pilD (PA4528, P22610) notes

No deep-research provider was available; this is my own literature review
(PubMed MCP plus cached publications).

Identity

UniProt P22610 (LEP4_PSEAE), 290 aa, Swiss-Prot reviewed; locus PA4528;
synonym xcpA. Matches the worklist accession.
Peptidase A24 family (MEROPS A24.001; Pfam PF01478 Peptidase_A24 and
PF06750 A24_N_bact; PANTHER PTHR30487:SF0). Six predicted TM helices,
cytoplasmic N-terminal domain with four conserved Cys (Zn ligands).
EC 3.4.23.43 (prepilin peptidase) plus an N-methyltransferase activity.

Bifunctional: cleaves the short basic leader peptide of type IV prepilin
and then N-methylates the new N-terminal Phe using SAM PMID:8096341.
The four conserved cytoplasmic Cys are needed for full peptidase and
methylase activity PMID:8340405.
Gly95/Lys96 substitutions separate methylation from cleavage; loss of
methylation does not prevent pilus assembly PMID:9668097.
Purified PilD, made cell-free into liposomes, cleaves PilA and methylates
mature pilin; it binds zinc, which is needed for methylation but not
cleavage PMID:23255525.
Type 4 prepilin peptidases are aspartic proteases with an invariant Asp
pair [PMID:10625704 "In this report we show that the TFPPs represent a
novel family of bilobed aspartate proteases that is unlike any other
protease"; "Corresponding aspartate residues are completely conserved
throughout this extensive peptidase family"]. (Shown for V. cholerae TcpJ
and VcpD; for PilD the aspartic assignment is by family conservation.)
Also processes the T2SS pseudopilins XcpT-W, and pilD mutants fail to
secrete exoproteins (accumulate them in the periplasm) PMID:1671384;
PMID:8331069;
PMID:1588814.
Inner (cytoplasmic) membrane location PMID:1898929.

GO:0004190 aspartic-type endopeptidase activity: correct genus for EC
3.4.23.43 (under EC 3.4.23 aspartic endopeptidases). The specific term
GO:0008978 prepilin peptidase activity is obsolete; GO:0042500 (intramembrane
cleaving) not used: the cleavage site of prepilin is at the cytoplasmic face,
not clearly within the bilayer.
GO:0008170 N-methyltransferase activity is general; GO:0071885 N-terminal
protein N-methyltransferase activity ("transfer of a methyl group from
S-adenosyl-L-methionine (AdoMet) to the alpha-amino group of the N-terminal
amino or imino acid residue of a protein substrate") fits exactly.
GO:0015627 type II protein secretion system complex (part_of, PseudoCAP
IDA, PMID:1588814). The abstract shows in vivo processing of Xcp
pseudopilins by XcpA/PilD, not membership of the secretion complex. PilD is
shared with the T4P system and is a maturation enzyme. Comparator check
(UniProt reviewed members of PTHR30487, incl. PulO, OutO, E. coli GspO,
Vibrio TcpJ/VvpD): none carries GO:0015627 or GO:0015628; PilD is the only
family member with GO:0015627 in QuickGO experimental rows.

PTN000766410 is a Bacteria-level (taxon:2) node of PTHR30487 with 33 leaf IBAs
in 29 taxa (worklist).

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN000766410	GO:0004190 aspartic-type endopeptidase activity	1 (sole: P22610)	33 (29 taxa)	GO:0004190, IDA, PMID:23255525 (PseudoCAP); also UniProt EXP PMID:8096341	SOUND	Purified PilD cleaves the PilA leader peptide in vitro (23255525) and PilD was the first prepilin peptidase characterised biochemically (8096341). The aspartic mechanism is a family property with invariant Asp pairs (10625704). Endopeptidase activity on prepilin-like substrates is the defining property of A24 prepilin peptidases, so the term suits a Bacteria-level node.
PTN000766410	GO:0005886 plasma membrane	3 (P22610, E. coli GspO P25960, PppA Q46836)	33 (29 taxa)	GO:0005886, IDA, PMID:9466269 (PseudoCAP); also UniProt EXP PMID:8331069	UNVERIFIABLE (PseudoCAP row); IBD SOUND	The claim is right (six TM polytopic inner-membrane protein; PMID:1898929, PMID:8331069), and the IBD has two other seeds plus the UniProt EXP row. But the abstract of PMID:9466269 (xcpT ts mutants and xcpR suppressors) reports no PilD localization; full text not available. Row accepted, reference queried (SUSPECTED).

GO:0008170 N-methyltransferase activity (IDA 8096341): sound, MODIFY to
GO:0071885.
GO:0006480 N-terminal protein amino acid methylation (IDA 23255525): sound.
GO:0009297 pilus assembly (IDA 9668097): MODIFY to type IV pilus assembly;
the pilus-assembly part of this paper is an in vivo mutant analysis (IMP
rather than IDA, SUSPECTED defect).
GO:0043683 type IV pilus assembly (IMP 1671384): sound (restates Nunn et al.
1990 pilD mutant phenotype).
GO:0015627 T2SS complex (IDA 1588814): MARK_AS_OVER_ANNOTATED, PSEUDOCAP
defect PROBABLE.

ACCEPT: aspartic-type endopeptidase activity (EXP, IBA, IDA, IEA); plasma
membrane (EXP, IBA, IDA, IEA); N-terminal protein amino acid methylation
(IDA); type IV pilus assembly (IMP).
MODIFY: N-methyltransferase activity -> N-terminal protein
N-methyltransferase activity; pilus assembly -> type IV pilus assembly;
membrane -> plasma membrane.
MARK_AS_OVER_ANNOTATED: type II protein secretion system complex.