XcpQ (PA3105) is the GspD-family secretin of the Xcp type II secretion system of Pseudomonas aeruginosa. Fifteen subunits assemble into a gated, barrel-shaped channel that is embedded in the outer membrane and extends across the periplasm, where its N0-N3 ring domains engage the inner-membrane assembly platform. The channel is wide enough to pass folded exoproteins, and it is the outer-membrane conduit through which the machine releases elastase LasB, the protease PrpL, the chitin-binding protein CbpD, aminopeptidase PaAP, metalloprotease ImpA and other hydrolases. Unlike the other P. aeruginosa secretins it reaches and inserts into the outer membrane with little help from the Bam and Lol targeting machineries, and it can multimerise into lipid vesicles on its own.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0009279 cell outer membrane | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping (cell outer membrane) for the secretin. Reason: XcpQ is the outer-membrane channel of the Xcp T2SS; the curated UniProt location rests on the cryo-EM and cross-linking work on the purified complex, and the membrane-embedded secretin domain is explicit in the record. Supporting Evidence: file:PSEAE/xcpQ/xcpQ-uniprot.txt SUBCELLULAR LOCATION: Cell outer membrane file:PSEAE/xcpQ/xcpQ-uniprot.txt the secretin and S domains form a channel that is partially inserted in the outer membrane |
| GO:0009306 protein secretion | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping from the shared T2SS/T3SS secretin domain IPR004846 to protein secretion. Reason: Correct but general. IPR004846 is shared with the T3SS secretins, so the mapping stops at the generic term; for XcpQ the specific supported term is GO:0015628 protein secretion by the type II secretion system, which the gene already carries. Proposed replacements: protein secretion by the type II secretion system Supporting Evidence: file:PSEAE/xcpQ/xcpQ-uniprot.txt Belongs to the bacterial secretin family. GSP D subfamily. PMID:29042496 The T2SS containing XcpQ is responsible for the secretion of at least 19 substrates |
| GO:0015627 type II protein secretion system complex | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA from PTN000768388, the GspD subnode of PTHR30332, whose IBD was seeded by three P. aeruginosa secretins including this gene. Reason: The node seed is correct for XcpQ, and the family keeps the T3SS secretins on a separate node (PTN009110345), so a T2SS-complex term suits the clade that inherits it. XcpQ appearing in its own WITH/FROM reflects its experimental seed and is expected. Supporting Evidence: PMID:29042496 class averages revealed that XcpQ is a pentadecameric secretin complex file:PSEAE/xcpQ/xcpQ-uniprot.txt NCBIfam; TIGR02517; type_II_gspD |
| GO:0015627 type II protein secretion system complex | IDA PMID:9466268 Formation of oligomeric rings by XcpQ and PilQ, which are in... | ACCEPT | Summary: PseudoCAP IDA from Bitter et al. 1998, which purified XcpQ as a ring-forming homomultimer; one of three seeds of the PTN000768388 IBD. Reason: Direct evidence. The purified protein forms stable ring-shaped multimers of the size expected for the T2SS outer-membrane channel, and the complex was later resolved as a pentadecameric secretin that engages the inner-membrane platform. Only the abstract is cached, but the claim is confirmed independently. Supporting Evidence: PMID:9466268 C-terminal part of XcpQ is sufficient for the formation of the multimer. PMID:29042496 class averages revealed that XcpQ is a pentadecameric secretin complex |
| GO:0015627 type II protein secretion system complex | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from the GspD entry IPR013356 to the T2SS complex. Reason: Reinforces the IDA and IBA rows for the same term; the signature is the T2SS-specific GspD entry, not the shared secretin domain, so the mapping is at the right granularity. Supporting Evidence: file:PSEAE/xcpQ/xcpQ-uniprot.txt InterPro; IPR013356; T2SS_GspD. |
| GO:0015628 protein secretion by the type II secretion system | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA from PTN000768388, whose IBD for this term rests solely on the PseudoCAP row for XcpQ that cites the review PMID:9818381. Reason: The biological claim holds for XcpQ and for GspD secretins generally - the deletion mutant loses export of the Xcp substrates - so the node placement is sound even though the seed row carries the wrong evidence code (the cited paper is a review; full text checked). The seed should be re-keyed, not the node removed. Supporting Evidence: file:PSEAE/xcpQ/xcpQ-uniprot.txt Loss of export of PrpL, elastase LasB, chitin PMID:29042493 the supernatant profile of the wild-type strain producing vHH04 is similar to that of an xcpQ deletion mutant |
| GO:0015628 protein secretion by the type II secretion system | IDA PMID:9818381 GSP-dependent protein secretion in gram-negative bacteria: t... | ACCEPT | Summary: PseudoCAP IDA citing Filloux, Michel and Bally 1998, a review of the Xcp system; sole seed of the PTN000768388 IBD for this term. Reason: The term is right for XcpQ, but a review with no original secretion data (full text checked) cannot support IDA. Either the evidence should become TAS for this reference, or the row should be re-keyed to a primary paper - the deletion-mutant secretome work (PMID:29042493) would support IMP. The same mis-coding sits on the xcpX row for the same term and the same reference, so this is a pattern across the PseudoCAP xcp rows. Supporting Evidence: PMID:29042493 the supernatant profile of the wild-type strain producing vHH04 is similar to that of an xcpQ deletion mutant file:PSEAE/xcpQ/xcpQ-uniprot.txt Among its substrates are PrpL, elastase LasB, chitin binding protein D |
| GO:0015628 protein secretion by the type II secretion system | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from the GspD entry IPR013356 to T2SS protein secretion. Reason: Reinforces the same claim from the T2SS-specific signature; correct and at the right granularity. Supporting Evidence: file:PSEAE/xcpQ/xcpQ-uniprot.txt NCBIfam; TIGR02517; type_II_gspD |
| GO:0019867 outer membrane | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping from IPR013356 to the generic outer membrane term. Reason: Correct but general. GO:0019867 does not say which outer membrane; XcpQ is in the bacterial cell outer membrane, and the gene already carries GO:0009279 cell outer membrane. Proposed replacements: cell outer membrane Supporting Evidence: file:PSEAE/xcpQ/xcpQ-uniprot.txt SUBCELLULAR LOCATION: Cell outer membrane |
| GO:0042802 identical protein binding | IPI PMID:24657091 Independent domain assembly in a trapped folding intermediat... | KEEP AS NON CORE | Summary: Self-association of XcpQ, from the secretin folding-intermediate study. Reason: True and informative at the level the term allows - XcpQ is an obligate homo-oligomer, and the substitution that traps PulD at the prepore stage does the same to XcpQ. The self-association is already stated more precisely by the pentadecameric secretin complex (GO:0015627), so the term is peripheral rather than the gene's core molecular function; it is as specific as GO offers for homo-oligomerisation, so there is nothing to modify it to. Supporting Evidence: PMID:24657091 in the Pseudomonas aeruginosa secretin XcpQ PMID:9466268 C-terminal part of XcpQ is sufficient for the formation of the multimer. |
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Download this section (compressed HTML)Q: Does the proposed C15-to-C6 symmetry transition of the XcpQ N-terminal domains happen during a secretion cycle, and can it be captured with substrate engaged?
Q: Should XcpQ carry a channel or protein-transmembrane-transporter molecular function term, given that the secretin forms the gated outer-membrane pore itself rather than only being part of the complex?
Experiment: Cryo-EM of the assembled Xcp secreton with a trapped substrate to test whether the central gate opens at the proposed pivot residue and whether the N0 ring changes symmetry.
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