PA1810 (OppB, 615 aa) is one of two periplasmic solute-binding proteins (bacterial solute-binding protein family 5, SBP_bac_5 / Peptide/Ni-binding) of the Opp oligopeptide ABC importer encoded by the oppABCDE-fabI operon (PA1811-PA1806). It carries an N-terminal signal peptide and acts in the periplasm with its paralogue OppA (PA1811, about 42% identical); OppC and OppD form the membrane permease and OppE the ATPase. Defined oppB mutants are highly resistant to the uridyl peptide antibiotic pacidamycin, and opp mutants take up less of the dipeptide Phe-Arg-beta-naphthylamide. Neither binding protein can substitute for the other, which suggests that OppA and OppB act together, possibly as a heteromeric binding protein. The operon is also needed for uptake of the tripeptide herbicide bialaphos. The natural peptide substrates have not been defined.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0006857 oligopeptide transport | IMP PMID:23979749 High-level pacidamycin resistance in Pseudomonas aeruginosa ... | ACCEPT | Summary: PseudoCAP IMP and one of the seven seeds of the PTN008624512 IBD (peptide transport). The full text shows that the transposon insertion in mutant PAM1194 (pacidamycin resistant, reduced PAbetaN uptake) maps to oppB, and that an unmarked deletion of oppB (PAO1284) is highly pacidamycin resistant even though it still expresses OppA. The binding protein of an ABC importer captures the substrate and delivers it to the permease, so it takes part in the transport step itself; the phenotype is not an indirect one. Reason: Sound seed. The full text shows that the oppB gene product is required for uptake of a peptide antibiotic through the Opp importer and that the Opp system transports a dipeptide substrate. As a periplasmic binding protein, PA1810 is a direct participant. Supporting Evidence: PMID:23979749 This mutant analysis also indicated that both OppA and OppB periplasmic binding proteins were required for pacidamycin uptake and that they cannot compensate for each other. PMID:23979749 The Opp system was shown to be a bona fide oligopeptide transport system by demonstrating that transport of PAΞ²N is impaired in opp mutants. |
| GO:0015833 peptide transport | IBA GO_REF:0000033 | TOO GENERAL | Summary: IBA from the PTN008624512 IBD (peptide transport), seeded by E. coli OppA, DppA, YejA, GsiB and MppA (EcoCyc IDA/EXP/IMP) and by the two P. aeruginosa Opp binding proteins (PseudoCAP IMP). PA1810 appearing in its own WITH/FROM is expected. The node term is a sound clade-level claim for SBP family 5 binding proteins, and it stands on the E. coli seeds alone. Reason: True, but GO:0006857 oligopeptide transport (is_a GO:0015833), accepted on the IMP row, already entails it. The phylogenetic inference itself is not disputed. Supporting Evidence: PMID:23979749 The Opp system was shown to be a bona fide oligopeptide transport system by demonstrating that transport of PAΞ²N is impaired in opp mutants. |
| GO:0030288 outer membrane-bounded periplasmic space | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN008624519, seeded by E. coli YejA (periplasm, IDA). PA1810 has a SignalP-predicted signal peptide and the paper describes OppA and OppB as periplasmic binding proteins of a Gram-negative ABC importer, where SBP family 5 members act. Reason: Signal peptide plus SBP family membership in a diderm bacterium place the protein in the periplasm, where substrate capture happens. Supporting Evidence: PMID:23979749 The first two genes, oppA and oppB , whose coding sequences overlap, contain type I signal peptides; thus, they are probably periplasmic binding proteins. file:PSEAE/PA1810/PA1810-uniprot.txt PF00496; SBP_bac_5 |
| GO:0042597 periplasmic space | IEA GO_REF:0000120 | TOO GENERAL | Summary: Electronic periplasm assignment. Correct, and the more specific GO:0030288 outer membrane-bounded periplasmic space is accepted above. Reason: GO:0030288 (is_a GO:0042597), accepted on the IBA row, entails this term. |
| GO:0042884 microcin transport | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: IBA from PTN008624519, seeded only by E. coli YejA, the binding protein of the YejABEF importer that takes up microcin C. Microcins are ribosomally made peptide antibiotics of enteric bacteria. No microcin uptake has been reported for P. aeruginosa Opp. Its known substrates are pacidamycin (a non-ribosomal uridyl peptide), PAbetaN and bialaphos. Reason: The substrate specificity of one E. coli binding protein is pushed to a subnode that includes the P. aeruginosa Opp binding proteins, which have no microcin data. Substrate specificity varies among SBP family 5 members, so it does not transfer reliably. The broader oligopeptide transport claim is what the evidence supports. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN008624519 Β· PTN008624519 SUPPORTS SOURCE BUT NOT TARGET Microcin C import is a YejA-specific substrate specificity; it does not extend to the P. aeruginosa OppA/OppB binding proteins. UniProtKB:P33913 Β· E. coli YejA (IMP/IDA PMID:17873039) SUPPORTS SOURCE BUT NOT TARGET Sound for YejA itself. Supporting Evidence: PMID:23979749 The Opp system was shown to be a bona fide oligopeptide transport system by demonstrating that transport of PAΞ²N is impaired in opp mutants. |
| GO:0043190 ATP-binding cassette (ABC) transporter complex | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO from the Peptide/Ni-binding SBP signature. PA1810 is the binding-protein subunit of the OppABCDE ABC importer, which includes the membrane components OppC and OppD and the ATPase OppE. Reason: The binding protein is a component of the binding protein-dependent Opp ABC transporter. Both binding proteins are needed for function. Supporting Evidence: PMID:23979749 indicative of an oligomeric binding protein requiring both OppA and OppB subunits |
| GO:0055085 transmembrane transport | IEA GO_REF:0000002 | MODIFY | Summary: Generic InterPro2GO process term. Correct but uninformative. The Opp system imports oligopeptides across the inner membrane. Reason: The evidence supports GO:0035672 oligopeptide transmembrane transport (is_a GO:0055085 and is_a GO:0006857), the specific descendant. Proposed replacements: oligopeptide transmembrane transport Supporting Evidence: PMID:23979749 These results are consistent with the notion that the Opp system is required for uptake of pacidamycin across the inner membrane |
| GO:1904680 peptide transmembrane transporter activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN008624512, seeded by M. tuberculosis OppA (MTBBASE IDA). By GO convention the transporter activity of a binding protein-dependent ABC importer is annotated to its subunits, including the periplasmic binding protein, which captures the substrate for the permease. Reason: Consistent with the Opp mutant data for P. aeruginosa and with the family-level evidence. PA1810 contributes peptide recognition to the importer's transmembrane transporter activity. Supporting Evidence: PMID:23979749 This mutant analysis also indicated that both OppA and OppB periplasmic binding proteins were required for pacidamycin uptake and that they cannot compensate for each other. |
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Download this section (compressed HTML)Q: Do OppA (PA1811) and OppB (PA1810) form a heteromeric binding protein, and which natural peptides (length, sequence) does each bind?
Experiment: Purify OppA and OppB and measure binding of a peptide library and of pacidamycin by ITC or thermal shift, alone and mixed, to test whether binding needs both proteins.
Type: biochemical binding assay
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