Bacterial dimethylglycine and sarcosine catabolism

A reusable two-step bacterial module for sequential N-demethylation of dimethylglycine to sarcosine and then glycine. In the first step a DgcA-type flavoprotein oxidizes dimethylglycine and reduces a membrane-anchored DgcB-type 2[4Fe-4S] ferredoxin. Reduced DgcB is proposed to pass the electrons to a pathway-associated heterodimeric ETF. The second step is performed either by a tetrahydrofolate-coupled heterotetrameric SoxABDG sarcosine oxidase or by a monomeric sarcosine oxidase that releases formaldehyde. Upstream glycine-betaine demethylation and downstream glycine cleavage or serine conversion are outside the module boundary.

MODULE:bacterial_dimethylglycine_sarcosine_catabolismCOMPLETECONCRETEMetabolic Pathwaymodules/bacterial_dimethylglycine_sarcosine_catabolism.yaml
PMID:17951379
Identification of two gene clusters and a transcriptional regulator required for Pseudomonas aeruginosa glycine betaine catabolism.
Mutant growth and isotope-tracing experiments support DgcAB-dependent dimethylglycine-to-sarcosine and SoxBDAG-dependent sarcosine-to-glycine conversion in Pseudomonas aeruginosa.
Similar experiments showed that strains with mutations in the dgcAB (PA5398-PA5399) genes, which exhibit homology to genes that encode other enzymes with demethylase activity, are required for the conversion of DMG to sarcosine.
PMID:35266867
Creatine utilization as a sole nitrogen source in Pseudomonas putida KT2440 is transcriptionally regulated by CahR.
The KT2440 creatine-utilization study identifies SoxBDAG as pathway background for conversion of sarcosine to glycine and formaldehyde.
sarcosine is then converted to glycine and formaldehyde by the tetrameric sarcosine oxidase (SoxBDAG)
PMID:32631860
Role of N,N-Dimethylglycine and Its Catabolism to Sarcosine in Chromohalobacter salexigens DSM 3043.
Biochemical analysis directly establishes DdhC as an FAD-containing dimethylglycine and sarcosine dehydrogenase with bound NAD(P), while disruption of the adjacent ferredoxin and ETF genes supports their pathway participation. The ordered DdhC-to-ferredoxin-to-ETF relay is a mechanistic inference.
gene disruption and complementation assays indicated that the csal_0990, csal_0991, csal_0992, and csal_0993 genes are responsible for DMG degradation to sarcosine.
PMID:9185627
Folate utilization by monomeric versus heterotetrameric sarcosine oxidases.
Biochemical comparison shows that heterotetrameric sarcosine oxidases efficiently couple the one-carbon unit to tetrahydrofolate, whereas monomeric enzymes predominantly release formaldehyde.
The results show that only the heterotetrameric sarcosine oxidases can use tetrahydrofolates as substrates
PMID:15946648
Crystal structure of heterotetrameric sarcosine oxidase from Corynebacterium sp. U-96.
The structure assigns NAD and folate binding to SoxA, FAD and FMN to SoxB, and a Cys3His-bound zinc atom to SoxD.
The alpha subunit is composed of two domains, contains NAD(+), and binds folinic acid. The beta subunit contains dimethylglycine, FAD, and FMN, and these flavins are approximately 10A apart.
UniProtKB:Q1QYW1
Reviewed DgcA-like bacterial dimethylglycine dehydrogenase
Q1QYW1 is the directly characterized DgcA-like bacterial dehydrogenase, a monomer with noncovalent FAD and bound NAD(P) that reduces the [4Fe-4S] ferredoxin Q1QYW0 (EC 1.5.7.3). Onward transfer to ETF rests on the genetically required four-gene locus.
UniProtKB:Q1QYW0
Reviewed DgcB-like membrane-anchored ferredoxin
Q1QYW0 is a reviewed membrane-anchored ferredoxin and a genetically required member of the Q1QYW1-associated degradation locus; direct electron transfer between the purified proteins has not been shown.
UniProtKB:Q50LF0
Reviewed tetrameric sarcosine oxidase alpha subunit
Q50LF0 and its reviewed Corynebacterium partner entries ground the tetrahydrofolate-coupled SoxABDG complex.
UniProtKB:P40873
Reviewed monomeric sarcosine oxidase
P40873 grounds the alternative single-chain sarcosine oxidase.

