Acd (3-sulfinopropanoyl-CoA desulfinase, B9U6P5) in Variovorax paradoxus strain TBEA6 (locus VPARA_05440) is a 399-amino-acid cytosolic homotetrameric flavoprotein (EC 3.13.1.4) that has been neo-functionalized from the acyl-CoA dehydrogenase (ACAD) structural superfamily. Rather than catalyzing an oxidative CH-CH dehydrogenation, Acd uses a non-redox, structurally bound FAD cofactor to catalyze the non-oxidative C-S bond cleavage (desulfination) of 3-sulfinopropanoyl-CoA (3SP-CoA) into propanoyl-CoA and inorganic sulfite, constituting the terminal step in the degradation of the organosulfur compounds 3,3'-thiodipropionic acid (TDP) and 3-sulfinopropionate (3SP).
Definition: Catalysis of the reaction: 3-sulfinopropanoyl-CoA + H2O = propanoyl-CoA + sulfite + H+ (EC 3.13.1.4, RHEA:41560).
Justification: Experimentally characterized in Variovorax paradoxus TBEA6 Acd (B9U6P5, PMID:24317404) and assigned IUBMB EC 3.13.1.4 and RHEA:41560, but currently lacks a dedicated Molecular Function term in the Gene Ontology.
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003995 acyl-CoA dehydrogenase activity | IEA GO_REF:0000120 | REMOVE | Reason: Direct biochemical assays of purified recombinant Variovorax paradoxus TBEA6 Acd (B9U6P5) in PMID:24317404 demonstrated that it lacks acyl-CoA dehydrogenase activity and instead functions as a non-oxidative 3-sulfinopropanoyl-CoA desulfinase (EC 3.13.1.4) that has been neo-functionalized from the ACAD fold. Supporting Evidence: PMID:24317404 Only AcdTBEA6, AcdN-1, and AcdLB400 desulfinated 3SP-CoA and were thus identified as 3SP-CoA desulfinases within the acyl-CoA dehydrogenase family, although none of these three Acds dehydrogenated any of the tested acyl-CoA thioesters. |
| GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors | IEA GO_REF:0000120 | REMOVE | Reason: Directly refuted by PMID:24317404: V. paradoxus Acd (B9U6P5) is not an oxidoreductase acting on CH-CH groups; its bound FAD cofactor does not undergo redox cycling, and the enzyme catalyzes a non-oxidative C-S bond cleavage (EC 3.13.1.4). Supporting Evidence: PMID:24317404 Due to the fact that the 3SP-CoA desulfination reaction is basically a hydrolysis and occurs in the absence of an additional electron acceptor, it was postulated that the FAD cofactor in Acd DPN7 is not directly involved in the catalytic mechanism. It was proposed that it is necessary for the structural integrity of the enzyme and for the proper positioning of the substrate during catalysis. |
| GO:0033539 fatty acid beta-oxidation using acyl-CoA dehydrogenase | IEA GO_REF:0000118 | REMOVE | Reason: Directly refuted by PMID:24317404 and PMID:19001372: B9U6P5 does not participate in fatty acid beta-oxidation; it functions in the catabolism of 3,3'-thiodipropionic acid (TDP) and 3-sulfinopropionate (3SP) by cleaving 3-sulfinopropanoyl-CoA into propanoyl-CoA and sulfite. Supporting Evidence: PMID:19001372 Insertion of Tn5::mob in a gene putatively coding for a family III acyl-CoA-transferase resulted in the accumulation of 3-sulfinopropionate during cultivation on 3,3-thiodipropionic acid, indicating that this compound is further metabolized to 3-sulfinopropionyl-CoA and subsequently to propionyl-CoA. |
| GO:0046359 butyrate catabolic process | IEA GO_REF:0000118 | REMOVE | Reason: TreeGrafter over-propagated butyrate catabolic process (GO:0046359) from short-chain acyl-CoA dehydrogenases. PMID:24317404 demonstrated that V. paradoxus Acd (B9U6P5) has no activity on butyryl-CoA and instead catalyzes 3-sulfinopropanoyl-CoA desulfination in the 3,3'-thiodipropionate/3-sulfinopropionate degradation pathway. Supporting Evidence: PMID:24317404 Only AcdTBEA6, AcdN-1, and AcdLB400 desulfinated 3SP-CoA and were thus identified as 3SP-CoA desulfinases within the acyl-CoA dehydrogenase family, although none of these three Acds dehydrogenated any of the tested acyl-CoA thioesters. |
