PA1055 (Q9I4R9, ShaC) notes

2026-10-28 review (PseudoCAP IBA-seed worklist, rank 21)

No deep-research provider was available; literature collected by PubMed search
and cached abstracts or full texts. The PseudoCAP-cited paper (PMID:16030218,
Kosono et al. 2005) is abstract-only here: its PMC copy (PMC1196046) is a
scanned PDF with no text, and the PDF could not be retrieved.

Identity

UniProt Q9I4R9 (unreviewed), 112 aa, two predicted TM helices (Phobius
32-57, 69-90). InterPro IPR050601 CPA3_antiporter_subunitC and IPR039428
NUOK/Mnh_C1-like; Pfam PF00420 (Oxidored_q2, the NuoK/ND4L family);
PANTHER PTHR34583:SF2 [file:PSEAE/PA1055/PA1055-uniprot.txt].
Second gene of the six-gene sha cluster PA1054-PA1059. The authors name the
cluster shaABCDEFG for six genes, as in other Gram-negative Mrp operons,
where mrpA and mrpB are fused PMID:29218041. So
PA1054 = ShaAB and, by gene order and family, PA1055 = ShaC (MrpC). The
abstract names only PA1054 (shaA) explicitly; the PA1055 = ShaC mapping is
an inference.

What PMID:16030218 shows

The whole cluster PA1054-PA1059, but not the cluster with PA1054 deleted,
complemented Na+ sensitivity and the antiport defect of E. coli TO114
PMID:16030218.
The abstract reports disruption of PA1054 only in P. aeruginosa PMID:16030218.
So the abstract describes no PA1055 mutant (full text not read). The IMP rows on PA1055 rest on a PA1054
mutant plus whole-cluster complementation. The cluster data do show that
the six gene products together make a Na+/H+ antiporter that is largely
responsible for Na+ extrusion.

Mrp/Sha complex biology (family)

Activity needs the hetero-oligomeric complex of all subunits
PMID:20624916, PMID:29218041.
MrpC is the NuoK/ND4L homologue PMID:29218041. In the 2.2 A B. pseudofirmus structure, MrpC sits at a
hydrated region proposed to carry Na+ PMID:36241630. The
MrpC-Q70A mutant keeps antiport activity but loses the monomeric complex
PMID:20624916.
Archaeal membrane-bound hydrogenase (MBH) contains an Mrp-like
Na+-translocating module PMID:29754813.

Annotation decisions (summary)

GO:0015385 sodium:proton antiporter activity (IBA, IMP): ACCEPT as the core
activity, but as a subunit contribution: contributes_to, not enables.
Defects filed for the qualifier (PSEUDOCAP, GO_CENTRAL) and the IMP code.
GO:0035725 sodium ion transmembrane transport (IBA, IMP): ACCEPT; IMP code
flagged.
GO:0005886 plasma membrane (IEA): ACCEPT.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN002160376	GO:0015385 sodium:proton antiporter activity	1 (sole)	24	GO:0015385, IMP, PMID:16030218	INDIRECT-PHENOTYPE	The abstract describes no PA1055 mutant. The row rests on a PA1054 (shaA) disruption and on complementation of E. coli TO114 by the whole PA1054-PA1059 cluster. That shows the Sha complex is a Na+/H+ antiporter, not that PA1055 enables antiport alone. Biologically right as `contributes_to` (a subunit of the antiporter complex), wrong as `enables` + IMP. The node is the LUCA root of the subunit-C family and includes MBH/MBX hydrogenase subunits (TK2086, TK1221), for which a stand-alone antiporter MF is doubtful.
PTN002160376	GO:0035725 sodium ion transmembrane transport	1 (sole)	24	GO:0035725, IMP, PMID:16030218	SOUND	As a subunit of the complex responsible for Na+ extrusion, PA1055 takes part in Na+ transmembrane transport. Structural work places MrpC at the putative Na+ pathway. The process fits the whole clade, MBH Na+-translocating modules included. Caveat: the IMP code looks wrong for PA1055, since the abstract describes no PA1055 mutant; filed as a CHECK.

Audit 2026-10-29: confidence matched to what was read

PMID:16030218 is still abstract-only here: the PubMed MCP returns no body
text (the PMC copy, PMC1196046, is a scanned PDF the publisher does not
release as XML), and the PMC, Europe PMC and ASM pages were not retrievable.
The WRONG_EVIDENCE_CODE (IMP) defects on this gene rest on the abstract not
describing a mutant of this gene, so they are lowered from PROBABLE to
SUSPECTED. The WRONG_QUALIFIER defects (enables vs contributes_to) rest on
positive statements in other Mrp papers and stay PROBABLE. The reference
correctness for PMID:16030218 is changed from MISCITED to UNVERIFIED.
Annotation actions are unchanged.

Full-text check of PMID:16030218 (2026-11-05)

The full text of Kosono et al. 2005 was supplied by the user and read. It
supersedes the earlier notes above that describe this paper as abstract-only.
The only sha mutant the paper constructs is the PA1054 insertion; the
cluster-level evidence comes from expressing the whole PA1054-PA1059 cluster,
or the cluster with PA1054 disrupted, in an antiporter-deficient E. coli
strain. There is no PA1055 mutant, so the IMP evidence-code defects on PA1055 are CONFIRMED.