The module is species-neutral. The dgcA-dgcB-etfA-etfB and soxBDAG loci are conserved among glycine-betaine-degrading Pseudomonadota, and monomeric sarcosine oxidases occur in Actinomycetota and Bacillota. Representative members were chosen for experimental evidence: Chromohalobacter salexigens DdhC, Csal_0991 and EtfAB (purified DdhC biochemistry and gene disruption of all four genes), Corynebacterium sp. U-96 SoxABDG (purification, cofactor analysis and crystal structure), and Arthrobacter sp. TE1826 monomeric sarcosine oxidase. Pseudomonas putida KT2440 is kept as a genome-scale exemplar with orthologous loci. Its own proteins are not reconstituted; DgcA and DgcB are 81% and 72% identical to DdhC and Csal_0991. Pseudomonas aeruginosa PAO1 dgcAB and soxBDAG mutant genetics (PMID:17951379) are cited as evidence, but its proteins are not added as members, because they would add no independent biochemical evidence. Family grounding: the ETF subunits are grounded on PANTHER PTHR43153 and PTHR21294, whose electron transfer activity is family-wide; the beta-oxidation process propagated to the dimethylglycine-locus ETFs is treated as over-annotation in their reviews. The Sox subunits are grounded on the subunit-specific NCBIfam TIGR01372-TIGR01375 models. PANTHER places SoxA in the aminomethyltransferase family (PTHR43757) and SoxB in a subfamily shared with FOXRED1 (PTHR13847:SF287); neither is role-specific, and both are reviewed. The monomeric enzyme is grounded at PTHR10961:SF7, because sarcosine oxidase activity is not family-wide in PTHR10961. DgcA and DgcB assert no family id: their PANTHER families (PTHR43656, PTHR43255) are reviewed but functionally heterogeneous. These choices differ deliberately from the family ids proposed for this module in open PR #5076. The folate-coupled SoxABDG reaction (EC 1.5.3.24) and the ferredoxin-linked dimethylglycine dehydrogenase reaction (EC 1.5.7.3) have no GO molecular-function terms; the member gene reviews carry proposed new terms. Subunit convention for the SoxABDG heterotetramer, applied identically to the Corynebacterium and KT2440 reviews: SoxB, which carries the sarcosine site and covalent FMN plus FAD, enables the activity, while SoxA, SoxD and SoxG contribute to it; their GOA enables qualifiers on sarcosine oxidase activity are recorded as WRONG_QUALIFIER source defects. All four use the proposed folate-coupled term as their core function, and GO:0008115 (the folate-free, formaldehyde-forming reaction) is kept as non-core. A bifunctional monomeric dimethylglycine oxidase (Arthrobacter globiformis DMGO) is a further first-step variant that is not yet modeled.

5Nodes
2Parts
1Variant Sets
2Variants
5Annotons
3Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✓ present

  • bacterial_dimethylglycine_sarcosine_catabolism-deep-research-openscientist.md (openscientist)

