Bacterial 3-mercaptopropionate and 3-sulfinopropionate desulfination pathway

Three-step aerobic catabolic pathway by which Variovorax paradoxus strain TBEA6 and related betaproteobacteria degrade the organosulfur compounds 3-mercaptopropionate (3MP, generated by cleavage of the thioether 3,3'-thiodipropionate, TDP) and 3-sulfinopropionate (3SP) into propanoyl-CoA and inorganic sulfite. First, the cysteine dioxygenase homolog Mdo (3-mercaptopropionate dioxygenase) catalyzes the O2-dependent dioxygenation of 3-mercaptopropionate to 3-sulfinopropionate (PMID:19001372). Second, the homodimeric class III CoA-transferase Act (succinyl-CoA:3-sulfinopropionate CoA-transferase, UniProtKB:B9U6P4, VPARA_05450) transfers CoA from succinyl-CoA (or itaconyl-CoA/glutaryl-CoA) to 3-sulfinopropionate to form 3-sulfinopropanoyl-CoA (3SP-CoA) and succinate (PMID:23772073); in V. paradoxus TBEA6, an unmarked delta-act deletion mutant retains growth on TDP and 3SP, indicating that at least one additional uncharacterized CoA-activating enzyme can partially substitute for Act in vivo (PMID:23772073). Third, the homotetrameric FAD-containing 3-sulfinopropanoyl-CoA desulfinase Acd (EC 3.13.1.4; Variovorax paradoxus TBEA6 UniProtKB:B9U6P5, VPARA_05440, encoded immediately downstream of act; orthologous to Advenella mimigardefordensis DPN7 Acd UniProtKB:Q705F0) catalyzes the non-oxidative C-S bond cleavage (desulfination) of 3-sulfinopropanoyl-CoA into propanoyl-CoA and sulfite (PMID:24317404).

MODULE:bacterial_3sp_thioether_desulfinationCOMPLETEMetabolic Pathwaymodules/bacterial_3sp_thioether_desulfination.yaml
sulfur compound catabolic processGO:0044273
PMID:19001372
3-mercaptopropionate dioxygenase, a cysteine dioxygenase homologue, catalyzes the initial step of 3-mercaptopropionate catabolism in the 3,3-thiodipropionic acid-degrading bacterium variovorax paradoxus.
Demonstrates Mdo-catalyzed oxygenation of 3-mercaptopropionate to 3-sulfinopropionate in vivo and in vitro using purified Variovorax paradoxus TBEA6 enzyme, with no activity toward cysteine or cysteamine.
Detection of 3-sulfinopropionate in the supernatant of one of these mutants during cultivation on 3,3-thiodipropionic acid as well as in vivo and in vitro enzyme assays using purified protein demonstrated oxygenation of 3-mercaptopropionic acid to 3-sulfinopropionate by this enzyme; cysteine and cysteamine were not used as substrate.
PMID:19001372
3-mercaptopropionate dioxygenase, a cysteine dioxygenase homologue, catalyzes the initial step of 3-mercaptopropionate catabolism in the 3,3-thiodipropionic acid-degrading bacterium variovorax paradoxus.
Shows that Tn5::mob insertion in a family III acyl-CoA-transferase gene causes accumulation of 3-sulfinopropionate during cultivation on 3,3'-thiodipropionic acid, indicating that 3-sulfinopropionate is further metabolized to 3-sulfinopropionyl-CoA and subsequently to propionyl-CoA.
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.
PMID:23772073
Succinyl-CoA:3-sulfinopropionate CoA-transferase from Variovorax paradoxus strain TBEA6, a novel member of the class III coenzyme A (CoA)-transferase family.
Purifies and kinetically characterizes Variovorax paradoxus TBEA6 Act (B9U6P4) as a homodimeric class III succinyl-CoA:3-sulfinopropionate CoA-transferase that converts 3-sulfinopropionate into 3-sulfinopropanoyl-CoA.
The act gene of Variovorax paradoxus TBEA6 encodes a succinyl-CoA:3-sulfinopropionate coenzyme A (CoA)-transferase, Act(TBEA6) (2.8.3.x), which catalyzes the activation of 3-sulfinopropionate (3SP), an intermediate during 3,3'-thiodipropionate (TDP) degradation.
PMID:24317404
Identification of 3-sulfinopropionyl coenzyme A (CoA) desulfinases within the Acyl-CoA dehydrogenase superfamily.
Purifies and characterizes Variovorax paradoxus TBEA6 Acd (B9U6P5) and orthologous bacterial Acd enzymes as homotetrameric FAD-dependent 3-sulfinopropanoyl-CoA desulfinases (EC 3.13.1.4) that cleave 3SP-CoA into propanoyl-CoA and sulfite.
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.
4Nodes
3Parts
0Variant Sets
0Variants
3Annotons
2Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:bacterial_3sp_thioether_desulfination deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Function consistency and core coverage

