ligD curation notes

2026-09-01

Applied the annotation-reviewer workflow to all four GOA rows and evaluated
three missing activities/process annotations. No annotation remains PENDING or
UNDECIDED.

• Q88HU3 is an unreviewed KT2440 protein with the complete LigD domain
  architecture: IPR014144 phosphoesterase, IPR014145 polymerase, and IPR014146
  ligase [file:PSEPK/ligD/ligD-uniprot.txt "InterPro; IPR014144;
  LigD_PE_domain."] [file:PSEPK/ligD/ligD-uniprot.txt "InterPro; IPR014145;
  LigD_pol_dom."] [file:PSEPK/ligD/ligD-uniprot.txt "InterPro; IPR014146;
  LigD_ligase_dom."].
• PTHR42705 PAINT places DNA polymerase activity, ATP-dependent DNA ligase
  activity, and NHEJ at PTN001627042
  [file:interpro/panther/PTHR42705/PTHR42705-paint.tsv
  "PTN001627042 GO:0003887"].
• Direct work on Pseudomonas aeruginosa LigD supports polymerase-mediated end
  remodeling PMID:20018881.
• The phosphoesterase domain is not modeled as generic exonuclease activity.
  Pseudomonas LigD removes a terminal ribonucleotide and then hydrolyzes the
  resulting 3-prime phosphate on a DNA repair intermediate
  PMID:15897197. A
  general RNA exonuclease term is not asserted because the demonstrated
  substrate is ribonucleotide-terminated DNA, and the isolated nuclease domain
  did not behave as an independent processive 3-prime-to-5-prime exonuclease
  PMID:16023671.
• The POL domain prefers ribonucleotides in biochemical assays, but
  GO:0003887 is retained as the PAINT- and UniProt-grounded polymerase term;
  no more specific MF term is asserted without a verified ontology match
  PMID:16023671.
• Direct P. putida genetics links LigD and both its PE and POL domains to
  stationary-phase mutation spectra PMID:25942369. The cached paper is abstract-only, so the
  catalytic assignments remain grounded in domain/family biochemistry.
• Target-organism Cas9 work perturbed NHEJ-associated KT2440 enzymes during DSB
  repair PMID:36475478, directly supporting the pathway assignment.

GO:0006310 is modified laterally to GO:0006303 because bacterial NHEJ is a DNA
repair route, not a child of generic DNA recombination. The three distinct LigD
molecular functions are represented separately in the core-functions list.