AcdS (Q6J256, 1A1D_VARPD) is a 338-amino-acid homotrimeric pyridoxal 5'-phosphate (PLP)-dependent 1-aminocyclopropane-1-carboxylate (ACC) deaminase (EC 3.5.99.7) in Variovorax paradoxus. It catalyzes the cyclopropane ring-opening deamination of ACC, the immediate biosynthetic precursor of the plant stress hormone ethylene, yielding 2-oxobutanoate (alpha-ketobutyrate) and ammonium. At its active site, the PLP cofactor is covalently linked via a Schiff base to Lys51 alongside the nucleophilic residue Ser78. In plant-associated Variovorax paradoxus strains, AcdS acts as a rhizosphere ethylene sink that lowers stress ethylene accumulation in host roots to maintain root elongation under biotic and abiotic stress.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003824 catalytic activity | IEA GO_REF:0000117 | TOO GENERAL | Summary: AcdS is an enzyme with 1-aminocyclopropane-1-carboxylate deaminase activity (EC 3.5.99.7). Reason: The root-adjacent term catalytic activity (GO:0003824) is true of AcdS but uninformative because the specific term 1-aminocyclopropane-1-carboxylate deaminase activity (GO:0008660) is already accepted on this record via HAMAP rule MF_00807. Supporting Evidence: UniProtKB:Q6J256 CC -!- CATALYTIC ACTIVITY: CC Reaction=1-aminocyclopropane-1-carboxylate + H2O = 2-oxobutanoate + CC NH4(+); Xref=Rhea:RHEA:16933, ChEBI:CHEBI:15377, ChEBI:CHEBI:16763, CC ChEBI:CHEBI:28938, ChEBI:CHEBI:58360; EC=3.5.99.7; CC Evidence={ECO:0000255|HAMAP-Rule:MF_00807}; |
| GO:0008660 1-aminocyclopropane-1-carboxylate deaminase activity | IEA GO_REF:0000120 | ACCEPT | Summary: AcdS catalyzes the deamination of 1-aminocyclopropane-1-carboxylate (ACC) into 2-oxobutanoate and ammonium (EC 3.5.99.7). Reason: Core enzymatic activity supported by HAMAP rule MF_00807, NCBIfam TIGR01274, and InterPro family IPR005965. Supporting Evidence: UniProtKB:Q6J256 CC -!- CATALYTIC ACTIVITY: CC Reaction=1-aminocyclopropane-1-carboxylate + H2O = 2-oxobutanoate + CC NH4(+); Xref=Rhea:RHEA:16933, ChEBI:CHEBI:15377, ChEBI:CHEBI:16763, CC ChEBI:CHEBI:28938, ChEBI:CHEBI:58360; EC=3.5.99.7; CC Evidence={ECO:0000255|HAMAP-Rule:MF_00807}; |
| GO:0009310 amine catabolic process | IEA GO_REF:0000002 | MODIFY | Summary: AcdS catabolizes the cyclic non-protein amino acid 1-aminocyclopropane-1-carboxylate (ACC). Reason: In GO, 1-aminocyclopropane-1-carboxylate catabolic process (GO:0042217) is classified under non-proteinogenic alpha-amino acid catabolic process rather than amine catabolic process (GO:0009310); this InterPro2GO mapping should be replaced by the specific process GO:0042217. Proposed replacements: 1-aminocyclopropane-1-carboxylate catabolic process Supporting Evidence: UniProtKB:Q6J256 CC -!- FUNCTION: Catalyzes a cyclopropane ring-opening reaction, the CC irreversible conversion of 1-aminocyclopropane-1-carboxylate (ACC) to CC ammonia and alpha-ketobutyrate. Allows growth on ACC as a nitrogen CC source. {ECO:0000255|HAMAP-Rule:MF_00807}. |
| GO:0019148 D-cysteine desulfhydrase activity | IEA GO_REF:0000118 | REMOVE | Summary: TreeGrafter over-propagated D-cysteine desulfhydrase activity from paralogous PALP-family enzymes in PTHR43780; AcdS is a dedicated 1-aminocyclopropane-1-carboxylate deaminase. Reason: PANTHER family PTHR43780 encompasses both ACC deaminases (AcdS) and D-cysteine desulfhydrases (DcyD). Q6J256 matches the strict ACC deaminase models HAMAP MF_00807 and NCBIfam TIGR01274 (IPR020601), not D-cysteine desulfhydrase. Supporting Evidence: UniProtKB:Q6J256 DR HAMAP; MF_00807; ACC_deaminase; 1. UniProtKB:Q6J256 DR NCBIfam; TIGR01274; ACC_deam; 1. |
| GO:0030170 pyridoxal phosphate binding | IEA GO_REF:0000002 | ACCEPT | Summary: AcdS binds pyridoxal 5'-phosphate (PLP) covalently via Lys51 as an essential catalytic cofactor. Reason: Supported by the conserved PALP domain (PF00291) and Schiff-base lysine residue Lys51 in HAMAP rule MF_00807. Supporting Evidence: UniProtKB:Q6J256 FT MOD_RES 51 FT /note="N6-(pyridoxal phosphate)lysine" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00807" |
| GO:0042217 1-aminocyclopropane-1-carboxylate catabolic process | IEA GO_REF:0000104 | ACCEPT | Summary: AcdS catalyzes the irreversible catabolism of 1-aminocyclopropane-1-carboxylate (ACC) into 2-oxobutanoate and ammonia. Reason: Directly supported by HAMAP rule MF_00807 and UniRule UR000100241. Supporting Evidence: UniProtKB:Q6J256 CC -!- FUNCTION: Catalyzes a cyclopropane ring-opening reaction, the CC irreversible conversion of 1-aminocyclopropane-1-carboxylate (ACC) to CC ammonia and alpha-ketobutyrate. Allows growth on ACC as a nitrogen CC source. {ECO:0000255|HAMAP-Rule:MF_00807}. |
| GO:0005829 cytosol | IC UniProtKB:Q6J256 | NEW | Summary: AcdS is a soluble cytoplasmic homotrimer that lacks signal peptides or transmembrane helices. Reason: Inferred by curator (IC) because bacterial ACC deaminase (AcdS, HAMAP MF_00807) is a soluble homotrimeric enzyme lacking signal peptides or transmembrane helices that degrades ACC imported into the bacterial cytosol. Supporting Evidence: UniProtKB:Q6J256 CC -!- SUBUNIT: Homotrimer. {ECO:0000255|HAMAP-Rule:MF_00807}. |
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Download this section (compressed HTML)Q: How is expression of acdS regulated relative to the iad auxin-catabolic operon in Variovorax paradoxus strains that carry both loci when colonizing plant roots?
Experiment: Construct single and double knockouts of acdS and iadDE in an acdS-positive Variovorax paradoxus strain and quantify Arabidopsis root elongation under combined auxin and ethylene-inducing microbial community challenges.
Hypothesis: Dual presence of AcdS and IadCDE provides additive protection against root growth inhibition under high-auxin conditions where auxin stimulates host ACC synthase activity.
Type: Bacterial genetics and gnotobiotic plant root elongation assay
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