methylthiopropanoate degradation I (cleavage)

MetaCyc:PWY-6048

The complete three-reaction MetaCyc route converts 3-(methylthio)propionate (MMPA) to methanethiol, acetaldehyde and carbon dioxide in Ruegeria pomeroyi DSS-3. DmdB2 activates MMPA with ATP and CoA; DmdC1 oxidizes the thioester to trans-methylthioacryloyl-CoA; DmdD-dependent hydration and hydrolysis complete cleavage. The terminal net reaction includes spontaneous methanethiol elimination and expected spontaneous decarboxylation. Generic electron-transfer flavoprotein redox states retain the MetaCyc/Rhea database convention: the physiological partner remains unidentified, and direct DmdC1 assays used artificial acceptors. DmdB2 and DmdC1 are experimentally supported homodimers and DmdD a homohexamer; protein enables edges represent their functional roles without asserting monomer sufficiency. DmdB magnesium dependence and DmdC inferred FAD cofactor are distinguished from the whole carrier. DMSP-dependent DmdB2 inhibition and its conditional relief by MMPA are supported in vitro. The route starts after DMSP demethylation and stops before acetaldehyde oxidation or methanethiol assimilation; it does not assert these adjacent pathways or flux in every environmental condition.

Pathway type

organosulfur catabolism

Organism scope

Ruegeria pomeroyi DSS-3 NCBITaxon:246200

Read the source YAML

Pathway network

24 nodes · 29 asserted directed edges

Arrows show recorded subject → object relationships, not necessarily metabolic flow. Select a node for details or an arrow for evidence. Scroll, zoom or find a node to explore.

Reaction / activity
Chemical / cofactor
Protein / complex
Pathway
Solid arrow: mechanistic relation
Dashed arrow: membership, location or cofactor relation

Show at full size (scroll to explore)

Components and activities

Declared biological components and source reaction directions
Node	Kind or role	Source direction
Ruegeria pomeroyi DSS-3 `NCBITaxon:246200`	taxon
3-(methylthio)propionate `CHEBI:49016`	small molecule
ATP(4-) `CHEBI:30616`	small molecule
coenzyme A(4-) `CHEBI:57287`	small molecule
3-(methylthio)propanoyl-CoA(4-) `CHEBI:82815`	small molecule
adenosine 5'-monophosphate(2-) `CHEBI:456215`	small molecule
diphosphate(3-) `CHEBI:33019`	small molecule
oxidized [electron-transfer flavoprotein] `RHEA-COMP:10685`	protein
hydron `CHEBI:15378`	small molecule
3-(methylthio)acryloyl-CoA(4-) `CHEBI:84994`	small molecule
reduced [electron-transfer flavoprotein] `RHEA-COMP:10686`	protein
water `CHEBI:15377`	small molecule
methanethiol `CHEBI:16007`	small molecule
acetaldehyde `CHEBI:15343`	small molecule
carbon dioxide `CHEBI:16526`	small molecule
magnesium(2+) `CHEBI:18420`	cofactor
FAD(3-) `CHEBI:57692`	cofactor
S,S-dimethyl-beta-propiothetin `CHEBI:16457`	small molecule
3-methylmercaptopropionyl-CoA ligase `UniProtKB:Q5LRT0`	protein
3-methylmercaptopropionyl-CoA dehydrogenase `UniProtKB:Q5LLW7`	protein
Methylthioacryloyl-CoA hydratase `UniProtKB:Q5LLW6`	protein
3-(methylsulfanyl)propanoate + ATP + CoA => 3-(methylsulfanyl)propanoyl-CoA + AMP + diphosphate `RHEA:43053`	molecular activity	left to right
3-(methylsulfanyl)propanoyl-CoA + oxidized [electron-transfer flavoprotein] + H(+) => 3-(methylsulfanyl)acryloyl-CoA + reduced [electron-transfer flavoprotein] `RHEA:52613`	molecular activity	left to right
3-(methylsulfanyl)acryloyl-CoA + 2 H2O => methanethiol + acetaldehyde + CO2 + CoA `RHEA:45145`	molecular activity	left to right

