id: P0A434 gene_symbol: opd product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:293 label: Brevundimonas diminuta description: >- OPD (phosphotriesterase, PTE) is a binuclear Zn(2+) metallo-dependent hydrolase of the amidohydrolase superfamily that hydrolyses the triester linkage of organophosphate compounds, releasing an aryl alcohol from an aryl dialkyl phosphate. Its substrates are synthetic organophosphate insecticides and phosphorofluoridate nerve agents; UniProt records that every phosphate triester found to be a substrate is a synthetic compound and that no naturally occurring substrate is known. The enzyme hydrolyses the insecticide paraoxon at a rate approaching the diffusion limit, which is exceptional for a reaction on a compound first synthesized in the twentieth century, and it has no detectable activity on phosphate mono- or diesters and none as an esterase or protease. OPD is exported by the twin-arginine translocation (Tat) system and associates with the membrane as a peripheral protein after signal peptide processing. Homologues annotated as putative PTEs turn out to be proficient lactonases (PTE-like lactonases, PLLs) that hydrolyse quorum-sensing N-acyl homoserine lactones with only weak phosphotriesterase side activity, identifying the ancestral function from which OPD's paraoxonase activity was recruited. reference_proteome_assessments: - reference_proteomes: - UP000596117 status: NO_SUPPORTED_COUNTERPART reviewed_on: '2026-10-19' reason: Retain P0A434 as the primary Swiss-Prot accession. No significant reference-proteome hit was returned for the characterized parathion hydrolase from strain MG. Strain/accessory-genome differences are plausible context, but the search alone does not establish why UniProt omitted the proteome association or that the gene is absent from the species. evidence: - type: PROTEOME_SEARCH description: MMseqs2 searched 3,387 sequences across UP000596117 at E <= 1e-5 and sensitivity 7.5, returning 0 hits. The search table and candidate FASTA are empty; no alignments were generated. The heuristic search does not establish genomic absence or unique locus identity. supported_by: - reference_id: file:BREDI/opd/opd-record-evidence.yaml supporting_text: 'target_sequence_count: 3387' - reference_id: file:BREDI/opd/opd-record-evidence.yaml supporting_text: 'candidate_count: 0' - type: PROTEOME_MEMBERSHIP description: The primary accession is outside every searched exact-taxon reference proteome. supported_by: - reference_id: file:BREDI/opd/opd-record-evidence.yaml supporting_text: 'primary_in_any_reference_proteome: false' - type: RECORD_HISTORY description: 'Sampled UniSave observations: 11-NOV-2015, entry version 74.: no Proteomes cross-reference; 12-AUG-2020, entry version 93.: no Proteomes cross-reference; 27-NOV-2024, entry version 105.: no Proteomes cross-reference. These dated observations do not establish uninterrupted membership/absence, the exact change date, or UniProt''s motivation.' supported_by: - reference_id: file:BREDI/opd/opd-record-evidence.yaml supporting_text: |- entry_date: 11-NOV-2015, entry version 74. proteomes: [] - reference_id: file:BREDI/opd/opd-record-evidence.yaml supporting_text: |- entry_date: 12-AUG-2020, entry version 93. proteomes: [] - reference_id: file:BREDI/opd/opd-record-evidence.yaml supporting_text: |- entry_date: 27-NOV-2024, entry version 105. proteomes: [] - type: CURATION_CONTEXT description: The primary UniProt entry records plasmid origin. Reference-proteome membership at species or strain level does not ensure coverage of every accessory plasmid. supported_by: - reference_id: file:BREDI/opd/opd-record-evidence.yaml supporting_text: 'geneEncodingType: Plasmid' existing_annotations: - term: id: GO:0004063 label: aryldialkylphosphatase activity evidence_type: IDA original_reference_id: PMID:23574004 qualifier: enables review: summary: >- Direct annotation of the organophosphate-hydrolysing activity that defines this enzyme. action: ACCEPT reason: >- The cited study expressed OPD heterologously and showed hydrolysis of a range of organophosphate insecticides, consistent with the extensive earlier enzymology on paraoxon and nerve agents. Although the substrates are entirely synthetic, this activity is the enzyme's own, kinetically near-perfect function and is the right core molecular function. The evidence is a CACAO community annotation on a paper whose