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

5 gene-function check(s) reflected in core functions · 0 conflict(s) · 2 evidence or coverage gap(s) (10 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
dgca_dehydrogenase_activity DgcA (Pseudomonas putida KT2440)
UniProtKB:Q88R24
Family Representative 		N,N-dimethylglycine/sarcosine dehydrogenase (ferredoxin) activity
GO:0033694 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
dgca_dehydrogenase_activity DdhC (Chromohalobacter salexigens)
UniProtKB:Q1QYW1
Family Representative 		N,N-dimethylglycine/sarcosine dehydrogenase (ferredoxin) activity
GO:0033694 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
dgcb_ferredoxin_activity DgcB (Pseudomonas putida KT2440)
UniProtKB:Q88R23
Family Representative 		electron transfer from DgcA to the pathway ETF
GO:0009055 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
dgcb_ferredoxin_activity Csal_0991 (Chromohalobacter salexigens)
UniProtKB:Q1QYW0
Family Representative 		electron transfer from DgcA to the pathway ETF
GO:0009055 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
dimethylglycine_catabolism_etf_activity PROTEIN_COMPLEX
Gene 		electron transfer from reduced DgcB toward an unresolved acceptor
GO:0009055 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
soxabdg_complex_activity PROTEIN_COMPLEX
Gene 		sarcosine oxidase (5,10-methylenetetrahydrofolate-forming) activity
No function ID 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
monomeric_sarcosine_oxidase_activity soxA (Arthrobacter sp. TE1826 monomeric sarcosine oxidase)
UniProtKB:P40873
Family Representative 		sarcosine oxidase activity
GO:0008115 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
dgca_dehydrogenase_activity DgcA flavin oxidoreductase family
Family 		N,N-dimethylglycine/sarcosine dehydrogenase (ferredoxin) activity
GO:0033694 		Family Id Missing
The family has no identifier linking it to a curated family review.
dgcb_ferredoxin_activity DgcB membrane-anchored 2[4Fe-4S] ferredoxin family
Family 		electron transfer from DgcA to the pathway ETF
GO:0009055 		Family Id Missing
The family has no identifier linking it to a curated family review.
monomeric_sarcosine_oxidase_activity monomeric sarcosine oxidase family
PANTHER:PTHR10961:SF7
Family 		sarcosine oxidase activity
GO:0008115 		Family Supported
Family review supports GO:0008115 for PANTHER:PTHR10961:SF7. Sarcosine oxidase activity is established for bacterial MSOX in SF7 (reference protein P40873) and animal PIPOX in SF46, but not for the fructosyl amino acid (SF24) or saccharopine (SF26) oxidases. Within SF7 the enterobacterial MTOX enzymes prefer N-methyl-L-tryptophan, so sarcosine oxidase is the primary activity only of the MSOX members.

Gene-review completeness (17/17 grounded genes reviewed)

17 complete review(s) · 1 with deep research · 0 missing review · 16 reviewed but lacking deep research

Gene Review Complete Deep research
Csal_0991 Q1QYW0 ✓ ✓ ✗
ddhC Q1QYW1 ✓ ✓ ✗
dgcA Q88R24 ✓ ✓ ✗
dgcB Q88R23 ✓ ✓ ✗
etfA Q1QYV9 ✓ ✓ ✗
etfB Q1QYV8 ✓ ✓ ✗
PP_0312 Q88R22 ✓ ✓ ✗
PP_0313 Q88R21 ✓ ✓ ✗
soxA P40873 ✓ ✓ ✗
soxA Q50LF0 ✓ ✓ ✗
soxA Q88R09 ✓ ✓ ✓
soxB Q50LF2 ✓ ✓ ✗
soxB Q88R11 ✓ ✓ ✗
soxD Q50LF1 ✓ ✓ ✗
soxD Q88R10 ✓ ✓ ✗
soxG Q50LE9 ✓ ✓ ✗
soxG Q88R08 ✓ ✓ ✗

Details

Context
bacteriaNCBITaxon:2
Bacterial dimethylglycine and sarcosine catabolismMetabolic Pathwaybacterial_dimethylglycine_sarcosine_catabolism
Context
bacteriaNCBITaxon:2

Connections

Dimethylglycine oxidation by DgcA reduces the DgcB 2[4Fe-4S] ferredoxin, which is the electron acceptor of EC 1.5.7.3.
Reduced DgcB is proposed to pass electrons to the pathway EtfAB heterodimer; this step is inferred from the genetically required four-gene locus.
Sarcosine formed by dimethylglycine demethylation is the substrate of sarcosine oxidase.
Part 1: dimethylglycine demethylation to sarcosine
Dimethylglycine conversion to sarcosineReactiondimethylglycine_to_sarcosine