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
3-(methylthio)propionate `CHEBI:49016`	consumes	3-(methylsulfanyl)propanoate + ATP + CoA => 3-(methylsulfanyl)propanoyl-CoA + AMP + diphosphate `RHEA:43053`	RHEA:43053 Source assertion: Rhea places CHEBI:49016 on the substrates side of directed RHEA:43053, with coefficient 1. Source location `http://rdf.rhea-db.org/43053/rh:substrates; http://rdf.rhea-db.org/43052_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_43052_compound_6054/rh:compound -> http://rdf.rhea-db.org/Compound_6054/rh:chebi`
ATP(4-) `CHEBI:30616`	consumes	3-(methylsulfanyl)propanoate + ATP + CoA => 3-(methylsulfanyl)propanoyl-CoA + AMP + diphosphate `RHEA:43053`	RHEA:43053 Source assertion: Rhea places CHEBI:30616 on the substrates side of directed RHEA:43053, with coefficient 1. Source location `http://rdf.rhea-db.org/43053/rh:substrates; http://rdf.rhea-db.org/43052_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_43052_compound_6372/rh:compound -> http://rdf.rhea-db.org/Compound_6372/rh:chebi`
coenzyme A(4-) `CHEBI:57287`	consumes	3-(methylsulfanyl)propanoate + ATP + CoA => 3-(methylsulfanyl)propanoyl-CoA + AMP + diphosphate `RHEA:43053`	RHEA:43053 Source assertion: Rhea places CHEBI:57287 on the substrates side of directed RHEA:43053, with coefficient 1. Source location `http://rdf.rhea-db.org/43053/rh:substrates; http://rdf.rhea-db.org/43052_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_43052_compound_1264/rh:compound -> http://rdf.rhea-db.org/Compound_1264/rh:chebi`
3-(methylsulfanyl)propanoate + ATP + CoA => 3-(methylsulfanyl)propanoyl-CoA + AMP + diphosphate `RHEA:43053`	produces	3-(methylthio)propanoyl-CoA(4-) `CHEBI:82815`	RHEA:43053 Source assertion: Rhea places CHEBI:82815 on the products side of directed RHEA:43053, with coefficient 1. Source location `http://rdf.rhea-db.org/43053/rh:products; http://rdf.rhea-db.org/43052_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_43052_compound_10325/rh:compound -> http://rdf.rhea-db.org/Compound_10325/rh:chebi`
3-(methylsulfanyl)propanoate + ATP + CoA => 3-(methylsulfanyl)propanoyl-CoA + AMP + diphosphate `RHEA:43053`	produces	adenosine 5'-monophosphate(2-) `CHEBI:456215`	RHEA:43053 Source assertion: Rhea places CHEBI:456215 on the products side of directed RHEA:43053, with coefficient 1. Source location `http://rdf.rhea-db.org/43053/rh:products; http://rdf.rhea-db.org/43052_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_43052_compound_2590/rh:compound -> http://rdf.rhea-db.org/Compound_2590/rh:chebi`
3-(methylsulfanyl)propanoate + ATP + CoA => 3-(methylsulfanyl)propanoyl-CoA + AMP + diphosphate `RHEA:43053`	produces	diphosphate(3-) `CHEBI:33019`	RHEA:43053 Source assertion: Rhea places CHEBI:33019 on the products side of directed RHEA:43053, with coefficient 1. Source location `http://rdf.rhea-db.org/43053/rh:products; http://rdf.rhea-db.org/43052_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_43052_compound_2106/rh:compound -> http://rdf.rhea-db.org/Compound_2106/rh:chebi`
3-(methylthio)propanoyl-CoA(4-) `CHEBI:82815`	consumes	3-(methylsulfanyl)propanoyl-CoA + oxidized [electron-transfer flavoprotein] + H(+) => 3-(methylsulfanyl)acryloyl-CoA + reduced [electron-transfer flavoprotein] `RHEA:52613`	RHEA:52613 Source assertion: Rhea places CHEBI:82815 on the substrates side of directed RHEA:52613, with coefficient 1. Source location `http://rdf.rhea-db.org/52613/rh:substrates; http://rdf.rhea-db.org/52612_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_52612_compound_10325/rh:compound -> http://rdf.rhea-db.org/Compound_10325/rh:chebi`
oxidized [electron-transfer flavoprotein] `RHEA-COMP:10685`	consumes This whole generic carrier state is the curated database acceptor-class convention, not a specific DSS-3 protein. Primary assays establish MMPA-CoA oxidation with artificial acceptors; the physiological flavoprotein partner remains unresolved. Carrier-bound FAD is not a substitute node for the carrier.	3-(methylsulfanyl)propanoyl-CoA + oxidized [electron-transfer flavoprotein] + H(+) => 3-(methylsulfanyl)acryloyl-CoA + reduced [electron-transfer flavoprotein] `RHEA:52613`	RHEA:52613 Source assertion: Rhea places RHEA-COMP:10685 on the substrates side of directed RHEA:52613, with coefficient 1. Source location `http://rdf.rhea-db.org/52613/rh:substrates; http://rdf.rhea-db.org/52612_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_52612_compound_10685/rh:compound -> http://rdf.rhea-db.org/Compound_10685/rh:id, rh:name, rdfs:subClassOf` MetaCyc:RXN-12572 Source assertion: The native reaction explicitly places the generic protein class ETF-Oxidized on its left side; it does not identify a strain-specific ETF protein. Source location `Reaction[@frameid="RXN-12572"]/left/Protein[@frameid="ETF-Oxidized"]` UniProtKB:Q5LLW7 Source assertion: The reviewed catalytic-activity entry cross-references RHEA:52612 and both generic ETF components. Its attached 2011 citation does not experimentally identify the physiological carrier. Source location `comments[1].reaction.reactionCrossReferences; comments[1].reaction.evidences`
