OprD (OccD1, protein D2, PA0958) is the archetypal member of the outer membrane carboxylate channel (Occ) family of Pseudomonas aeruginosa: an 18-stranded beta-barrel, substrate-specific channel in the outer membrane. It has a binding site for basic amino acids and lysine-containing peptides and mediates their uptake across the outer membrane; carbapenems such as imipenem and meropenem enter through the same channel, which is why loss of OprD is the commonest cause of carbapenem resistance in clinical isolates. A serine-protease activity has also been reported for the purified protein.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0008236 serine-type peptidase activity | IDA PMID:8843159 Protein D2 porin of the Pseudomonas aeruginosa outer membran... | KEEP AS NON CORE | Summary: UniProt IDA serine-type peptidase activity: purified D2 hydrolyses synthetic peptides, is inhibited and labelled by DFP; UniProt also lists active-site residues from a later mutagenesis paper. Reason: A measured, inhibitor-sensitive activity reported by one group; the channel function is the protein's established role and the physiological relevance of the protease activity is unknown. Supporting Evidence: PMID:8843159 purified protein D2 hydrolyzed several synthetic peptides according to the |
| GO:0009279 cell outer membrane | EXP PMID:2109575 Outer membrane protein D2 catalyzes facilitated diffusion of... | ACCEPT | Summary: UniProt EXP cell outer membrane. Reason: Purified from and functional in the outer membrane. Supporting Evidence: PMID:2109575 Protein D2 was purified and was shown |
| GO:0009279 cell outer membrane | EXP PMID:2118530 Protein D2 channel of the Pseudomonas aeruginosa outer membr... | ACCEPT | Summary: UniProt EXP cell outer membrane. Reason: Outer membrane channel. Supporting Evidence: PMID:2118530 Wild type cells transported tripeptide Thr-Ser-Lys into the |
| GO:0009279 cell outer membrane | IDA PMID:8012497 Two-dimensional polyacrylamide gel electrophoresis isolation... | ACCEPT | Summary: UniProt IDA cell outer membrane from 2-D gels of OM fractions. Reason: OprD identified in the OM fraction by N-terminal sequencing. Supporting Evidence: PMID:8012497 Outer membrane (OM) proteins of beta-lactam-susceptible and -resistant strains |
| GO:0009279 cell outer membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Cell outer membrane from UniProt subcellular location. Reason: Consistent with the experimental rows. Supporting Evidence: PMID:2118530 Wild type cells transported tripeptide Thr-Ser-Lys into the |
| GO:0015288 porin activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN002160747; this gene is one of three seeds and the one with direct experimental evidence. Reason: Sound: OprD is a well-characterised channel, and its own IDA is among the IBD's descendant evidence (expected self-appearance). Supporting Evidence: PMID:2118530 Wild type cells transported tripeptide Thr-Ser-Lys into the PMID:22272184 uptake of this antibiotic is only mediated by OccD1 and not by OccD2/D3 |
| GO:0015288 porin activity | IDA PMID:2118530 Protein D2 channel of the Pseudomonas aeruginosa outer membr... | ACCEPT | Summary: UniProt IDA porin activity: competitive inhibition of imipenem diffusion by basic amino acids and faster Thr-Ser-Lys uptake by D2+ cells. Reason: Core activity of this substrate-specific outer membrane channel. Supporting Evidence: PMID:2118530 Wild type cells transported tripeptide Thr-Ser-Lys into the PMID:2118530 L- and D-lysine were found |
| GO:0015288 porin activity | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO porin activity from the OprD family signature. Reason: Core activity of this substrate-specific outer membrane channel. Supporting Evidence: PMID:22272184 uptake of this antibiotic is only mediated by OccD1 and not by OccD2/D3 |
| GO:0015288 porin activity | IMP PMID:2120174 Outer membrane proteins responsible for the penetration of b... | ACCEPT | Summary: PseudoCAP IMP porin activity, one of the three PTN002160747 seed rows. The abstract reports mutants that lost four OM proteins (C, D2, E1, E2) together and concludes only that at least one of them is a porin. Reason: The claim is correct and well supported by other evidence on OprD, so the row is kept consistent with the other porin rows; the IMP evidence from this paper cannot attribute porin activity to OprD alone, recorded as a PseudoCAP CHECK defect. Supporting Evidence: PMID:2118530 Wild type cells transported tripeptide Thr-Ser-Lys into the PMID:2120174 decreased amounts of outer membrane proteins C, D2, E1, and E2 lowered the |
| GO:0015802 basic amino acid transport | IDA PMID:2118530 Protein D2 channel of the Pseudomonas aeruginosa outer membr... | MODIFY | Summary: UniProt IDA basic amino acid transport. Reason: Correct; the transport is across the outer membrane, so the specific term is basic amino acid transmembrane transport (GO:1990822), a descendant of this term. Proposed replacements: basic amino acid transmembrane transport Supporting Evidence: PMID:2118530 Wild type cells transported tripeptide Thr-Ser-Lys into the file:PSEAE/oprD/oprD-uniprot.txt Porin with a specificity for basic amino acids |
| GO:0016020 membrane | IEA GO_REF:0000002 | TOO GENERAL | Summary: Membrane from InterPro. Reason: Cell outer membrane (GO:0009279), accepted here, is_a membrane. |
| GO:0019867 outer membrane | IDA PMID:2120174 Outer membrane proteins responsible for the penetration of b... | TOO GENERAL | Summary: PseudoCAP IDA outer membrane from OM-protein profiles of the mutants. Reason: Cell outer membrane (GO:0009279), accepted here, is_a outer membrane. |
| GO:0055085 transmembrane transport | IEA GO_REF:0000108 | MODIFY | Summary: Transmembrane transport inferred from porin activity. Reason: Correct but general; the supported process is basic amino acid transmembrane transport (GO:1990822). Proposed replacements: basic amino acid transmembrane transport Supporting Evidence: PMID:2118530 Wild type cells transported tripeptide Thr-Ser-Lys into the |
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Download this section (compressed HTML)Q: Is the reported serine-protease activity of OprD intrinsic to the channel or due to a co-purifying protease, given that the structures show a classical channel barrel?
Experiment: Assay protease activity of OprD purified from a heterologous porin-deficient host, with and without mutation of the proposed catalytic residues, alongside channel conductance.
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