xcpX (PA3097, Q00518) review notes

Review session 2026-10-28 (PseudoCAP IBA-seed protocol)

Fetched with just fetch-gene PSEAE xcpX; accession Q00518 matches the worklist (rank 15,
PA3097). No deep-research provider was used; these are manual notes from the cached
publications and the UniProt record.

What XcpX is

XcpX is the GspK-family minor pseudopilin of the Xcp type II secretion system (T2SS).
UniProt: "Belongs to the GSP K family"; Pfam PF03934 (T2SSK), NCBIfam NF037980 (T2SS_GspK),
PANTHER PTHR38831.
It is a bitopic inner-membrane protein processed by the prepilin peptidase PilD/XcpA
[PMID:9466253 "we characterized the xcpX gene product, a bitopic cytoplasmic membrane protein";
"We show that XcpX could be processed by the prepilin peptidase, PilD/XcpA, and that the highly
conserved glycine residue preceding the hydrophobic segment could not be mutated without loss of
the XcpX function"]. UniProt: TRANSMEM 8..29, periplasmic domain 30..333.
XcpX controls the length of the XcpT pseudopilus and binds XcpT directly
[PMID:16012171 "when the number of XcpX subunits increases, the length of the pseudopilus
decreases. Conversely, in the absence of XcpX, the pseudopilus length is abnormally long";
"Our results indicate that XcpT and XcpX directly interact with each other"].
XcpX forms the tip complex with XcpU, XcpV and XcpW PMID:19828448. Crystal structure of XcpVWX (Zhang et al. 2018) places XcpX on top of the
tip complex PMID:30346996 and shows
a third Ca2+ site confirmed by ITC PMID:30346996.

Conflict on secretion requirement

Bleves et al. 1998 (abstract) report loss of XcpX function on mutating the conserved glycine.
Zhang et al. 2018, using PAO1 transposon mutants from the Manoil library, found the xcpX mutant
still secreted protease PMID:30346996. The insertion site was not given; a late insertion could leave a functional protein, and
in Klebsiella PulK deletion affects PulA secretion (cited in the same paper). The weight of
evidence (classic Xcp genetics, the GspK family role in tip assembly) still supports involvement in
T2SS secretion, but the necessity of XcpX for every substrate is open. Recorded as a question.

PseudoCAP row details

GO:0015627 IDA PMID:9466253: the abstract shows membrane location, PilD processing and
pseudopilin classification; the full text (Mol Microbiol 1998) is not in PMC. Membership in the
T2SS complex is independently shown by the tip-complex biochemistry (PMID:19828448) and the
XcpVWX structure (PMID:30346996). The term is correct.
GO:0015628 IDA PMID:9818381: this paper is a review (Filloux, Michel & Bally 1998, FEMS
Microbiol Rev; PubMed type Review). The IDA is not supported: the full text has no original secretion data. The term is correct, and the
primary evidence is Bleves et al. 1998 (mutational loss of function, i.e. IMP). Source defect
recorded as WRONG_EVIDENCE_CODE / CHECK.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN000475915	GO:0015627 type II protein secretion system complex	1 (sole seed)	35 (28 taxa)	GO:0015627, IDA, PMID:9466253	SOUND	XcpX is a GspK pseudopilin and is part of the pseudopilus tip complex (PMID:19828448, PMID:30346996). The cited abstract alone only shows membrane location and PilD processing, but the claim is correct and GspK is a conserved T2SS component, so the node term suits the GspK clade.
PTN000475915	GO:0015628 protein secretion by the type II secretion system	1 (sole seed)	35 (28 taxa)	GO:0015628, IDA, PMID:9818381	SOUND (term); evidence code WRONG (cited paper is a review with no original secretion data; full text checked)	Term is correct for GspK proteins. PMID:9818381 is a review, so IDA is not valid; the primary support is PMID:9466253 (IMP, glycine mutant loses function). A 2018 transposon mutant still secreted protease (PMID:30346996), a caveat but not a refutation. The IBD conclusion is sound; the seed should be re-keyed to PMID:9466253 IMP (or TAS for the review).