hydron `CHEBI:15378`	consumes	3-(methylsulfanyl)propanoyl-CoA + oxidized [electron-transfer flavoprotein] + H(+) => 3-(methylsulfanyl)acryloyl-CoA + reduced [electron-transfer flavoprotein] `RHEA:52613`	RHEA:52613 Source assertion: Rhea places CHEBI:15378 on the substrates side of directed RHEA:52613, with coefficient 1. Source location `http://rdf.rhea-db.org/52613/rh:substrates; http://rdf.rhea-db.org/52612_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_52612_compound_3249/rh:compound -> http://rdf.rhea-db.org/Compound_3249/rh:chebi`
3-(methylsulfanyl)propanoyl-CoA + oxidized [electron-transfer flavoprotein] + H(+) => 3-(methylsulfanyl)acryloyl-CoA + reduced [electron-transfer flavoprotein] `RHEA:52613`	produces	3-(methylthio)acryloyl-CoA(4-) `CHEBI:84994`	RHEA:52613 Source assertion: Rhea places CHEBI:84994 on the products side of directed RHEA:52613, with coefficient 1. Source location `http://rdf.rhea-db.org/52613/rh:products; http://rdf.rhea-db.org/52612_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_52612_compound_11096/rh:compound -> http://rdf.rhea-db.org/Compound_11096/rh:chebi`
3-(methylsulfanyl)propanoyl-CoA + oxidized [electron-transfer flavoprotein] + H(+) => 3-(methylsulfanyl)acryloyl-CoA + reduced [electron-transfer flavoprotein] `RHEA:52613`	produces This whole generic carrier state is the curated database acceptor-class convention, not a specific DSS-3 protein. Primary assays establish MMPA-CoA oxidation with artificial acceptors; the physiological flavoprotein partner remains unresolved. Carrier-bound FAD is not a substitute node for the carrier.	reduced [electron-transfer flavoprotein] `RHEA-COMP:10686`	RHEA:52613 Source assertion: Rhea places RHEA-COMP:10686 on the products side of directed RHEA:52613, with coefficient 1. Source location `http://rdf.rhea-db.org/52613/rh:products; http://rdf.rhea-db.org/52612_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_52612_compound_10686/rh:compound -> http://rdf.rhea-db.org/Compound_10686/rh:id, rh:name, rdfs:subClassOf` MetaCyc:RXN-12572 Source assertion: The native reaction explicitly places the generic protein class ETF-Reduced on its right side; it does not identify a strain-specific ETF protein. Source location `Reaction[@frameid="RXN-12572"]/right/Protein[@frameid="ETF-Reduced"]` UniProtKB:Q5LLW7 Source assertion: The reviewed catalytic-activity entry cross-references RHEA:52612 and both generic ETF components. Its attached 2011 citation does not experimentally identify the physiological carrier. Source location `comments[1].reaction.reactionCrossReferences; comments[1].reaction.evidences`
3-(methylthio)acryloyl-CoA(4-) `CHEBI:84994`	consumes This is a side of the single terminal net reaction. DmdD catalyzes hydration and hydrolysis; methanethiol elimination and subsequent decarboxylation are spontaneous or expected spontaneous steps within that net conversion.	3-(methylsulfanyl)acryloyl-CoA + 2 H2O => methanethiol + acetaldehyde + CO2 + CoA `RHEA:45145`	RHEA:45145 Source assertion: Rhea places CHEBI:84994 on the substrates side of directed RHEA:45145, with coefficient 1. Source location `http://rdf.rhea-db.org/45145/rh:substrates; http://rdf.rhea-db.org/45144_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_45144_compound_11096/rh:compound -> http://rdf.rhea-db.org/Compound_11096/rh:chebi`
water `CHEBI:15377`	consumes This is a side of the single terminal net reaction. DmdD catalyzes hydration and hydrolysis; methanethiol elimination and subsequent decarboxylation are spontaneous or expected spontaneous steps within that net conversion.	3-(methylsulfanyl)acryloyl-CoA + 2 H2O => methanethiol + acetaldehyde + CO2 + CoA `RHEA:45145`	RHEA:45145 Source assertion: Rhea places CHEBI:15377 on the substrates side of directed RHEA:45145, with coefficient 2. Source location `http://rdf.rhea-db.org/45145/rh:substrates; http://rdf.rhea-db.org/45144_L/rh:contains2 -> http://rdf.rhea-db.org/Participant_45144_compound_1283/rh:compound -> http://rdf.rhea-db.org/Compound_1283/rh:chebi`
