S. pombe vms1 (O74977): VLRF1 catalytic-site conservation

Question

S. pombe vms1 has no experimental molecular-function annotation (GOA carries
GO:0003674 molecular_function with evidence ND). Its only biological-process
annotation is an IBA to GO:0036503 ERAD pathway. The Vms1/ANKZF1 family's
best-characterised activity is instead cleavage of polypeptidyl-tRNA on stalled
60S ribosome-nascent-chain complexes, which in human ANKZF1 depends on a single
catalytic glutamine in the VLRF1 (Vms1-like release factor 1) domain.

Does S. pombe vms1 retain that catalytic glutamine, i.e. is it plausibly a
catalytically competent family member rather than a degenerate pseudoenzyme?

Method

vlrf1_catalytic_conservation.py performs global BLOSUM62 pairwise alignments
(Biopython PairwiseAligner, gap open -11 / extend -1) of full-length UniProt
sequences and projects the human ANKZF1 catalytic position onto each ortholog:

Human ANKZF1 is used as the reference because it is the only family member whose
catalytic residue has direct mutagenesis evidence in UniProt.

Reproduce with:

cd genes/SCHPO/vms1/vms1-bioinformatics
uv run python vlrf1_catalytic_conservation.py

FASTA inputs were downloaded from https://rest.uniprot.org/uniprotkb/<ACC>.fasta.

Results

Reference: Q9H8Y5 (human ANKZF1), 726 aa
  annotated catalytic site 246: AKRGTA[Q]GLRDAR

Q04311 (S. cerevisiae Vms1), 632 aa  [alignment score 242.0]
  UniProt ACT_SITE           : 295  RKQGGS[Q]SAMDNA
  aligned to Q9H8Y5:246      : 295  RKQGGS[Q]SAMDNA
  alignment agrees with ACT_SITE annotation: yes
  residue at aligned position: Q

O74977 (S. pombe vms1), 600 aa  [alignment score 313.0]
  UniProt ACT_SITE           : 249  RKQGGS[Q]GAADNT
  aligned to Q9H8Y5:246      : 249  RKQGGS[Q]GAADNT
  alignment agrees with ACT_SITE annotation: yes
  residue at aligned position: Q

Interpretation

• The alignment independently reproduces the UniProt ACT_SITE call for both
  yeasts: human ANKZF1 Q246 aligns to S. cerevisiae Q295 and S. pombe Q249.
• The glutamine is present in S. pombe vms1, in an RKQGGSQ motif that is
  identical to the S. cerevisiae Vms1 context and corresponds to the
  eRF1 GGQ-motif position repurposed in the VLRF1 clade.
• Conclusion: S. pombe vms1 retains the catalytic residue required for
  polypeptidyl-tRNA cleavage in this family. There is no evidence here of
  pseudoenzyme degeneration in the fission-yeast ortholog.

Caveats

• Residue conservation supports catalytic competence but does not demonstrate
  it. No fission-yeast biochemistry for vms1 has been published; the proposed
  molecular-function annotation should therefore rest on sequence/ortholog
  evidence (ISS-level), not be asserted as experimentally established.
• Only three sequences were compared (the two model yeasts and human). This is
  a targeted check of one residue, not a family-wide phylogenetic analysis.
• Global pairwise alignment of full-length, domain-shuffled proteins can be
  unreliable outside conserved cores; the agreement between the projected
  position and the independently annotated ACT_SITE in both queries is the
  control that the projection is trustworthy here.