1 gene-function check(s) reflected in core functions · 0 conflict(s) · 4 evidence or coverage gap(s) (5 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

AnnotonParticipantFunctionAssessment
mdo_dioxygenase_activity mdo (Variovorax paradoxus TBEA6)
Family Representative 		3-mercaptopropionate dioxygenase activity
GO:0016702 		Participant Id Missing
The participant lacks a UniProt identifier for joining a gene review.
act_coa_transferase_activity act (Variovorax paradoxus TBEA6)
UniProtKB:B9U6P4
Family Representative 		succinyl-CoA:3-sulfinopropionate CoA-transferase activity
GO:0008410 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
acd_desulfinase_activity acd (Variovorax paradoxus TBEA6)
UniProtKB:B9U6P5
Gene 		3-sulfinopropanoyl-CoA desulfinase activity
No function ID 		No Function Id
A gene review exists, but this function lacks a GO identifier. Free-text chemistry is not automatically compared.
mdo_dioxygenase_activity Mdo 3-mercaptopropionate dioxygenases (cysteine dioxygenase homologs)
Family 		3-mercaptopropionate dioxygenase activity
GO:0016702 		Family Id Missing
The family has no identifier linking it to a curated family review.
act_coa_transferase_activity Act family III succinyl-CoA:3-sulfinopropionate CoA-transferases
Family 		succinyl-CoA:3-sulfinopropionate CoA-transferase activity
GO:0008410 		Family Id Missing
The family has no identifier linking it to a curated family review.

Gene-review completeness (2/2 grounded genes reviewed)

2 complete review(s) · 0 with deep research · 0 missing review · 2 reviewed but lacking deep research

Gene Review Complete Deep research
acd B9U6P5 ✓ ✓ ✗
act B9U6P4 ✓ ✓ ✗

Details

Context
Variovorax paradoxusNCBITaxon:34073
Bacterial 3-mercaptopropionate and 3-sulfinopropionate desulfination pathwayMetabolic Pathwaybacterial_3sp_thioether_desulfination
sulfur compound catabolic processGO:0044273
Context
Variovorax paradoxusNCBITaxon:34073

Grounded on the Variovorax paradoxus strain TBEA6 (NCBITaxon:34073) 3,3'-thiodipropionate (TDP) and 3-sulfinopropionate (3SP) catabolic pathway comprising Mdo (PMID:19001372), Act (UniProtKB:B9U6P4, VPARA_05450; PMID:23772073), and Acd (UniProtKB:B9U6P5, VPARA_05440; PMID:24317404, complemented in vivo by Advenella mimigardefordensis DPN7 Acd UniProtKB:Q705F0 in PMID:23772073). An unmarked delta-act mutant in V. paradoxus TBEA6 remains able to utilize TDP and 3SP as sole carbon sources, demonstrating functional redundancy at the 3SP CoA-activation step via an uncharacterized alternative CoA-transferase or acyl-CoA synthetase (PMID:23772073). Step 1 (mdo_3mp_dioxygenase_step) intentionally omits a representative_members UniProt accession because the V. paradoxus TBEA6 Mdo UniProt record is not cached locally and its accession cannot be confirmed from the cited publications alone.

