, ANKZF1/Vms1 can act on ribosomes stalled at any codon and generate a CCA-less tRNA intermediate incompatible with aminoacylation [1,2,3,4,5].

The ANKZF1/Vms1 Vms1-like release factor 1 (VLRF1) domain, which acts as a peptidyl-tRNA hydrolase, has a catalytic loop bearing a conserved glutamine. In addition to the glutamine in the active site, the VLRF1 domain also contains conserved vicinal arginines in the α-helix immediately following the active-site loop. The cleavage mechanism involves remodelling and cleavage of the ribose-phosphate backbone of the tRNA by a tyrosine and the GSQ motif (see <PDB:5WHG>) [2,3].

The profile we developed covers the entire VLRF1 domain.