PA1056 encodes subunit D (ShaD/MrpD) of the Sha (Mrp/Mnh/Pha) multisubunit Na+/H+ antiporter of Pseudomonas aeruginosa PAO1. It is a 499-residue integral membrane protein with 14 predicted transmembrane helices, in the CPA3 subunit D family, homologous to the antiporter-like NuoM and NuoN subunits of respiratory complex I. It is the third gene of the six-gene sha cluster PA1054-PA1059, in which shaA and shaB are fused. The cluster restores Na+ tolerance and Na+/H+ antiport to an E. coli strain lacking its major antiporters, and in P. aeruginosa the Sha antiporter is largely responsible for Na+ extrusion and supports virulence in mouse infection models. In Bacillus Mrp antiporters, MrpD is needed for Na+ tolerance and for assembly of the complex, and with MrpA it is proposed to carry the proton-translocating part of the antiport cycle. Antiport needs the hetero-oligomeric complex of all subunits.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Subcellular location mapping (cell membrane, multi-pass). PA1056 has 14 predicted TM helices and is a subunit of an inner-membrane Na+/H+ antiporter complex. Reason: Correct location for a subunit of the Na+-extruding membrane complex. Supporting Evidence: file:PSEAE/PA1056/PA1056-uniprot.txt TRANSMEM 6..24 PMID:16030218 genes PA1054 to PA1059 encode a Na+/H+ antiporter that is largely responsible for Na+ extrusion in P. aeruginosa |
| GO:0008137 NADH dehydrogenase (ubiquinone) activity | IEA GO_REF:0000002 | REMOVE | Summary: InterPro2GO from IPR003918 (NADH:quinone oxidoreductase membrane subunit), a signature shared by complex I NuoM/NuoN and by Mrp antiporter subunit D. PA1056 is ShaD of the Sha Na+/H+ antiporter; the sha cluster has no NADH-oxidizing or quinone-reducing subunits. Reason: Demonstrably wrong electronic mapping for this protein. PA1056 belongs to the CPA3 antiporter subunit D family and the six-gene cluster it is part of is a Na+/H+ antiporter, not a complex I. Homology to NuoM/NuoN does not confer NADH dehydrogenase activity on a subunit that lacks the peripheral redox arm. Supporting Evidence: file:PSEAE/PA1056/PA1056-uniprot.txt IPR050586; CPA3_Na-H_Antiporter_D PMID:16030218 genes PA1054 to PA1059 encode a Na+/H+ antiporter that is largely responsible for Na+ extrusion in P. aeruginosa PMID:29218041 MrpA has the closest homology to the NuoL subunit of complex I and MrpD has the closest homology to complex I NuoM and NuoN subunits. |
| GO:0015385 sodium:proton antiporter activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN001865541, the Eubacteria node of PTHR42703 (16 reference leaves), seeded by B. subtilis MrpD (O05229, IMP) and by the PseudoCAP IMP row for this gene. PA1056 is ShaD of the Sha antiporter. The activity belongs to the hetero-oligomeric complex, so a subunit contributes to it. The archaeal MBH/MBX subunit-H proteins of the family sit outside this node. Reason: Core activity of the complex this protein belongs to; kept, with the qualifier corrected to contributes_to (GO_CENTRAL defect below). Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN001865541 · PTN001865541 SUPPORTS TRANSFER Bacterial MrpD clade; right as a contribution to complex activity. MBH hydrogenase subunits are outside the node. Minor caveat: a Leptospira leaf named formate hydrogenase subunit B. UniProtKB:O05229 · B. subtilis MrpD SUPPORTS TRANSFER Independent experimental seed: B. subtilis mrpD deletion is Na+ sensitive and complemented in trans by MrpD. UniProtKB:Q9I4R8 · PA1056 (shaD) SOURCE WEAK OR INFERRED PseudoCAP IMP, but the PMID:16030218 abstract reports a disruption of PA1054 only. The cluster-level complementation supports a contribution by the complex; an IMP for this gene is not shown in the abstract. Supporting Evidence: PMID:16030218 The gene cluster PA1054 to PA1059, but not the cluster with a deletion of PA1054, complemented a growth defect in the presence of 0.2 M NaCl and a defect in Na+/H+ antiport activity of the Escherichia coli TO114 mutant lacking the three major Na+/H+ antiporters PMID:21236240 Deletion of either mrpA or mrpD from the Bacillus subtilis chromosome resulted in a Na+ and pH sensitive growth phenotype. PMID:29218041 In previous studies, none of the Mrp antiporters exhibited antiport activity with MrpA or MrpD alone. file:PSEAE/PA1056/PA1056-bioinformatics/RESULTS.md PTN001865541 is not the family root. |
