PA1056 (Q9I4R8, ShaD) notes

2026-10-28 review (PseudoCAP IBA-seed worklist, rank 69)

No deep-research provider was available; literature collected by PubMed search
and cached abstracts or full texts. PMID:16030218 (Kosono et al. 2005) is
abstract-only here (PMC1196046 is a scanned PDF). Verdicts kept consistent
with the completed PA1055 (ShaC) and PA1057 (ShaE) reviews.

Identity

UniProt Q9I4R8 (unreviewed, PE 3), 499 aa, 14 predicted TM helices.
InterPro IPR050586 CPA3_Na-H_Antiporter_D, IPR003918 NADH_UbQ_OxRdtase,
IPR001750 ND/Mrp_TM; Pfam PF00361; PANTHER PTHR42703:SF1
[file:PSEAE/PA1056/PA1056-uniprot.txt]. "Probable NADH dehydrogenase" is
the submitter's name.
Third gene of the sha cluster PA1054-PA1059. With PA1054 = ShaAB (fused,
PMID:29218041) and PA1055 = ShaC, gene order and family (CPA3 subunit D)
make PA1056 = ShaD (MrpD).

What PMID:16030218 shows

Whole-cluster complementation of E. coli TO114, lost when PA1054 is
deleted; the abstract reports disruption of PA1054 only in P. aeruginosa PMID:16030218. So the abstract describes no PA1056 mutant, and IMP looks wrong for PA1056 (full text not read).

MrpD biology (family)

B. subtilis mrpD deletion is Na+ and pH sensitive PMID:21236240; proposed H+
carrier PMID:21236240.
MrpD needed for complex formation PMID:29218041; no antiport with MrpD alone PMID:29218041.
Structural model PMID:36241630.
MrpD is homologous to complex I NuoM/NuoN PMID:29218041, which explains the
IPR003918 InterPro2GO rows (NADH dehydrogenase, respiratory electron
transport). The sha cluster has no redox subunits, so those are wrong for
PA1056.

PAINT node (PA1056-bioinformatics/RESULTS.md)

PTN001865541 = Eubacteria node of PTHR42703 (root PTN000511965, LUCA, 28
leaves), 16 leaves/13 taxa, 16 GO_Central IBAs per term. GO:0015385 seeds:
B. subtilis MrpD O05229 (IMP, PMID:20509166) and PA1056. GO:0035725 seed:
PA1056 only. The archaeal MBH/MBX subunit-H proteins (TK2087, TK1220,
TK1219) are in the Archaea-Eukaryota branch, outside the node. Possible
non-antiporter leaves: Leptospira LA_4273 ("Formate hydrogenase subunit B"),
Thermotoga TM_1105/TM_1211, Rhodopirellula RB1430/RB1431.

Annotation decisions

GO:0015385 (IBA, IMP): ACCEPT (core) as contributes_to; defects: PSEUDOCAP
WRONG_EVIDENCE_CODE CHECK and WRONG_QUALIFIER REPOINT; GO_CENTRAL
WRONG_QUALIFIER CHECK.
GO:0035725 (IBA, IMP): ACCEPT; IMP code flagged (CHECK).
GO:0008137 NADH dehydrogenase (ubiquinone) and GO:0042773 ATP synthesis
coupled electron transport (InterPro2GO IPR003918): REMOVE.
GO:1902600 proton transmembrane transport (GO_REF:0000108 from GO:0008137):
ACCEPT; true on its own grounds for an antiporter subunit.
GO:0005886 plasma membrane: ACCEPT; GO:0016020 membrane: MODIFY.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN001865541	GO:0015385 sodium:proton antiporter activity	2	16	GO:0015385, IMP, PMID:16030218	INDIRECT-PHENOTYPE	The abstract describes no PA1056 mutant; the evidence is a PA1054 disruption plus whole-cluster complementation of E. coli TO114. Right only as `contributes_to` (subunit of the antiporter complex). The IBD itself survives: an independent B. subtilis MrpD IMP seed supports it, and the bacterial node excludes the archaeal MBH subunits. The IBD qualifier should still be `contributes_to`.
PTN001865541	GO:0035725 sodium ion transmembrane transport	1 (sole)	16	GO:0035725, IMP, PMID:16030218	SOUND	As a subunit of the complex responsible for Na+ extrusion, PA1056 takes part in Na+ transmembrane transport; structural models couple MrpD protonation to Na+ transfer. The process fits the bacterial MrpD clade. Caveat: IMP looks like the wrong code for PA1056 (no mutant in the abstract); 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 PA1056 mutant, so the IMP evidence-code defects on PA1056 are CONFIRMED.