LolD (PA2987) is the ATP-binding cassette (nucleotide-binding) subunit of the LolCDE lipoprotein release complex of Pseudomonas aeruginosa, encoded between the two permease subunits PA2988 and PA2986. Two LolD subunits sit on the cytoplasmic face of the inner membrane and power the complex by ATP binding and hydrolysis. The purified P. aeruginosa LolCDE complex, reconstituted into proteoliposomes, extracts outer-membrane-specific lipoproteins from the inner membrane and hands them to the periplasmic chaperone LolA in an ATP-dependent manner, after which LolB inserts them into the outer membrane. P. aeruginosa LolCDE does not release lipoproteins carrying the Lys3-Ser4 inner-membrane retention signal, so it sets the lipoprotein sorting specificity of the organism.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005524 ATP binding | IEA GO_REF:0000002 | ACCEPT | Summary: ATP binding from ABC transporter nucleotide-binding domain signatures. Reason: LolD has the ABC nucleotide-binding domain with a Walker A P-loop, and release of lipoproteins by the reconstituted complex required ATP. Supporting Evidence: file:PSEAE/lolD/lolD-uniprot.txt PROSITE; PS50893; ABC_TRANSPORTER_2; 1. PMID:17350955 When incubated in the presence of ATP and a LolA homologue, the reconstituted LolCDE homologue released lipoproteins, leading to the formation of a LolA-lipoprotein complex. |
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | ACCEPT | Summary: IBA plasma membrane from a broad ABC ATPase node. Reason: LolD acts on the cytoplasmic face of the inner membrane as part of LolCDE, which was purified from membranes and reconstituted into proteoliposomes. Supporting Evidence: PMID:17350955 The LolCDE homologue thus purified was reconstituted into proteoliposomes with lipoproteins. |
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Inner membrane (peripheral) from the UniProt subcellular-location mapping. Reason: Same claim as the IBA row. Supporting Evidence: file:PSEAE/lolD/lolD-uniprot.txt Part of the ABC transporter complex LolCDE involved in the translocation of mature outer membrane-directed lipoproteins, from the inner membrane to the periplasmic chaperone, LolA. |
| GO:0016020 membrane | IEA GO_REF:0000002 | MODIFY | Summary: Generic membrane location. Reason: Correct but general; the specific location is the cytoplasmic (plasma) membrane, which the gene already carries (GO:0005886). Proposed replacements: plasma membrane Supporting Evidence: PMID:17350955 The LolCDE homologue thus purified was reconstituted into proteoliposomes with lipoproteins. |
| GO:0016887 ATP hydrolysis activity | IEA GO_REF:0000002 | ACCEPT | Summary: ATP hydrolysis from ABC transporter signatures. Reason: LolD is the ATPase subunit that energises lipoprotein release; release by the reconstituted P. aeruginosa complex depended on ATP. Supporting Evidence: file:PSEAE/lolD/lolD-uniprot.txt PROSITE; PS00211; ABC_TRANSPORTER_1; 1. PMID:17350955 When incubated in the presence of ATP and a LolA homologue, the reconstituted LolCDE homologue released lipoproteins, leading to the formation of a LolA-lipoprotein complex. |
| GO:0022857 transmembrane transporter activity | IBA GO_REF:0000033 | MODIFY | Summary: IBA transmembrane transporter activity from the deep ABC ATPase node PTN000655654, seeded only by M. tuberculosis Rv2688c (P9WQL7, a fluoroquinolone efflux ATPase). Reason: LolCDE does not move its substrate across a membrane; it extracts lipoproteins from the outer leaflet of the inner membrane and transfers them to LolA in the periplasm. GO models this as GO:0140306 lipoprotein releasing activity, which is_a transporter activity but not transmembrane transporter activity, and which E. coli LolD carries by IDA. The transporter essence holds; the transmembrane part does not fit the LolD subclade. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: FUNCTIONAL DIVERGENCE GRANULARITY MISMATCH Sources checked: PANTHER:PTN000655654 · PTN000655654 SUPPORTS SOURCE BUT NOT TARGET Deep ABC ATPase node spanning importers, exporters and type VII (MacB/LolD/FtsE-like) machines. Transmembrane transport suits its classical transporter members but not the LolD clade, whose complex releases lipoproteins to a periplasmic chaperone. UniProtKB:P9WQL7 · M. tuberculosis Rv2688c SUPPORTS SOURCE BUT NOT TARGET Fluoroquinolone efflux ATPase; a genuine transporter, but functionally distant from LolD. Proposed replacements: lipoprotein releasing activity Supporting Evidence: PMID:17350955 When incubated in the presence of ATP and a LolA homologue, the reconstituted LolCDE homologue released lipoproteins, leading to the formation of a LolA-lipoprotein complex. |
| GO:0044873 lipoprotein localization to membrane | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro2GO lipoprotein localization to membrane. Reason: True but uninformative; GO:0044874 lipoprotein localization to outer membrane, accepted in this review, is an is_a descendant of GO:0044873. |
| GO:0044874 lipoprotein localization to outer membrane | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN000656700 (LolD clade, 2 seeds, 15 leaf IBAs). Seeds are E. coli LolD (P75957, IDA PMID:17509078 and IMP PMID:10783239) and LolD itself (PseudoCAP IDA, PMID:17350955). Reason: The node term suits a LolD clade, LolD has its own reconstitution evidence, and the IBD stands on E. coli LolD alone. This node is distinct from the permease node PTN002524722 recorded on PA2988. Supporting Evidence: PMID:17350955 These results indicate that Lol proteins are responsible for the sorting of lipoproteins to the outer membrane of P. aeruginosa |