Annotons

DgcA dimethylglycine dehydrogenase
dgca_dehydrogenase_activity
Participant: Family: DgcA flavin oxidoreductase family
Family:
DgcA flavin oxidoreductase family Two-domain flavoproteins (an Old Yellow Enzyme-like barrel fused to an FAD/NAD(P)-binding domain) encoded in a conserved dgcA-dgcB-etfA-etfB neighborhood. No PANTHER id is asserted: PTHR43656 and its SF2 subfamily also contain unrelated single-domain flavin oxidoreductases (see the PTHR43656 family review).
Representative Members: DgcA (Pseudomonas putida KT2440)UniProtKB:Q88R24 DdhC (Chromohalobacter salexigens)UniProtKB:Q1QYW1

Function

N,N-dimethylglycine/sarcosine dehydrogenase (ferredoxin) activityGO:0033694
Substrates: N,N-dimethylglycine oxidized 2[4Fe-4S] ferredoxin (DgcB) water
Products: sarcosine formaldehyde reduced 2[4Fe-4S] ferredoxin (DgcB) 2 protons

EC 1.5.7.3 (RHEA:74167). DdhC is active as a monomer containing noncovalent FAD and bound NAD(P), and the membrane ferredoxin DgcB is the electron acceptor it reduces, so the activity belongs to DgcA alone. GO has no term for this reaction; the member reviews propose "N,N-dimethylglycine/sarcosine dehydrogenase (ferredoxin) activity" under GO:0033694 (oxidoreductase activity, acting on the CH-NH group of donors, iron-sulfur protein as acceptor). GO:0047865 is not used because its definition names electron-transfer flavoprotein as the direct acceptor. Purified DdhC also demethylates sarcosine in vitro (RHEA:74155), but the disruption mutant still grows on sarcosine, so the in vivo role modeled here is the dimethylglycine step.

DgcB membrane ferredoxin electron transfer
dgcb_ferredoxin_activity
Participant: Family: DgcB membrane-anchored 2[4Fe-4S] ferredoxin family
Family:
DgcB membrane-anchored 2[4Fe-4S] ferredoxin family Membrane-anchored ferredoxins with a Csal_0991-like N-terminal region and CCG/4Fe-4S domains, encoded beside DgcA and the pathway ETF. No PANTHER id is asserted: PTHR43255:SF1 also contains archaeal heterodisulfide reductase HdrC subunits and other bacterial electron-transfer subunits (see the PTHR43255 family review).
Representative Members: DgcB (Pseudomonas putida KT2440)UniProtKB:Q88R23 Csal_0991 (Chromohalobacter salexigens)UniProtKB:Q1QYW0

Function

electron transfer from DgcA to the pathway ETFGO:0009055

DgcB is reduced by DgcA and is proposed to reoxidize by passing electrons to the EtfAB heterodimer. Its disruption abolishes growth on dimethylglycine but not on sarcosine; direct electron transfer between the purified proteins has not been shown.

Pathway-associated electron transfer flavoprotein
dimethylglycine_catabolism_etf_activity
Participant: Protein Complex: dimethylglycine catabolism ETF heterodimer
Protein Complex:
dimethylglycine catabolism ETF heterodimer
Active units:
ETF alpha subunit
Participant: Family: dimethylglycine catabolism ETF alpha-subunit family
Family:
dimethylglycine catabolism ETF alpha-subunit familyPANTHER:PTHR43153 Pathway assignment requires an exact curated representative in the conserved dgcA-dgcB-etfA-etfB neighborhood; generic ETF alpha/FixB family membership is insufficient.
Representative Members: PP_0312 (Pseudomonas putida KT2440)UniProtKB:Q88R22 EtfA (Chromohalobacter salexigens)UniProtKB:Q1QYV9
ETF beta subunit
Participant: Family: dimethylglycine catabolism ETF beta-subunit family
Family:
dimethylglycine catabolism ETF beta-subunit familyPANTHER:PTHR21294 Pathway assignment requires an exact curated representative paired with the pathway ETF alpha subunit beside dgcAB; generic ETF beta/FixA family membership is insufficient.
Representative Members: PP_0313 (Pseudomonas putida KT2440)UniProtKB:Q88R21 EtfB (Chromohalobacter salexigens)UniProtKB:Q1QYV8

Function

electron transfer from reduced DgcB toward an unresolved acceptorGO:0009055

The ETF heterodimer is proposed to accept reducing equivalents from reduced DgcB. Direct transfer and the downstream acceptor have not been established for KT2440.