3-(methylsulfanyl)acryloyl-CoA + 2 H2O => methanethiol + acetaldehyde + CO2 + CoA `RHEA:45145`	produces This is a side of the single terminal net reaction. DmdD catalyzes hydration and hydrolysis; methanethiol elimination and subsequent decarboxylation are spontaneous or expected spontaneous steps within that net conversion.	methanethiol `CHEBI:16007`	RHEA:45145 Source assertion: Rhea places CHEBI:16007 on the products side of directed RHEA:45145, with coefficient 1. Source location `http://rdf.rhea-db.org/45145/rh:products; http://rdf.rhea-db.org/45144_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_45144_compound_2831/rh:compound -> http://rdf.rhea-db.org/Compound_2831/rh:chebi`
3-(methylsulfanyl)acryloyl-CoA + 2 H2O => methanethiol + acetaldehyde + CO2 + CoA `RHEA:45145`	produces This is a side of the single terminal net reaction. DmdD catalyzes hydration and hydrolysis; methanethiol elimination and subsequent decarboxylation are spontaneous or expected spontaneous steps within that net conversion.	acetaldehyde `CHEBI:15343`	RHEA:45145 Source assertion: Rhea places CHEBI:15343 on the products side of directed RHEA:45145, with coefficient 1. Source location `http://rdf.rhea-db.org/45145/rh:products; http://rdf.rhea-db.org/45144_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_45144_compound_3952/rh:compound -> http://rdf.rhea-db.org/Compound_3952/rh:chebi`
3-(methylsulfanyl)acryloyl-CoA + 2 H2O => methanethiol + acetaldehyde + CO2 + CoA `RHEA:45145`	produces This is a side of the single terminal net reaction. DmdD catalyzes hydration and hydrolysis; methanethiol elimination and subsequent decarboxylation are spontaneous or expected spontaneous steps within that net conversion.	carbon dioxide `CHEBI:16526`	RHEA:45145 Source assertion: Rhea places CHEBI:16526 on the products side of directed RHEA:45145, with coefficient 1. Source location `http://rdf.rhea-db.org/45145/rh:products; http://rdf.rhea-db.org/45144_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_45144_compound_4391/rh:compound -> http://rdf.rhea-db.org/Compound_4391/rh:chebi`
3-(methylsulfanyl)acryloyl-CoA + 2 H2O => methanethiol + acetaldehyde + CO2 + CoA `RHEA:45145`	produces This is a side of the single terminal net reaction. DmdD catalyzes hydration and hydrolysis; methanethiol elimination and subsequent decarboxylation are spontaneous or expected spontaneous steps within that net conversion.	coenzyme A(4-) `CHEBI:57287`	RHEA:45145 Source assertion: Rhea places CHEBI:57287 on the products side of directed RHEA:45145, with coefficient 1. Source location `http://rdf.rhea-db.org/45145/rh:products; http://rdf.rhea-db.org/45144_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_45144_compound_1264/rh:compound -> http://rdf.rhea-db.org/Compound_1264/rh:chebi`
3-methylmercaptopropionyl-CoA ligase `UniProtKB:Q5LRT0`	enables DmdB2 (SPO2045) enables MMPA activation as a functional gene-product role. Purified recombinant DSS-3 enzyme was a homodimer by gel filtration; this edge does not assert monomer sufficiency. DmdB1 is a separately characterized isozyme outside this native catalyst projection.	3-(methylsulfanyl)propanoate + ATP + CoA => 3-(methylsulfanyl)propanoyl-CoA + AMP + diphosphate `RHEA:43053`	MetaCyc:ENZRXN-19462 Source assertion: The native enzymatic-reaction object assigns MONOMER-16783 to RXN-12571. Source location `Enzymatic-Reaction[@frameid="ENZRXN-19462"]/enzyme/Protein; reaction/Reaction` MetaCyc:MONOMER-16783 Source assertion: The native protein frame cross-references UniProt Q5LRT0; this establishes the gene-product identity, not a monomeric active assembly. Source location `Protein[@frameid="MONOMER-16783"]/dblink[dblink-db="UNIPROT"]/dblink-oid` UniProtKB:Q5LRT0 Source assertion: The reviewed catalytic-activity annotation assigns RHEA:43052 with experimental evidence ECO:0000269. The selected forward direction is independently read from Rhea. Source location `comments[1].reaction.reactionCrossReferences; comments[1].reaction.evidences` PMID:21562561 Source assertion: Partially purified native MMPA-CoA ligase identified SPO2045; recombinant expression confirmed activity, with ATP consumption and AMP production. Source location `Printed p.208, MMPA-CoA ligase purification and recombinant expression paragraphs; Figure 1 p.209` PMID:24443527 Source assertion: SPO2045 is RPO_DmdB2. Purified recombinant DmdB2 has MMPA-CoA ligase activity and a native gel-filtration mass consistent with a dimer. Source location `Figure 2 caption; Results, DmdBs are dimers with MMPA-CoA ligase activity, section sec3-1; Table 1` UniProtKB:Q5LRT0 Source assertion: The reviewed entry identifies Ruegeria pomeroyi strain ATCC 700808 / DSM 15171 / DSS-3 and taxon 246200. Source location `organism.scientificName; organism.taxonId; genes`
