LinA is the gamma-hexachlorocyclohexane (lindane) dehydrochlorinase of Sphingobium indicum UT26, a small cofactor-independent lyase that defines its own family (HCH dehydrochlorinase) with a scytalone dehydratase-like fold. It catalyses two successive 1,2-anti dehydrochlorinations, converting gamma-HCH to gamma-pentachlorocyclohexene and then to 1,3,4,6-tetrachloro-1,4-cyclohexadiene, releasing chloride at each step and requiring no metal or redox cofactor. The reaction demands a 1,2-biaxial H-Cl pair on the substrate ring, which explains why LinA acts on the alpha, gamma and delta isomers of HCH but not on the beta isomer, whose substituents are all equatorial. LinA initiates the pathway that allows UT26 to grow on lindane, a persistent organochlorine insecticide used worldwide since the 1940s, as sole carbon and energy source. The protein is found in the periplasm without N-terminal processing, by an export route that has not been identified.
Definition: Catalysis of the reaction: gamma-hexachlorocyclohexane = (3R,4S,5S,6R)-pentachlorocyclohexene + chloride + H+. The enzyme eliminates HCl across a 1,2-biaxial hydrogen-chlorine pair and requires no cofactor, and also dehydrochlorinates the resulting pentachlorocyclohexene to 1,3,4,6-tetrachlorocyclohexa-1,4-diene.
Justification: This restores GO:0018830, obsoleted in the bulk action of go-ontology#28108 with the comment "there is no evidence that this specific activity exists". The activity is in fact well characterized: LinA from Sphingobium indicum UT26 has been studied by Tn5 mutagenesis, in vitro complementation, GC-MS, NMR and CD, and its stereochemical requirements are defined. The bulk criteria selected terms with no annotations and no Rhea mapping, which at the time was true of this term but reflected curation coverage, not absence of evidence; UniProt now maps the reaction to RHEA:45480, which has no GO term. Without it, a well-studied enzyme has no molecular function annotation. Should be placed under GO:0016848 carbon-halide lyase activity, beside the surviving sibling GO:0018833 DDT-dehydrochlorinase activity.
Parent term: carbon-halide lyase activity
Mappings:
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0018919 gamma-1,2,3,4,5,6-hexachlorocyclohexane catabolic process | IDA PMID:7686793 Isolation and characterization of Tn5-induced mutants of Pse... | ACCEPT | Summary: Tn5 mutants mapping to linA lose gamma-HCH degradation, and purified LinA restores both pathway steps in vitro. Reason: Two independent Tn5 insertions in linA abolished or crippled gamma-HCH degradation in a host that grows on lindane as sole carbon and energy source, and in vitro complementation of the null mutant's extract with partially purified LinA restored both the first and second steps. The evidence is mutant-based, so IMP would fit better than IDA, but the process assignment itself is well supported. Supporting Evidence: PMID:7686793 An in vitro complementation test with a crude extract from UT64 plus partially purified LinA protein showed that LinA was essential not only for the first-step reaction (gamma-HCH to gamma-pentachloro-cyclohexene; gamma-PCCH), but also for the second-step reaction (gamma-PCCH to compound B) of gamma-HCH degradation in UT26. |
| GO:0042597 periplasmic space | IEA GO_REF:0000044 | ACCEPT | Summary: Keyword-mapped periplasm, resting on a direct localization study, though the export mechanism is unexplained. Reason: UniProt's periplasm assignment carries experimental evidence (ECO:0000269) from a dedicated localization study, not a sequence prediction, which is notable because LinA has no cleaved signal peptide and the export route remains unknown. The keyword-to-GO mapping therefore transmits a real finding here rather than a prediction. |
| GO:0016848 carbon-halide lyase activity | IDA PMID:11099497 Reaction mechanism and stereochemistry of gamma-hexachlorocy... | NEW | Summary: Proposed annotation to fill a gap left by the bulk obsoletion of the specific term: LinA currently has no molecular function annotation at all. Reason: GOA carries no MF annotation for LinA. The specific term GO:0018830 gamma-hexachlorocyclohexane dehydrochlorinase activity was obsoleted in the bulk action of go-ontology#28108, whose stated criteria were leaf catalytic terms with a partial EC xref, zero annotations, no RHEA xref and no MetaCyc/KEGG xref, and whose obsoletion comment reads "there is no evidence that this specific activity exists". For this term that conclusion was incorrect: the activity has been characterized by GC-MS, NMR and CD, its stereochemical requirement for a 1,2-biaxial H-Cl pair is established, and UniProt now records the reaction as RHEA:45480. The term was swept up because it had no annotations and no Rhea mapping at the time, which is a reflection of curation coverage rather than of the biology. GO:0016848 carbon-halide lyase activity is the correct live ancestor and is proposed here as an interim annotation; the specific term should be restored (see proposed_new_terms). The sibling term GO:0018833 DDT-dehydrochlorinase activity survived the same bulk action because it had an EC number and a Rhea mapping. No proposed_replacement_terms are listed on this row because a NEW annotation replaces nothing; the request to restore GO:0018830 is carried by the proposed_new_terms entry below and by core_functions.proposed_molecular_function. Supporting Evidence: PMID:11099497 LinA requires the presence of a 1,2-biaxial HCl pair on a substrate molecule. PMID:11099497 delta-PCCH was detected as the only product of dehydrochlorination of delta-HCH. |
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Download this section (compressed HTML)Q: How many other terms from the go-ontology#28108 bulk obsoletion describe activities that are in fact well characterized? The selection criteria (no annotations, no Rhea xref) correlate with curation coverage rather than with evidence, and LinA shows the two can diverge.
Q: Is there a naturally occurring polychlorinated alicyclic substrate for LinA? The enzyme needs no cofactor and only a 1,2-biaxial H-Cl pair, which is a permissive requirement.
Q: How is LinA exported to the periplasm without N-terminal processing?
Experiment: Audit the 160 terms obsoleted in go-ontology#28108 against current UniProt catalytic activity records and Rhea mappings, listing those that now have experimental evidence or a Rhea reaction and therefore may need restoring.
Hypothesis: A minority of the bulk-obsoleted terms describe genuinely characterized activities that were unannotated at the time, and LinA is not the only case.
Type: curation audit
Experiment: Assay purified LinA against naturally occurring chlorinated cyclohexanes and related alicyclic halides, chosen for a 1,2-biaxial H-Cl pair, to look for an ancestral substrate.
Hypothesis: LinA's dehydrochlorination capability predates lindane and acts on a natural polychlorinated compound.
Type: enzyme kinetics
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