Connections

Mdo oxidizes 3-mercaptopropionate to 3-sulfinopropionate (3SP), the carboxylate substrate activated by Act.
Act converts 3-sulfinopropionate into 3-sulfinopropanoyl-CoA (3SP-CoA), the direct thioester substrate desulfinated by Acd (UniProtKB:B9U6P5).
Part 1: dioxygenation of 3-mercaptopropionate to 3-sulfinopropionate
Mdo 3-mercaptopropionate dioxygenationReactionmdo_3mp_dioxygenase_step

Annotons

Mdo 3-mercaptopropionate dioxygenase
mdo_dioxygenase_activity
Participant: Family: Mdo 3-mercaptopropionate dioxygenases (cysteine dioxygenase homologs)
Family:
Mdo 3-mercaptopropionate dioxygenases (cysteine dioxygenase homologs)
Representative Members: mdo (Variovorax paradoxus TBEA6)

Function

3-mercaptopropionate dioxygenase activityGO:0016702
Substrates: 3-mercaptopropionate dioxygen
Products: 3-sulfinopropionate

Catalyzes the O2-dependent oxidation of the thiol group of 3-mercaptopropionate to form 3-sulfinopropionate (3SP).

Part 2: CoA-transferase activation of 3-sulfinopropionate to 3-sulfinopropanoyl-CoA
Act succinyl-CoA:3-sulfinopropionate CoA transferReactionact_3sp_coa_transferase_step

Annotons

Act succinyl-CoA:3-sulfinopropionate CoA-transferase
act_coa_transferase_activity
Participant: Family: Act family III succinyl-CoA:3-sulfinopropionate CoA-transferases
Family:
Act family III succinyl-CoA:3-sulfinopropionate CoA-transferases
Representative Members: act (Variovorax paradoxus TBEA6)UniProtKB:B9U6P4

Function

succinyl-CoA:3-sulfinopropionate CoA-transferase activityGO:0008410
Substrates: 3-sulfinopropionate succinyl-CoA
Products: 3-sulfinopropanoyl-CoA succinate

Transfers the CoA moiety from succinyl-CoA (or itaconyl-CoA/glutaryl-CoA) to 3-sulfinopropionate to generate 3-sulfinopropanoyl-CoA (3SP-CoA). In V. paradoxus TBEA6, an uncharacterized backup enzyme can bypass delta-act during growth on TDP or 3SP (PMID:23772073).

Part 3: non-oxidative FAD-dependent desulfination of 3-sulfinopropanoyl-CoA to propanoyl-CoA and sulfite
Acd 3-sulfinopropanoyl-CoA desulfinationReactionacd_3sp_coa_desulfinase_step

Annotons

Acd 3-sulfinopropanoyl-CoA desulfinase
acd_desulfinase_activity
Participant: Gene Product: acd (Variovorax paradoxus TBEA6)
Gene Product:
acd (Variovorax paradoxus TBEA6)UniProtKB:B9U6P5 Variovorax paradoxus TBEA6 3-sulfinopropanoyl-CoA desulfinase (EC 3.13.1.4; UniProtKB:B9U6P5, SPCAD_VARPD, VPARA_05440) purified and kinetically characterized in PMID:24317404; the previously characterized orthologous Advenella mimigardefordensis DPN7 enzyme (UniProtKB:Q705F0) complements the V. paradoxus act::Tn5::mob polar mutant in PMID:23772073.

Function

3-sulfinopropanoyl-CoA desulfinase activity Catalyzes the non-oxidative C-S bond cleavage (desulfination, EC 3.13.1.4) of 3-sulfinopropanoyl-CoA into propanoyl-CoA and sulfite; left ungrounded to a GO ID because GO lacks a term for carbon-sulfur lyase/desulfinase activity on sulfinylacyl-CoA thioesters (consistent with proposed_molecular_function in genes/VARPD/acd/acd-ai-review.yaml).
Substrates: 3-sulfinopropanoyl-CoA water
Products: propanoyl-CoA sulfite

Uses a non-redox, structurally bound FAD cofactor to catalyze the C-S bond cleavage (desulfination, EC 3.13.1.4) of 3-sulfinopropanoyl-CoA into propanoyl-CoA and inorganic sulfite.