primary purpose is biocatalyst construction, which is worth noting: this gene is a case where the biocatalysis literature and the physiological literature are the same literature. supported_by: - reference_id: PMID:23574004 supporting_text: >- Organophosphate hydrolase (OPH), the product of an organophosphate-degrading (opd) gene cloned from Brevundimonas diminuta, hydrolyses the triester linkage found in neurotoxic organophosphate (OP) insecticides and nerve agents. - term: id: GO:0004063 label: aryldialkylphosphatase activity evidence_type: IEA original_reference_id: GO_REF:0000003 qualifier: enables supporting_entities: - EC:3.1.8.1 review: summary: EC-mapped IEA duplicating the experimentally supported activity. action: ACCEPT reason: >- EC 3.1.8.1 is an exactMatch of GO:0004063, so the mapping is sound and agrees with the IDA. It is redundant with the direct annotation but not misleading, and the EC entry itself rests on this enzyme's characterization. - term: id: GO:0005886 label: plasma membrane evidence_type: IDA original_reference_id: PMID:23574004 qualifier: part_of review: summary: >- Membrane association shown for the mature Tat-processed protein; the term is right, though the part_of qualifier would be better as located_in. action: ACCEPT reason: >- The localization finding is sound: the mature form was targeted to the membrane after Tat-dependent export, consistent with the experimentally confirmed signal peptide cleavage. The term is correct and is accepted. One caveat that no action in this vocabulary expresses: part_of asserts that the gene product is a constituent of the plasma membrane, whereas UniProt describes OPD as a peripheral membrane protein, for which located_in (as used by the parallel IEA row) is the better qualifier. A second caveat is that the experiment used OPD expressed in Pseudomonas sp. Ind01 rather than in B. diminuta, so this is strictly a heterologous-host localization. Both points are raised in suggested_questions rather than being forced into an annotation action. supported_by: - reference_id: PMID:23574004 supporting_text: >- The heterologously expressed OPH, which is a substrate of twin arginine transport (Tat) pathway, successfully targeted to the membrane of Pseudomonas sp. Ind01. - term: id: GO:0005886 label: plasma membrane evidence_type: IEA original_reference_id: GO_REF:0000044 qualifier: located_in supporting_entities: - UniProtKB-SubCell:SL-0039 review: summary: Keyword-mapped plasma membrane location with the correct qualifier. action: ACCEPT reason: >- This row uses located_in, which is appropriate for a peripheral membrane protein, and agrees with the Tat-export and membrane-targeting data and with the experimentally confirmed signal peptide cleavage site. - term: id: GO:0008270 label: zinc ion binding evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: enables supporting_entities: - InterPro:IPR001559 - InterPro:IPR017947 review: summary: Binuclear zinc centre, well established for this enzyme. action: ACCEPT reason: >- OPD binds two Zn(2+) ions per subunit, and the binuclear metal centre is the catalytic machinery that activates water for attack on the phosphorus. The InterPro phosphotriesterase signature prediction matches extensive direct metal-substitution and structural work on this protein. - term: id: GO:0016788 label: hydrolase activity, acting on ester bonds evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: enables supporting_entities: - InterPro:IPR017947 review: summary: >- Broad ester-hydrolase ancestor of the specific activity, and potentially misread as general esterase activity, which OPD lacks. action: MARK_AS_OVER_ANNOTATED reason: >- GO:0016788 is an ancestor of GO:0004063 via phosphoric triester hydrolase activity, so it is formally correct and redundant. It is worth flagging rather than simply accepting because OPD has no activity as an esterase in the colloquial sense, nor on phosphate mono- or diesters, and the broad term invites that reading. The specific term conveys the real specificity. core_functions: - description: >- OPD hydrolyses the triester linkage of synthetic organophosphates at a binuclear Zn(2+) centre, cleaving aryl dialkyl phosphates such as paraoxon to the dialkyl phosphate and aryl alcohol. Catalysis approaches the diffusion limit on paraoxon, and the enzyme reaches the periplasmic face of the membrane via the Tat pathway. molecular_function: id: GO:0004063 label: aryldialkylphosphatase activity locations: - id: GO:0005886 label: plasma membrane supported_by: - reference_id: PMID:23574004 supporting_text: >- Organophosphate hydrolase (OPH), the product of an organophosphate-degrading (opd) gene cloned from Brevundimonas diminuta, hydrolyses the triester linkage found in neurotoxic organophosphate (OP) insecticides and nerve agents. knowledge_gaps: - gap_statement: >- No naturally occurring substrate of OPD has been identified, so it is undetermined what, if anything, the enzyme hydrolyses in the absence of synthetic organophosphates. boundary: >- The substrate range among synthetic organophosphates and phosphorofluoridates is mapped in detail, paraoxon turnover approaches the diffusion limit, and activity on phosphate mono- and diesters, esters generally and peptides is absent. The PLL lactonase homologues identify N-acyl homoserine lactone hydrolysis as the likely progenitor activity, and OPD retains promiscuous lactonase activity. gap_kind: - BIOLOGY significance: >- OPD is the strongest known case of a near-catalytically-perfect enzyme for a substrate that has existed for under a century, so establishing whether it retains any native role bounds how fast such optimization happens. resolution: >- Quantitative comparison of OPD's lactonase activity against the PLL family's, and a search for an endogenous phosphotriester or lactone substrate in B. diminuta. proposed_new_terms: [] suggested_questions: - question: >- Does OPD retain enough lactonase activity to serve a quorum-sensing-related role in B. diminuta, or has the paraoxonase specialization abolished the ancestral function? The PLL work establishes the progenitor family but not the extent of trade-off in OPD itself. - question: >- How should GO handle an activity that is both the gene product's genuine, highly optimized function and defined entirely by man-made substrates? OPD sits at the opposite end of the spectrum from the benzil reductase case: the substrate is synthetic in both, but here the catalytic efficiency shows selection, not an assay artefact. - question: >- Is the part_of GO:0005886 qualifier on the CACAO annotation a systematic issue? A peripheral membrane protein localized by fractionation should be located_in, and the distinction matters for complex-membership inference. suggested_experiments: - description: >- Measure OPD's catalytic efficiency on a panel of N-acyl homoserine lactones and other lactones side by side with characterized PLL enzymes, and test whether an opd deletion in B. diminuta alters any lactone-dependent phenotype. experiment_type: enzyme kinetics and genetics hypothesis: >- OPD retains measurable but much reduced lactonase activity relative to PLLs, consistent with specialization onto organophosphates at the cost of the ancestral function. references: - id: file:BREDI/opd/opd-record-evidence.yaml title: Compact archived record and sequence evidence for P0A434 - id: GO_REF:0000002 title: Gene Ontology annotation through association of InterPro records with GO terms findings: [] - id: GO_REF:0000003 title: Gene Ontology annotation based on Enzyme Commission mapping findings: [] - id: GO_REF:0000044 title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt findings: [] - id: PMID:23574004 title: Expression and subcellular localization of organophosphate hydrolase in acephate-degrading Pseudomonas sp. strain Ind01 and its use as a potential biocatalyst for elimination of organophosphate insecticides. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: >- Correctly cited and it does support both the hydrolase activity and Tat-dependent membrane targeting, but its aim is constructing a biocatalyst, and the localization was done in a heterologous Pseudomonas host rather than in B. diminuta. Abstract-only in cache; quoted text is in the abstract. - id: PMID:17105187 title: The latent promiscuity of newly identified microbial lactonases is linked to a recently diverged phosphotriesterase. findings: [] reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Identifies the PTE-like lactonase (PLL) family and argues that PTE evolved from a PLL member by exploiting latent promiscuous paraoxonase activity. The key reference for the evolutionary framing, though it characterizes the homologues rather than this accession, so it is cited in the description and questions rather than as annotation support.