xcpR (PA3103, Q00512) review notes

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

Fetched with just fetch-gene PSEAE xcpR; accession Q00512 matches the worklist entry (rank 72,
PA3103, reviewed Swiss-Prot entry GSPE_PSEAE). No deep-research provider key was available, so
these notes are manual, from the cached publications, the UniProt record and the cached PAINT
table interpro/panther/PTHR30258/PTHR30258-paint.tsv.

What XcpR is

XcpR is the GspE-family secretion ATPase of the Xcp type II secretion system (T2SS), the
cytoplasmic motor of the machine. UniProt: "Belongs to the GSP E family"; NCBIfam TIGR02533
(type_II_gspE), Pfam PF00437 T2SSE, PANTHER PTHR30258.
It was identified with the other xcp genes and recognised as a PilB homologue with a canonical
nucleotide-binding site PMID:1588814. UniProt records a Walker A motif
(FT:BINDING 263..270) and four further ATP/metal-binding residues.
Serine substitution of the conserved Walker A glycine abolishes exoprotein secretion, and
overexpression of the mutant protein is dominant-negative, causing periplasmic accumulation of
normally secreted enzymes PMID:8102361. UniProt CC:DISRUPTION PHENOTYPE:
"Mutants show complete loss of extracellular exotoxin A secretion."
XcpR dimerises through an 85-residue N-terminal region and that dimerisation is required for
secretion PMID:9426126.
It has no hydrophobic anchor of its own and reaches the cytoplasmic (inner) membrane only via
XcpY/GspL PMID:9882649.
Co-purification with His-tagged XcpZ isolated an XcpRSYZ inner-membrane platform subcomplex
PMID:16168578.
UniProt assigns EC 7.4.2.8 with ECO:0000305|PubMed:8102361, i.e. the catalytic activity is a
curator inference from the Walker-site genetics, not a measured ATPase rate for XcpR itself. A
Zn(2+) cofactor is asserted only by similarity (ECO:0000250|UniProtKB:P37093).

PseudoCAP row details

GO:0015627 IDA PMID:16168578 (Robert, Filloux & Michel 2005): the abstract itself reports the
native XcpRSYZ subcomplex, so the complex-membership claim is directly supported even though
only the abstract is cached. Sole seed of the PTN002016240 IBD for this term.
GO:0015628 IDA PMID:9818381: Filloux, Michel & Bally 1998 is a review (publication_type: REVIEW in the cached file; PubMed publication type Review). The same reference is mis-keyed as
IDA on the xcpQ and xcpX rows for the same term, so this is a systematic PseudoCAP pattern over
the xcp cluster rather than a single slip. The term is correct for XcpR - Walker-site mutants
lose exoprotein secretion entirely - and the right primary reference is PMID:8102361 (IMP).
Recorded as a WRONG_EVIDENCE_CODE source defect on both the xcpR and xcpQ reviews.

PAINT node context

interpro/panther/PTHR30258/PTHR30258-paint.tsv:

PTN001250205 (no taxon restriction): GO:0005886 IBD seeded by P0AFA5 and Q00512; GO:0016887 ATP
hydrolysis IBD seeded by P22608. This is the broad GspE/PilB-type ATPase node, and both terms
(inner-membrane localisation, ATP hydrolysis) are generic enough to suit it.
PTN002016240 (taxon:1236, Gammaproteobacteria): GO:0015627 and GO:0015628 IBDs, both sole-seeded
by Q00512. The T2SS-specific terms are confined to a Gammaproteobacterial subnode rather than
being pushed to the family root, which is the right shape - the family also contains type IV
pilus assembly ATPases (PilB) and other T4P-superfamily motors, for which T2SS terms would be
wrong.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN002016240	GO:0015628 protein secretion by the type II secretion system	1 (sole seed)	7 (6 taxa)	GO:0015628, IDA, PMID:9818381	SOUND (term); evidence code WRONG (cited paper is a review with no original secretion data; full text checked)	XcpR is the T2SS secretion ATPase: Walker A mutants lose exoprotein secretion and are dominant-negative (PMID:8102361), and dimerisation-defective variants cannot secrete (PMID:9426126). But PMID:9818381 is a review, so IDA cannot stand; the row should be re-keyed to PMID:8102361 as IMP (or downgraded to TAS). The IBD conclusion is unaffected, and the Gammaproteobacterial restriction of the node keeps the term off the PilB-type members.
PTN002016240	GO:0015627 type II protein secretion system complex	1 (sole seed)	7 (6 taxa)	GO:0015627, IDA, PMID:16168578	SOUND	The seed paper isolated the native XcpRSYZ inner-membrane platform subcomplex, which is direct evidence of membership; XcpR's membrane recruitment by XcpY (PMID:9882649) is consistent. The node term fits a Gammaproteobacterial GspE clade.

Open questions

No ATPase rate has been measured for XcpR itself; EC 7.4.2.8 and the GO:0008564
protein-exporting ATPase activity row both descend from the Walker-site genetics
(ECO:0000305|PubMed:8102361). A direct hydrolysis assay on purified XcpR, ideally in the
XcpRSYZ context, would settle it.
The Zn(2+) cofactor is asserted only by similarity to P37093, so no metal-binding GO row is
proposed here.
GO:0008564 is a transmembrane transporter activity. XcpR is the cytoplasmic motor, not the
conduit, so contributes_to would describe the row better than enables.