3-methylmercaptopropionyl-CoA dehydrogenase `UniProtKB:Q5LLW7`	enables DmdC1 (SPO3804) enables the oxidation in its experimentally supported homodimeric context. Current Rhea specifies a generic ETF acceptor class; this role does not claim that the exact carrier was tested. The 2022 study used recombinant DSS-3 enzyme and artificial electron acceptors.	3-(methylsulfanyl)propanoyl-CoA + oxidized [electron-transfer flavoprotein] + H(+) => 3-(methylsulfanyl)acryloyl-CoA + reduced [electron-transfer flavoprotein] `RHEA:52613`	MetaCyc:ENZRXN-19463 Source assertion: The native enzymatic-reaction object assigns MONOMER-16784 to RXN-12572. Source location `Enzymatic-Reaction[@frameid="ENZRXN-19463"]/enzyme/Protein; reaction/Reaction` MetaCyc:MONOMER-16784 Source assertion: The native protein frame cross-references UniProt Q5LLW7; this establishes the gene-product identity, not a monomeric active assembly. Source location `Protein[@frameid="MONOMER-16784"]/dblink[dblink-db="UNIPROT"]/dblink-oid` UniProtKB:Q5LLW7 Source assertion: The reviewed catalytic-activity annotation assigns RHEA:52612 with experimental evidence ECO:0000269. The selected forward direction is independently read from Rhea. Source location `comments[1].reaction.reactionCrossReferences; comments[1].reaction.evidences` PMID:21562561 Source assertion: Recombinant SPO3804 catalyzed MMPA-CoA oxidation. The dmdC mutant could not grow on MMPA, and SPO3804 complementation restored growth. Artificial electron acceptors supported the assay. Source location `Printed pp.208-209, MMPA-CoA dehydrogenation, recombinant expression and dmdC disruption/complementation paragraphs` PMID:34818101 Source assertion: The cloned DSS-3 SPO3804 enzyme forms a homodimer. Oxidation required PMS plus DCPIP or INT; free FAD, FMN and NADP+ alone did not support activity. An uncharacterized in vivo flavoprotein is inferred. Source location `Results, Properties of RPO_DmdC1 dehydrogenase, section s2-3 paragraphs 1-2; Materials and Methods, Plasmid construction and expression of recombinant protein, section s3-1` UniProtKB:Q5LLW7 Source assertion: The reviewed entry identifies Ruegeria pomeroyi strain ATCC 700808 / DSM 15171 / DSS-3 and taxon 246200. Source location `organism.scientificName; organism.taxonId; genes`
Methylthioacryloyl-CoA hydratase `UniProtKB:Q5LLW6`	enables DmdD (SPO3805) enables the observed net cleavage as a homohexamer (dimer of trimers), not an isolated monomer. The net equation includes spontaneous methanethiol elimination after hydration and expected spontaneous malonate-semialdehyde decarboxylation. It is not duplicated by component reaction nodes.	3-(methylsulfanyl)acryloyl-CoA + 2 H2O => methanethiol + acetaldehyde + CO2 + CoA `RHEA:45145`	MetaCyc:ENZRXN-19464 Source assertion: The native enzymatic-reaction object assigns MONOMER-16785 to RXN-12573. Source location `Enzymatic-Reaction[@frameid="ENZRXN-19464"]/enzyme/Protein; reaction/Reaction` MetaCyc:MONOMER-16785 Source assertion: The native protein frame cross-references UniProt Q5LLW6; this establishes the gene-product identity, not a monomeric active assembly. Source location `Protein[@frameid="MONOMER-16785"]/dblink[dblink-db="UNIPROT"]/dblink-oid` UniProtKB:Q5LLW6 Source assertion: The reviewed catalytic-activity annotation assigns RHEA:45144 with experimental evidence ECO:0000269. The selected forward direction is independently read from Rhea. Source location `comments[1].reaction.reactionCrossReferences; comments[1].reaction.evidences` PMID:21562561 Source assertion: Purified DmdD/SPO3805 and recombinant expression establish MTA-CoA cleavage; stoichiometric CoA and methanethiol and approximately 90% theoretical acetaldehyde were obtained. Lost carbon was presumed to be CO2. Source location `Printed pp.208-209, DmdD purification and product-identification paragraphs; Figure 1` PMID:23704947 Source assertion: DmdD is a homohexamer with two trimers and intersubunit active sites. The mechanism assigns enzymatic hydration and thioester hydrolysis; methanethiol release is spontaneous and final decarboxylation is expected spontaneous. Source location `Results and Discussion, The hexamer of DmdD (s2b), and Catalytic mechanism of DmdD (s2g); Figure 6` UniProtKB:Q5LLW6 Source assertion: The reviewed entry identifies Ruegeria pomeroyi strain ATCC 700808 / DSM 15171 / DSS-3 and taxon 246200. Source location `organism.scientificName; organism.taxonId; genes`