Part 2: sarcosine demethylation to glycine
Sarcosine conversion to glycineReactionsarcosine_to_glycine
Variant set: Sarcosine oxidase architecture by enzyme architecture (One Or More)
Tetrahydrofolate-coupled SoxABDG heterotetramerReactiontetrameric_soxabdg_variant

Annotons

SoxABDG sarcosine oxidase activity
soxabdg_complex_activity
Participant: Protein Complex: tetrameric sarcosine oxidase complex
Protein Complex:
tetrameric sarcosine oxidase complexGO:0032921
Active units:
SoxA alpha subunit
Participant: Family: tetrameric sarcosine oxidase alpha-subunit family
Family:
tetrameric sarcosine oxidase alpha-subunit familyNCBIfam:TIGR01372 Grounded on NCBIfam TIGR01372. PANTHER places SoxA in PTHR43757:SF2 with glycine cleavage T-proteins, so the PANTHER id is not role-specific.
Representative Members: SoxA (Pseudomonas putida KT2440)UniProtKB:Q88R09 SoxA (Corynebacterium sp. U-96)UniProtKB:Q50LF0
SoxB beta subunit
Participant: Family: tetrameric sarcosine oxidase beta-subunit family
Family:
tetrameric sarcosine oxidase beta-subunit familyNCBIfam:TIGR01373 Grounded on NCBIfam TIGR01373. PANTHER places SoxB in PTHR13847:SF287, a subfamily shared with FOXRED1, so the PANTHER id is not role-specific.
Representative Members: SoxB (Pseudomonas putida KT2440)UniProtKB:Q88R11 SoxB (Corynebacterium sp. U-96)UniProtKB:Q50LF2
SoxD delta subunit
Participant: Family: tetrameric sarcosine oxidase delta-subunit family
Family:
tetrameric sarcosine oxidase delta-subunit familyNCBIfam:TIGR01374
Representative Members: SoxD (Pseudomonas putida KT2440)UniProtKB:Q88R10 SoxD (Corynebacterium sp. U-96)UniProtKB:Q50LF1
SoxG gamma subunit
Participant: Family: tetrameric sarcosine oxidase gamma-subunit family
Family:
tetrameric sarcosine oxidase gamma-subunit familyNCBIfam:TIGR01375
Representative Members: SoxG (Pseudomonas putida KT2440)UniProtKB:Q88R08 SoxG (Corynebacterium sp. U-96)UniProtKB:Q50LE9

Function

sarcosine oxidase (5,10-methylenetetrahydrofolate-forming) activity
Substrates: sarcosine tetrahydrofolate oxygen
Products: glycine 5,10-methylenetetrahydrofolate hydrogen peroxide

This is EC 1.5.3.24 / RHEA:70455. No current GO molecular function term accurately represents the folate-coupled reaction; GO:0008115 is reserved for the water/formaldehyde chemistry. In low folate, the same complex can release formaldehyde conditionally.

Monomeric sarcosine oxidaseReactionmonomeric_sarcosine_oxidase_variant

Annotons

Monomeric sarcosine oxidase activity
monomeric_sarcosine_oxidase_activity
Participant: Family: monomeric sarcosine oxidase family
Family:
monomeric sarcosine oxidase familyPANTHER:PTHR10961:SF7 Grounded at PANTHER subfamily PTHR10961:SF7, where sarcosine oxidase activity is supported; the subfamily also contains enterobacterial N-methyl-L-tryptophan oxidase (SolA), whose sarcosine oxidation is secondary. Other PTHR10961 subfamilies oxidise pipecolate, saccharopine or fructosyl amino acids.
Representative Members: soxA (Arthrobacter sp. TE1826 monomeric sarcosine oxidase)UniProtKB:P40873

Function

sarcosine oxidase activityGO:0008115
Substrates: sarcosine oxygen water
Products: glycine formaldehyde hydrogen peroxide