| GO:0015385 sodium:proton antiporter activity | IMP PMID:16030218 Characterization of a multigene-encoded sodium/hydrogen anti... | ACCEPT | Summary: PseudoCAP IMP, one of two seeds of the PTN001865541 antiporter IBD. The paper shows antiport for the whole PA1054-PA1059 cluster, lost when PA1054 is deleted, and reports a P. aeruginosa disruption of PA1054 only. The abstract describes no PA1056 mutant, and the full text (read 2026-11-05) confirms none was made, so a mutant-phenotype code is wrong for PA1056. PA1056 is a subunit of the antiporter complex. Reason: PA1056 is part of the Na+/H+ antiporter, so the claim is kept as the core activity. It is a contribution (contributes_to), and the evidence is cluster-level, with no PA1056 mutant in the paper (full text checked). Both are flagged to PseudoCAP. Supporting Evidence: PMID:16030218 The gene cluster PA1054 to PA1059, but not the cluster with a deletion of PA1054, complemented a growth defect in the presence of 0.2 M NaCl and a defect in Na+/H+ antiport activity of the Escherichia coli TO114 mutant lacking the three major Na+/H+ antiporters PMID:20624916 Antiport activity requires hetero-oligomeric complexes of all six or seven hydrophobic Mrp proteins (MrpA-MrpG). |
| GO:0016020 membrane | IEA GO_REF:0000044 | MODIFY | Summary: Generic membrane location from the subcellular location mapping. Reason: True but general; GO:0005886 plasma membrane (already on this gene) is the supported location. Proposed replacements: plasma membrane Supporting Evidence: file:PSEAE/PA1056/PA1056-uniprot.txt TRANSMEM 6..24 |
| GO:0035725 sodium ion transmembrane transport | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN001865541 (bacterial MrpD clade), sole-seeded by the PseudoCAP IMP row. MrpD-type subunits take part in Na+ translocation by the Mrp complex. The term suits the clade. Reason: Core process of the Sha complex in which this subunit participates; structural models couple proton binding at MrpD to Na+ transfer. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN001865541 · PTN001865541 SUPPORTS TRANSFER Na+ transmembrane transport fits bacterial MrpD subunits of Mrp antiporters. UniProtKB:Q9I4R8 · PA1056 (shaD) SOURCE WEAK OR INFERRED Sole seed; process supported by cluster-level evidence, but the IMP code looks wrong for PA1056 (see the IMP row). Supporting Evidence: PMID:16030218 genes PA1054 to PA1059 encode a Na+/H+ antiporter that is largely responsible for Na+ extrusion in P. aeruginosa PMID:36241630 Binding of the first proton to the Lys/Glu pair of MrpD drives the transfer of sodium bound at SLS1 |
| GO:0035725 sodium ion transmembrane transport | IMP PMID:16030218 Characterization of a multigene-encoded sodium/hydrogen anti... | ACCEPT | Summary: PseudoCAP IMP, the sole seed of the PTN001865541 Na+ transport IBD. The Sha cluster is responsible for Na+ efflux, and PA1056 is one of its subunits. The IMP code looks wrong for PA1056 (no PA1056 mutant in the abstract). Reason: Process correct for this subunit of the Na+-extruding complex; evidence code flagged. Supporting Evidence: PMID:16030218 genes PA1054 to PA1059 encode a Na+/H+ antiporter that is largely responsible for Na+ extrusion in P. aeruginosa |
| GO:0042773 ATP synthesis coupled electron transport | IEA GO_REF:0000002 | REMOVE | Summary: InterPro2GO from IPR003918, the complex I membrane-subunit signature shared with Mrp subunit D. PA1056 is a Na+/H+ antiporter subunit, not a respiratory chain component. Reason: Demonstrably wrong electronic mapping for this protein: the sha cluster encodes a secondary Na+/H+ antiporter with no electron-transfer subunits, so PA1056 takes no part in respiratory electron transport. Supporting Evidence: PMID:16030218 genes PA1054 to PA1059 encode a Na+/H+ antiporter that is largely responsible for Na+ extrusion in P. aeruginosa file:PSEAE/PA1056/PA1056-uniprot.txt IPR050586; CPA3_Na-H_Antiporter_D |
| GO:1902600 proton transmembrane transport | IEA GO_REF:0000108 | ACCEPT | Summary: Inferred by GO logic from the (wrong) NADH dehydrogenase (ubiquinone) IEA. The claim stands on other grounds: Na+/H+ antiport moves H+ across the membrane, and MrpD is proposed to form part of the proton-translocating machinery of the Mrp complex. Reason: True for a subunit of a Na+/H+ antiporter, independent of the faulty source annotation; H+ movement is half of the core transport cycle. Supporting Evidence: PMID:21236240 Presumably, MrpA transports Na+ whereas MrpD transports H+ in opposite directions, resulting in antiporter activity. PMID:36241630 Steiner and Sazanov propose that trans-membrane proton transfer is carried out by the MrpA and MrpD subunits |
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Download this section (compressed HTML)Q: Should GO provide a cellular component term for the Mrp-type multisubunit Na+/H+ antiporter complex, by analogy with GO:1903103 potassium:proton antiporter complex, so that Sha/Mrp subunits can be annotated to the complex instead of each carrying the activity?
Q: Should the InterPro2GO mapping of IPR003918 to NADH dehydrogenase (ubiquinone) activity be restricted so it does not reach Mrp antiporter subunit D proteins (IPR050586)?
Experiment: Make an in-frame PA1056 (shaD) deletion in P. aeruginosa, then measure Na+ tolerance, Na+ efflux and Sha complex assembly (BN-PAGE), with complementation in trans; mutate the conserved MrpD Lys/Glu pair to test its role in the coupled H+ and Na+ movements.
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