3-methylmercaptopropionyl-CoA ligase `UniProtKB:Q5LRT0`	has_cofactor Magnesium dependence is reported for ligase activity. The sources do not establish an independent protein-binding stoichiometry or separate MgATP and free-ion mechanisms.	magnesium(2+) `CHEBI:18420`	UniProtKB:Q5LRT0 Source assertion: The Mg(2+) cofactor annotation is inferred by similarity, ECO:0000250 from Q5SKN9. Source location `comments[2].cofactors[0].cofactorCrossReference; comments[2].cofactors[0].evidences` PMID:24443527 Source assertion: The primary DmdB study explicitly states that Mg2+ was required for activity; divalent cations were consequently not tested in the salt-response experiment. Source location `Results, DmdBs show various activities in the presence of salts, section sec3-2 paragraph 1`
3-methylmercaptopropionyl-CoA dehydrogenase `UniProtKB:Q5LLW7`	has_cofactor The enzyme-bound FAD assignment is similarity-scoped and distinct from the generic whole ETF substrate. Free FAD did not act as the sole electron acceptor in the DSS-3 DmdC1 assay; cross-species DmdC activity with free FAD is not transferred here.	FAD(3-) `CHEBI:57692`	UniProtKB:Q5LLW7 Source assertion: FAD cofactor assignment is ECO:0000250, inferred by similarity to A3SI50; it is not a directly measured DSS-3 occupancy or stoichiometry. Source location `comments[2].cofactors[0].cofactorCrossReference; comments[2].cofactors[0].evidences`
S,S-dimethyl-beta-propiothetin `CHEBI:16457`	inhibits The physiological regulatory model is proposed from measured in vitro inhibition and cellular DMSP context; no direct regulator binding or universal in vivo flux assertion is made.	3-methylmercaptopropionyl-CoA ligase `UniProtKB:Q5LRT0`	PMID:24443527 Source assertion: DMSP strongly inhibits RPO_DmdB2, with the plotted concentration response measured using purified recombinant enzyme. This is an in vitro enzyme effect, not a transcription-factor claim. Source location `Results, DMSP inhibition of marine DmdBs, section sec3-5; Figure 3` UniProtKB:Q5LRT0 Source assertion: The DmdB2 activity-regulation annotation states inhibition by DMSP, with experimental evidence ECO:0000269 from PMID:24443527. Source location `comments[3].texts[0]`
3-(methylthio)propionate `CHEBI:49016`	activates Conditional relief of DMSP inhibition, not unqualified stimulation in the absence of inhibitor. MMPA is also the substrate of the activation reaction.	3-methylmercaptopropionyl-CoA ligase `UniProtKB:Q5LRT0`	PMID:24443527 Source assertion: MMPA above 2 mM relieves DMSP inhibition of RPO_DmdB2; about 80% activity is regained at 8 mM MMPA. ADP relief belongs to DmdB1 and is not transferred to DmdB2. Source location `Results, ADP and MMPA relieved inhibition by DMSP in R. pomeroyi DSS-3, section sec3-6 paragraph 1; Figure 5B` UniProtKB:Q5LRT0 Source assertion: The DmdB2 annotation records MMPA-dependent relief of DMSP inhibition, with ECO:0000269 from PMID:24443527. Source location `comments[3].texts[0]`
3-(methylsulfanyl)propanoate + ATP + CoA => 3-(methylsulfanyl)propanoyl-CoA + AMP + diphosphate `RHEA:43053`	part_of	`MetaCyc:PWY-6048`	MetaCyc:PWY-6048 Source assertion: The exact native pathway reaction-list includes RXN-12571. This is one of three complete native members. Source location `Pathway[@frameid="PWY-6048"]/reaction-list/Reaction` MetaCyc:RXN-12571 Source assertion: The native reaction is physiologically left-to-right and assigns ENZRXN-19462 as its enzymatic reaction. Source location `Reaction[@frameid="RXN-12571"]/reaction-direction; enzymatic-reaction/Enzymatic-Reaction` RHEA:43053 Source assertion: Rhea master 43052 explicitly links directed reaction 43053 through rh:directionalReaction. Source location `http://rdf.rhea-db.org/43052/rh:directionalReaction -> http://rdf.rhea-db.org/43053` MetaCyc:RXN-12571 Source assertion: The native reaction directly cross-references RHEA:43053. Source location `Reaction[@frameid="RXN-12571"]/dblink[dblink-db="RHEA"]/dblink-oid`
