id: P22643 gene_symbol: dhlA product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:280 label: Xanthobacter autotrophicus description: >- DhlA is the haloalkane dehalogenase of Xanthobacter autotrophicus GJ10, an alpha/beta-hydrolase-fold enzyme that hydrolytically cleaves carbon-halogen bonds in short halogenated aliphatic compounds, giving the corresponding primary alcohol, a halide ion and a proton. It requires no cofactor and uses an Asp-His-Asp catalytic triad in which the aspartate attacks the substrate carbon directly to form a covalent alkyl-enzyme intermediate that is then hydrolysed, a mechanism established by crystallography of trapped intermediates. Specificity covers terminally mono- and di-chlorinated and brominated alkanes up to C4, with highest activity on 1,2-dichloroethane, 1,3-dichloropropane and 1,2-dibromoethane. It catalyses the first of four steps that let X. autotrophicus GJ10 grow on 1,2-dichloroethane, a high-volume commodity chemical used in vinyl chloride manufacture, as sole carbon source. DhlA belongs to the same structural superfamily as epoxide hydrolases, which share the alpha/beta-hydrolase fold and a comparable nucleophile-His-acid triad, and that shared fold is the source of a misleading family-based annotation on this entry. reference_proteome_assessments: - reference_proteomes: - UP001161920 - UP001603991 status: NO_SUPPORTED_COUNTERPART reviewed_on: '2026-10-19' reason: Retain P22643 as the primary Swiss-Prot accession. Both exact-taxon reference proteomes were searched as a deduplicated union. The leading alpha/beta-hydrolase hits are remote (about 25% global identity) and do not establish haloalkane dehalogenase identity or substrate specificity. The source is strain GJ10; no supported counterpart was identified in either reference proteome. evidence: - type: PROTEOME_SEARCH description: MMseqs2 searched 9,703 sequences across UP001161920, UP001603991 at E <= 1e-5 and sensitivity 7.5, returning 9 hits. Every returned sequence was globally aligned using BLOSUM62 with gap-open -10 and extension -0.5. Scores and sequences for all 9 returned candidates are retained, with 9 detailed alignment files. The heuristic search does not establish genomic absence or unique locus identity. supported_by: - reference_id: file:XANAU/dhlA/dhlA-record-evidence.yaml supporting_text: 'target_sequence_count: 9703' - reference_id: file:XANAU/dhlA/dhlA-record-evidence.yaml supporting_text: 'candidate_count: 9' - type: PROTEOME_MEMBERSHIP description: The primary accession is outside every searched exact-taxon reference proteome. supported_by: - reference_id: file:XANAU/dhlA/dhlA-record-evidence.yaml supporting_text: 'primary_in_any_reference_proteome: false' - type: RECORD_HISTORY description: 'Sampled UniSave observations: 14-OCT-2015, entry version 97.: no Proteomes cross-reference; 02-DEC-2020, entry version 110.: no Proteomes cross-reference; 27-NOV-2024, entry version 122.: 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:XANAU/dhlA/dhlA-record-evidence.yaml supporting_text: |- entry_date: 14-OCT-2015, entry version 97. proteomes: [] - reference_id: file:XANAU/dhlA/dhlA-record-evidence.yaml supporting_text: |- entry_date: 02-DEC-2020, entry version 110. proteomes: [] - reference_id: file:XANAU/dhlA/dhlA-record-evidence.yaml supporting_text: |- entry_date: 27-NOV-2024, entry version 122. proteomes: [] existing_annotations: - term: id: GO:0003824 label: catalytic activity evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: enables supporting_entities: - InterPro:IPR000639 review: summary: >- Root catalytic activity term from the epoxide hydrolase-like InterPro signature; the least informative possible molecular function statement. action: MARK_AS_OVER_ANNOTATED reason: >- GO:0003824 is the root of the molecular function catalytic branch and is an ancestor of the specific haloalkane dehalogenase activity already annotated. IPR000639 is the epoxide hydrolase-like signature, which matches because DhlA shares the alpha/beta-hydrolase fold; mapping it only to the root is the conservative and correct choice for a signature whose members span several reaction types, but it contributes nothing for a gene with a solved structure and mechanism. - term: id: GO:0004301 label: epoxide hydrolase activity evidence_type: IEA original_reference_id: GO_REF:0000118 qualifier: enables supporting_entities: - PANTHER:PTN000107240 review: summary: >- TreeGrafter propagation of epoxide hydrolase activity onto a haloalkane dehalogenase; a fold-level transfer to the wrong reaction. action: REMOVE reason: >- Epoxide hydrolases and haloalkane dehalogenases share the alpha/beta-hydrolase fold and an analogous nucleophile-His-acid triad, so they group together in sequence-based family trees, but they catalyse different reactions on different substrates: an epoxide hydrolase opens a strained C-O-C ring to a diol, whereas DhlA displaces a halide from a saturated carbon. DhlA's substrate range was mapped directly and consists of halogenated alkanes; no epoxide is reported as a substrate, and the enzyme's covalent alkyl-enzyme mechanism is specific to halide displacement. This is the same failure mode as the GO:0016810 annotation on AtzA: a structural signature predicting the superfamily's prevalent chemistry rather than the member's own. Where the PAINT or TreeGrafter node genuinely covers both activities, the fix belongs at the node, not on this gene. propagation_review: root_cause: PROPAGATION_BAD failure_modes: - FUNCTIONAL_DIVERGENCE - WRONG_ORTHOLOG_OR_PARALOG