| GO:0050660 flavin adenine dinucleotide binding | IEA GO_REF:0000002 | ACCEPT | Reason: Confirmed experimentally in PMID:24317404: purified V. paradoxus Acd (B9U6P5) binds one non-covalent FAD cofactor per monomer, which is required structurally/electrostatically for 3-sulfinopropanoyl-CoA desulfination even though it does not undergo redox cycling. Supporting Evidence: PMID:24317404 Due to the fact that the 3SP-CoA desulfination reaction is basically a hydrolysis and occurs in the absence of an additional electron acceptor, it was postulated that the FAD cofactor in Acd DPN7 is not directly involved in the catalytic mechanism. It was proposed that it is necessary for the structural integrity of the enzyme and for the proper positioning of the substrate during catalysis. |
| GO:0044273 sulfur compound catabolic process | IDA PMID:24317404 Identification of 3-sulfinopropionyl coenzyme A (CoA) desulf... | NEW | Summary: Acd catalyzes the terminal desulfination of 3-sulfinopropanoyl-CoA into propanoyl-CoA and sulfite during catabolism of 3,3'-thiodipropionic acid and 3-sulfinopropionate. Reason: Direct biochemical characterization of purified recombinant Variovorax paradoxus TBEA6 Acd (B9U6P5) in PMID:24317404 demonstrated that it catalyzes the non-oxidative desulfination of 3-sulfinopropanoyl-CoA (3SP-CoA) into propanoyl-CoA and sulfite, constituting the terminal enzymatic step in the catabolism of the organosulfur compounds 3,3'-thiodipropionic acid (TDP) and 3-sulfinopropionate (3SP) established in PMID:19001372. Supporting Evidence: PMID:24317404 Only AcdTBEA6, AcdN-1, and AcdLB400 desulfinated 3SP-CoA and were thus identified as 3SP-CoA desulfinases within the acyl-CoA dehydrogenase family, although none of these three Acds dehydrogenated any of the tested acyl-CoA thioesters. PMID:19001372 Insertion of Tn5::mob in a gene putatively coding for a family III acyl-CoA-transferase resulted in the accumulation of 3-sulfinopropionate during cultivation on 3,3-thiodipropionic acid, indicating that this compound is further metabolized to 3-sulfinopropionyl-CoA and subsequently to propionyl-CoA. |
| GO:0005829 cytosol | IC PMID:24317404 Identification of 3-sulfinopropionyl coenzyme A (CoA) desulf... | NEW | Reason: Inferred by curator (IC) because V. paradoxus Acd (B9U6P5) was purified as a soluble homotetrameric enzyme lacking signal peptides or transmembrane domains (PMID:24317404) that acts on intracellular 3-sulfinopropanoyl-CoA. Supporting Evidence: PMID:24317404 All purified acyl-CoA dehydrogenases appeared as homotetramers, as revealed by size exclusion chromatography. |
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Download this section (compressed HTML)Q: What is the exact role of the oxidized FAD isoalloxazine ring in polarizing the beta-carbon or sulfinyl group of 3-sulfinopropanoyl-CoA during non-oxidative C-S cleavage by Variovorax paradoxus Acd?
Experiment: Reconstitute apo-Acd from Variovorax paradoxus with 5-deaza-FAD or redox-inactive flavin analogues and determine the X-ray crystal structure of Acd in complex with a non-hydrolyzable 3SP-CoA analogue.
Hypothesis: Redox-inactive flavin analogues preserve 3SP-CoA desulfinase activity, confirming that FAD acts purely as an electrostatic/structural cofactor in the active site.
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