3-(methylsulfanyl)propanoyl-CoA + oxidized [electron-transfer flavoprotein] + H(+) => 3-(methylsulfanyl)acryloyl-CoA + reduced [electron-transfer flavoprotein] `RHEA:52613`	part_of	`MetaCyc:PWY-6048`	MetaCyc:PWY-6048 Source assertion: The exact native pathway reaction-list includes RXN-12572. This is one of three complete native members. Source location `Pathway[@frameid="PWY-6048"]/reaction-list/Reaction` MetaCyc:RXN-12572 Source assertion: The native reaction is physiologically left-to-right and assigns ENZRXN-19463 as its enzymatic reaction. Source location `Reaction[@frameid="RXN-12572"]/reaction-direction; enzymatic-reaction/Enzymatic-Reaction` RHEA:52613 Source assertion: Rhea master 52612 explicitly links directed reaction 52613 through rh:directionalReaction. Source location `http://rdf.rhea-db.org/52612/rh:directionalReaction -> http://rdf.rhea-db.org/52613` UniProtKB:Q5LLW7 Source assertion: The native protein crosswalk resolves the reviewed DmdC entry, whose current catalytic-activity annotation links RHEA:52612. The older native reaction itself does not carry this Rhea cross-reference. Source location `primaryAccession; comments[1].reaction.reactionCrossReferences`
3-(methylsulfanyl)acryloyl-CoA + 2 H2O => methanethiol + acetaldehyde + CO2 + CoA `RHEA:45145`	part_of The selected terminal Rhea net includes all four native component transformations and is represented once.	`MetaCyc:PWY-6048`	MetaCyc:PWY-6048 Source assertion: The exact native pathway reaction-list includes RXN-12573. This is one of three complete native members. Source location `Pathway[@frameid="PWY-6048"]/reaction-list/Reaction` MetaCyc:RXN-12573 Source assertion: The native reaction is physiologically left-to-right and assigns ENZRXN-19464 as its enzymatic reaction. Source location `Reaction[@frameid="RXN-12573"]/reaction-direction; enzymatic-reaction/Enzymatic-Reaction` RHEA:45145 Source assertion: Rhea master 45144 explicitly links directed reaction 45145 through rh:directionalReaction. Source location `http://rdf.rhea-db.org/45144/rh:directionalReaction -> http://rdf.rhea-db.org/45145` MetaCyc:RXN-12573 Source assertion: The native reaction directly cross-references RHEA:45145. Source location `Reaction[@frameid="RXN-12573"]/dblink[dblink-db="RHEA"]/dblink-oid`
3-(methylsulfanyl)propanoate + ATP + CoA => 3-(methylsulfanyl)propanoyl-CoA + AMP + diphosphate `RHEA:43053`	provides_input_for The shared chemical is CHEBI:82815; this is material continuity, not an assumed regulatory relation.	3-(methylsulfanyl)propanoyl-CoA + oxidized [electron-transfer flavoprotein] + H(+) => 3-(methylsulfanyl)acryloyl-CoA + reduced [electron-transfer flavoprotein] `RHEA:52613`	MetaCyc:PWY-6048 Source assertion: The native reaction-list contains all three activation, oxidation and cleavage transformations. Exact ChEBI intermediate continuity is established separately from both current Rhea sides. Source location `Pathway[@frameid="PWY-6048"]/reaction-list/Reaction` RHEA:43053 Source assertion: Rhea places CHEBI:82815 on the products side of directed RHEA:43053, with coefficient 1. Source location `http://rdf.rhea-db.org/43053/rh:products; http://rdf.rhea-db.org/43052_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_43052_compound_10325/rh:compound -> http://rdf.rhea-db.org/Compound_10325/rh:chebi` RHEA:52613 Source assertion: Rhea places CHEBI:82815 on the substrates side of directed RHEA:52613, with coefficient 1. Source location `http://rdf.rhea-db.org/52613/rh:substrates; http://rdf.rhea-db.org/52612_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_52612_compound_10325/rh:compound -> http://rdf.rhea-db.org/Compound_10325/rh:chebi`
3-(methylsulfanyl)propanoyl-CoA + oxidized [electron-transfer flavoprotein] + H(+) => 3-(methylsulfanyl)acryloyl-CoA + reduced [electron-transfer flavoprotein] `RHEA:52613`	provides_input_for The shared chemical is CHEBI:84994; this is material continuity, not an assumed regulatory relation.	3-(methylsulfanyl)acryloyl-CoA + 2 H2O => methanethiol + acetaldehyde + CO2 + CoA `RHEA:45145`	MetaCyc:PWY-6048 Source assertion: The native reaction-list contains all three activation, oxidation and cleavage transformations. Exact ChEBI intermediate continuity is established separately from both current Rhea sides. Source location `Pathway[@frameid="PWY-6048"]/reaction-list/Reaction` RHEA:52613 Source assertion: Rhea places CHEBI:84994 on the products side of directed RHEA:52613, with coefficient 1. Source location `http://rdf.rhea-db.org/52613/rh:products; http://rdf.rhea-db.org/52612_R/rh:contains1 -> http://rdf.rhea-db.org/Participant_52612_compound_11096/rh:compound -> http://rdf.rhea-db.org/Compound_11096/rh:chebi` RHEA:45145 Source assertion: Rhea places CHEBI:84994 on the substrates side of directed RHEA:45145, with coefficient 1. Source location `http://rdf.rhea-db.org/45145/rh:substrates; http://rdf.rhea-db.org/45144_L/rh:contains1 -> http://rdf.rhea-db.org/Participant_45144_compound_11096/rh:compound -> http://rdf.rhea-db.org/Compound_11096/rh:chebi`

