oprD (PP_1206) encodes a substrate-selective outer membrane porin of the OprD/Occ (TC 1.B.25) family in Pseudomonas putida KT2440. The protein is a monomeric beta-barrel channel located in the bacterial outer membrane that mediates the facilitated diffusion of small, charged solutes from the extracellular space into the periplasm. As the archetypal OccD-subfamily porin (the founding member historically named OprD/OccD1), it is associated with the uptake of basic amino acids (e.g., arginine, lysine) and related small molecules, contributing to nutrient scavenging across the low-permeability Pseudomonas outer membrane. In P. putida its expression is integrated into carbon/nitrogen status regulatory networks: transcription is induced under dual carbon-plus-nitrogen limitation, and the carbon-status response regulator CbrB binds the oprD promoter directly. Although annotated with an EC 3.4.21.- (serine peptidase) keyword inherited from the source EMBL record, there is no biochemical or structural support for a hydrolase/peptidase activity; the protein is a channel-forming porin, not an enzyme.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0015288 porin activity | IEA GO_REF:0000120 | ACCEPT | Summary: Channel/porin activity is the well-supported molecular function for this protein. It belongs to the outer membrane porin (Opr, TC 1.B.25) family / OprD-Occ superfamily of substrate-selective beta-barrel channels, and the InterPro/PANTHER and Pfam (PF03573 OprD) signatures are diagnostic. Porin activity is the correct, appropriately general molecular function. Reason: Family membership (OprD/Occ porin), Pfam PF03573, and the OprD-family literature establish that this is a channel-forming outer membrane porin. A more specific "wide pore channel activity" subtype is plausible but the parent porin activity term is well supported and is the core molecular function. |
| GO:0016020 membrane | IEA GO_REF:0000002 | MODIFY | Summary: Localization to a membrane is correct but uninformatively general. OprD/Occ-family porins are integral outer membrane beta-barrel proteins; the protein carries a cleaved N-terminal signal peptide (residues 1-23) consistent with Sec-dependent export and outer membrane insertion. The annotation should be refined to the bacterial outer membrane. Reason: The protein is an established OprD/Occ-family outer membrane porin; the generic "membrane" term under-specifies its known compartment. GO:0019867 (outer membrane) is the appropriate, evidence-consistent refinement. Proposed replacements: outer membrane |
| GO:0055085 transmembrane transport | IEA GO_REF:0000108 | ACCEPT | Summary: As a porin, this protein mediates diffusion of small solutes across the outer membrane, so participation in transmembrane transport is the correct biological process. This is a reasonable, appropriately general process term inferred logically from the porin molecular function. Reason: Porin activity entails movement of solutes across a membrane; transmembrane transport is the consistent and correct BP annotation. A more specific child (e.g., amino acid transmembrane transport) is plausible based on family-level substrate preference but is not directly demonstrated for PP_1206 itself, so the general term is retained. |
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Download this section (compressed HTML)Q: What is the precise substrate specificity of P. putida KT2440 OprD (PP_1206) - does it transport basic amino acids (arginine/lysine) and/or other small solutes, and with what selectivity, when assayed directly (e.g., single-channel electrophysiology or proteoliposome flux)?
Q: Does loss of PP_1206 produce a measurable growth or outer membrane permeability phenotype in P. putida, or is its function masked by redundancy within the large OprD/Occ porin repertoire of this organism?
Experiment: Construct a clean PP_1206 deletion mutant in P. putida KT2440 and assess growth on basic amino acids (arginine, lysine, histidine) as sole nitrogen/carbon source and outer membrane permeability, complementing in trans to confirm specificity.
Experiment: Purify OprD (PP_1206), reconstitute into planar lipid bilayers or proteoliposomes, and measure single-channel conductance and substrate-dependent flux/competition to define the channel's selectivity profile.
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