source_entities: - source_id: PANTHER:PTN000107240 source_label: PTN000107240 source_status: SUPPORTS_SOURCE_BUT_NOT_TARGET comment: >- The node is appropriate for alpha/beta-hydrolase-fold epoxide hydrolases, but DhlA's demonstrated reaction is hydrolytic dehalogenation of haloalkanes, a different chemistry on a different substrate class within the same fold. - term: id: GO:0018786 label: haloalkane dehalogenase activity evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: enables supporting_entities: - InterPro:IPR023489 - RHEA:19081 - RHEA:25185 - EC:3.8.1.5 - UniRule:UR000101351 review: summary: >- The correct specific activity, converged on by a dedicated InterPro signature, a Rhea exactMatch, EC and a UniRule. action: ACCEPT reason: >- RHEA:19081 (1-haloalkane + H2O = halide + primary alcohol) is an exactMatch of GO:0018786 and RHEA:25185 (the 1,2-dichloroethane reaction) is a narrowMatch of the same term, which is the correct arrangement: the specific reaction maps as a narrowMatch to a term defined over the substrate class, rather than being pushed up to an EC-level grouping class. This is the pattern the RHEA:25968 case on GO:0016616 should follow. The activity itself has been characterized structurally and mechanistically; as with tfdA and pcpB, no experimental annotation exists in GOA despite that. - term: id: GO:0019260 label: 1,2-dichloroethane catabolic process evidence_type: IEA original_reference_id: GO_REF:0000041 qualifier: involved_in supporting_entities: - UniPathway:UPA00265 review: summary: >- UniPathway-mapped process term; DhlA is step 1 of 4 in a pathway supporting growth on 1,2-dichloroethane. action: ACCEPT reason: >- X. autotrophicus GJ10 was isolated for growth on 1,2-dichloroethane as sole carbon source, and DhlA catalyses the committed first step, converting it to 2-chloroethanol en route to glycolate. The process annotation reflects the host's demonstrated catabolic capability rather than inference from the activity alone. core_functions: - description: >- DhlA hydrolyses the carbon-halogen bond of short halogenated alkanes without any cofactor, using an Asp nucleophile that forms a covalent alkyl-enzyme intermediate, to give the primary alcohol and halide. Acting on 1,2-dichloroethane it provides the entry step of the catabolic pathway that allows X. autotrophicus GJ10 to grow on this industrial chemical. molecular_function: id: GO:0018786 label: haloalkane dehalogenase activity directly_involved_in: - id: GO:0019260 label: 1,2-dichloroethane catabolic process knowledge_gaps: - gap_statement: >- The natural substrate from which DhlA's dehalogenase activity derives is undetermined, and it is unresolved whether the activity predates industrial haloalkanes or was recruited from a related alpha/beta-hydrolase activity on another substrate. boundary: >- The reaction, the covalent-intermediate mechanism, the catalytic triad and the substrate range (terminal mono- and di-halogenated alkanes up to C4, best on 1,2-dichloroethane, 1,3-dichloropropane, 1,2-dibromoethane) are all established structurally and kinetically. Naturally occurring short-chain haloalkanes do exist, notably from marine and soil sources, but have not been tested as substrates for this enzyme. gap_kind: - BIOLOGY significance: >- 1,2-dichloroethane is an industrial commodity chemical, so whether DhlA's activity is ancient or recent bears directly on how quickly a cofactor-independent hydrolase can be recruited to a new substrate. resolution: >- Kinetic comparison of DhlA against naturally occurring halomethanes and haloethanes alongside its industrial substrates, and phylogenetic dating of the dehalogenase clade within the alpha/beta-hydrolase superfamily. proposed_new_terms: [] suggested_questions: - question: >- Does the PANTHER node PTN000107240 genuinely cover both epoxide hydrolases and haloalkane dehalogenases, and if so should the epoxide hydrolase assertion be moved to a descendant node? The fix for this propagation belongs upstream, not as a per-gene removal. - question: >- How many other alpha/beta-hydrolase-fold enzymes carry epoxide hydrolase annotations by family inference alone? The fold is large and functionally heterogeneous, so this may be a recurring pattern rather than a single case. - question: >- Is there a natural haloalkane substrate for DhlA? Biogenic halomethanes and haloethanes are produced in marine and soil environments, which would make an ancient origin plausible. suggested_experiments: - description: >- Assay purified DhlA against biogenic short-chain haloalkanes (for example bromomethane, chloromethane, bromoethane) and against a panel of epoxides, to test both the ancestral-substrate hypothesis and the epoxide hydrolase annotation directly. experiment_type: enzyme kinetics hypothesis: >- DhlA turns over at least one biogenic haloalkane efficiently and shows no detectable epoxide hydrolase activity, supporting both an ancient dehalogenase function and removal of the propagated epoxide hydrolase term. references: - id: file:XANAU/dhlA/dhlA-record-evidence.yaml title: Compact archived record and sequence evidence for P22643 - id: GO_REF:0000002 title: Gene Ontology annotation through association of InterPro records with GO terms findings: [] - id: GO_REF:0000041 title: Gene Ontology annotation based on UniPathway vocabulary mapping findings: [] - id: GO_REF:0000118 title: TreeGrafter-generated GO annotations findings: [] - id: GO_REF:0000120 title: Combined Automated Annotation using Multiple IEA Methods findings: []