References

MetaCyc:ENZRXN-19462 MetaCyc ENZRXN-19462 native XML (source version: MetaCyc 22.5; original native XML)
MetaCyc:ENZRXN-19463 MetaCyc ENZRXN-19463 native XML (source version: MetaCyc 22.5; original native XML)
MetaCyc:ENZRXN-19464 MetaCyc ENZRXN-19464 native XML (source version: MetaCyc 22.5; original native XML)
MetaCyc:MONOMER-16783 MetaCyc MONOMER-16783 native XML (source version: MetaCyc 22.5; original native XML)
MetaCyc:MONOMER-16784 MetaCyc MONOMER-16784 native XML (source version: MetaCyc 22.5; original native XML)
MetaCyc:MONOMER-16785 MetaCyc MONOMER-16785 native XML (source version: MetaCyc 22.5; original native XML)
MetaCyc:PWY-6048 MetaCyc PWY-6048 native XML (source version: MetaCyc 22.5; original native XML)
MetaCyc:RXN-12571 MetaCyc RXN-12571 native XML (source version: MetaCyc 22.5; original native XML)
MetaCyc:RXN-12572 MetaCyc RXN-12572 native XML (source version: MetaCyc 22.5; original native XML)
MetaCyc:RXN-12573 MetaCyc RXN-12573 native XML (source version: MetaCyc 22.5; original native XML)
PMID:21562561 Novel pathway for assimilation of dimethylsulphoniopropionate widespread in marine bacteria. (source version: Nature 473, 208-211 (2011); complete six-page author-hosted original PDF)
PMID:23704947 Crystal Structure of DmdD, a Crotonase Superfamily Enzyme That Catalyzes the Hydration and Hydrolysis of Methylthioacryloyl-CoA (source version: PLOS ONE 8:e63870 (2013); original full-text JATS)
PMID:24443527 Regulatory and Functional Diversity of Methylmercaptopropionate Coenzyme A Ligases from the Dimethylsulfoniopropionate Demethylation Pathway in Ruegeria pomeroyi DSS-3 and Other Proteobacteria (source version: Original full-text PMC HTML retrieved 2026-10-11)
PMID:34818101 Substrate Specificity of the 3-Methylmercaptopropionyl Coenzyme A Dehydrogenase (DmdC1) from Ruegeria pomeroyi DSS-3 (source version: Original full-text PMC HTML retrieved 2026-10-11)
RHEA:43053 Rhea 43053 directed MMPA cleavage reaction (source version: 142 (2026-09-02); complete compressed RDF body)
RHEA:45145 Rhea 45145 directed MMPA cleavage reaction (source version: 142 (2026-09-02); complete compressed RDF body)
RHEA:52613 Rhea 52613 directed MMPA cleavage reaction (source version: 142 (2026-09-02); complete compressed RDF body)
UniProtKB:Q5LLW6 UniProtKB Q5LLW6, Ruegeria pomeroyi DSS-3 (source version: 2026_03 (2026-09-02))
UniProtKB:Q5LLW7 UniProtKB Q5LLW7, Ruegeria pomeroyi DSS-3 (source version: 2026_03 (2026-09-02))
UniProtKB:Q5LRT0 UniProtKB Q5LRT0, Ruegeria pomeroyi DSS-3 (source version: 2026_03 (2026-09-02))

Curation history

2026-10-11T09:04:14Z codex
- CREATE — Add methylthiopropanoate degradation I (cleavage)
  Curated all three native methylthiopropanoate cleavage reactions, retaining generic electron-carrier conventions, measured enzyme/cofactor context and spontaneous components of the terminal net reaction. Maintained record MetaCyc:PWY-6048; creation bytes SHA256 7810e21c690b17fe781fd249ea6fc0ec86220913a55947df75ec29c15cffe5dd. Original-source projections, replay and identifier decisions are in research/pathway_additions/2026-10-11-next-203/. Duplicate searches included ignored and hidden files. Independent review and full integration gates are separate subsequent checks, not claimed by this creation event.
Read this curation session