| GO:0044874 lipoprotein localization to outer membrane | IDA PMID:17350955 Characterization of the Pseudomonas aeruginosa Lol system as... | ACCEPT | Summary: PseudoCAP IDA, the PTN000656700 seed row. Purified P. aeruginosa LolCDE released lipoproteins to LolA in an ATP-dependent reconstitution assay, and LolB then incorporated them into outer membranes. Reason: Seed verdict SOUND. Direct biochemical evidence on the complex that contains LolD; the ATP dependence is LolD's contribution. Supporting Evidence: PMID:17350955 When incubated in the presence of ATP and a LolA homologue, the reconstituted LolCDE homologue released lipoproteins, leading to the formation of a LolA-lipoprotein complex. |
| GO:0044874 lipoprotein localization to outer membrane | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA lipoprotein localization to outer membrane. Reason: Same claim as the IDA row. Supporting Evidence: PMID:17350955 These results indicate that Lol proteins are responsible for the sorting of lipoproteins to the outer membrane of P. aeruginosa |
| GO:0055085 transmembrane transport | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: IBA transmembrane transport from the deep ABC ATPase node PTN000655654 (seeds E. coli NikD, YejF and M. tuberculosis Rv2688c). Reason: The lipoproteins handled by LolCDE are not carried across the inner membrane; they are lifted out of its outer leaflet and passed to LolA. Transmembrane transport is true of the classical importers and exporters that seed this deep node but is an over-propagation to the LolD clade. The specific process is captured by GO:0044874. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN000655654 · PTN000655654 SUPPORTS SOURCE BUT NOT TARGET Deep ABC ATPase node; transmembrane transport fits its transporter members but not the lipoprotein-release LolD clade. UniProtKB:P33593 · E. coli NikD SUPPORTS SOURCE BUT NOT TARGET Nickel importer ATPase. UniProtKB:P33916 · E. coli YejF SUPPORTS SOURCE BUT NOT TARGET Peptide importer ATPase. UniProtKB:P9WQL7 · M. tuberculosis Rv2688c SUPPORTS SOURCE BUT NOT TARGET Fluoroquinolone efflux ATPase. Supporting Evidence: PMID:17350955 When incubated in the presence of ATP and a LolA homologue, the reconstituted LolCDE homologue released lipoproteins, leading to the formation of a LolA-lipoprotein complex. |
| GO:0089705 protein localization to outer membrane | IBA GO_REF:0000033 | ACCEPT | Summary: IBA protein localization to outer membrane from the LolD clade node. Reason: Lipoproteins are proteins sent to the outer membrane by LolCDE-LolA-LolB. GO:0089705 is not an ancestor of GO:0044874 in the current ontology, so it adds the protein-localization view of the same step. E. coli LolD carries it by IDA. Supporting Evidence: PMID:17350955 Lipoproteins were then incorporated into the outer membrane depending on a LolB homologue. |
| GO:0089705 protein localization to outer membrane | IDA PMID:17350955 Characterization of the Pseudomonas aeruginosa Lol system as... | ACCEPT | Summary: PseudoCAP IDA protein localization to outer membrane (also a PTN000656700 seed term). Reason: Seed verdict SOUND, on the same reconstitution evidence as GO:0044874. Supporting Evidence: PMID:17350955 Lipoproteins were then incorporated into the outer membrane depending on a LolB homologue. |
| GO:0089705 protein localization to outer membrane | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA protein localization to outer membrane. Reason: Same claim as the IDA row. Supporting Evidence: PMID:17350955 Lipoproteins were then incorporated into the outer membrane depending on a LolB homologue. |
| GO:0140306 lipoprotein releasing activity | IDA PMID:17350955 Characterization of the Pseudomonas aeruginosa Lol system as... | NEW | Summary: Proposed molecular function. The reconstituted P. aeruginosa LolCDE complex, which includes LolD, releases lipoproteins from the membrane to LolA in an ATP-dependent manner, the activity GO:0140306 describes. E. coli LolD carries this term by IDA and IMP, and the permease PA2988 review proposes the same term. Reason: The gene's only specific molecular function annotation is generic ATP hydrolysis; the release activity is that of LolCDE as a whole, as for the E. coli subunits. Supporting Evidence: PMID:17350955 When incubated in the presence of ATP and a LolA homologue, the reconstituted LolCDE homologue released lipoproteins, leading to the formation of a LolA-lipoprotein complex. |
| GO:0043190 ATP-binding cassette (ABC) transporter complex | IDA PMID:17350955 Characterization of the Pseudomonas aeruginosa Lol system as... | NEW | Summary: Proposed complex membership. LolD was purified as the ATPase subunit of the P. aeruginosa LolCDE homologue; E. coli LolD carries this term (ComplexPortal IPI), and the permease PA2988 review uses it. Reason: No complex term is annotated to LolD; LolCDE is an ABC transporter-family complex of two LolD ATPases and the LolC and LolE permeases. Supporting Evidence: PMID:17350955 The LolCDE homologue thus purified was reconstituted into proteoliposomes with lipoproteins. |
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