A0A1S3Y076 (Nicotiana tabacum LOC107770656) notes

2026-10-20 — Full re-review, independent of the ProtNLM2 predictions

No notes file existed before this session; this is the first entry. ProtNLM2 files were not opened.

Identity

• UniProt A0A1S3Y076 (TrEMBL, PE 3), 540 aa, RefSeq XP_016445475.1, chromosome 22. Full-length: PROP1-like PPR
  domain 4-208, PRORP nuclease domain 251-476, disordered C-terminal tail. Not a fragment or isoform.
• PANTHER PTHR13547:SF13 "PROTEINACEOUS RNASE P 2". The SF13 member list in
  interpro/panther/PTHR13547/PTHR13547-entries.csv includes Arabidopsis PRORP2 (Q680B9); PRORP3 (F4JKB6) is
  in SF20 and PRORP1 (Q66GI4) with animal mitochondrial PRORP in SF1.
• Own analysis (A0A1S3Y076-bioinformatics/RESULTS-rereview.md): 57% identity to PRORP2, 59% to PRORP3, 50%
  to PRORP1; all 8 PRORP1 Zn/Mn ligands conserved (D310, D386, D387, D405 catalytic); no transit-peptide
  extension. So the tobacco protein is the nuclear-type PRORP.

Literature (Arabidopsis PRORP2, the characterized SF13 member)

• Karasik 2016 PMID:26655022; crystal structure and Mg2+-dependent catalysis PMID:26655022.
• Gutmann 2012 PMID:22549728 (abstract only).
• Arrivé 2023 PMID:37945696; TRM1A/B facilitate nuclear RNase P activity. Not transferred to tobacco as a GO term.
• Gobert 2010 (PMID:20473316) and Gobert 2013 E. coli complementation (PMID:28499021) cached for context.

Problems found in the previous review

• The falcon deep research run states "no contexts were retrieved" — it is ungrounded, and it predicted
  organellar localization, which contradicts the SF13 placement and the lack of a transit peptide.
• Two supporting_text quotes attributed to the deep-research file were not present in that file (fabricated
  bracketed paraphrases). Replaced with verifiable PMID quotes.
• The description claimed Mg2+ cofactor and organellar/nuclear options without resolving compartment; now resolved
  to nucleus by subfamily.

Decisions

• GO:0004526 ribonuclease P activity (IBA, IEA): ACCEPT, core.
• GO:0001682 tRNA 5'-leader removal (IBA, IEA): ACCEPT, core.
• NEW GO:0005634 nucleus, by transfer from PRORP2 within SF13 (supported by no transit peptide). PAINT made no
  plant CC assertion at PTN001005190 (a eukaryote-wide node with mixed compartments), so this is not
  contradicting a curator decision.
• No TRM1 interaction or snoRNA/mRNA processing terms added (one-species, not PAINT-propagated).

Relative

• Arabidopsis PRORP2 (Q680B9, AT2G16650), same PANTHER subfamily SF13; no review in repo (genes/ARATH has no
  PRORP folder).