Glutathione-dependent formaldehyde detoxification

A detoxification module found in bacteria and eukaryotes in which formaldehyde is captured by glutathione as S-(hydroxymethyl)glutathione, the hemithioacetal is oxidized to S-formylglutathione by a class-III alcohol dehydrogenase, and the thioester is hydrolyzed to formate while regenerating glutathione. Chemical capture, oxidation, and hydrolysis are represented as separate steps; formate can then be oxidized to CO2 by an NAD-dependent formate dehydrogenase.

MODULE:glutathione_dependent_formaldehyde_detoxificationDRAFTBiological Processmodules/glutathione_dependent_formaldehyde_detoxification.yaml
formaldehyde catabolic processGO:0046294
PMID:21261833
Physiological responses of Pseudomonas putida to formaldehyde during detoxification
KT2440 oxidizes formaldehyde rather than assimilating it. PP_1616 and PP_1617 are induced by 0.5 mM formaldehyde, and their disruption impairs growth at 1.5 mM formaldehyde; the paper does not assign either protein to this glutathione-dependent reaction sequence.
PMID:21261833
Physiological responses of Pseudomonas putida to formaldehyde during detoxification
This study calls PP_3970 fhdA and glutathione-dependent, but reports a formaldehyde-sensitivity phenotype rather than a biochemical substrate or glutathione-dependence assay.
the fhdA gene encoding a glutathione‐dependent formaldehyde dehydrogenase (PP3970)
PMID:19304846
Redundancy of enzymes for formaldehyde detoxification in Pseudomonas putida
KT2440 PP_3970 knockout data support a contribution to labeled-formaldehyde mineralization, but do not establish the enzyme's substrate chemistry or glutathione dependence.
The results showed that both enzymes contributed to formaldehyde catabolism.
PMCID:PMC2687156
Open-access full text of PMID:19304846
The open-access full text calls PP_3970 fdhB during a comparative sequence-annotation analysis; its glutathione-independent classification is not established by a direct biochemical assay.
The PP0328 gene was annotated as fdhA, whereas the PP3970 gene was called fdhB (Table 1).
UniProtKB:Q88FV8
PSEPK PP_3970 UniProt record
The current unreviewed record names PP_3970 ybdR and assigns only a generic zinc-dependent, NAD(P)-binding oxidoreductase function; it does not assign formaldehyde as substrate or state glutathione dependence.
file:PSEPK/frmA/frmA-uniprot.txt
PSEPK FrmA UniProt record
Q88MF5 is an S-(hydroxymethyl)glutathione dehydrogenase.
UniProtKB:P25437
Reviewed Escherichia coli FrmA UniProt record
The reviewed E. coli FrmA record reports glutathione-dependent formaldehyde dehydrogenase activity, assigns GO:0051903 from direct assay, and classifies the protein in PTHR43880:SF12.
file:PSEPK/frmC/frmC-uniprot.txt
PSEPK FrmC UniProt record
Q88MF4 is an S-formylglutathione hydrolase.
file:interpro/panther/PTHR10061/PTHR10061-metadata.yaml
PANTHER PTHR10061 family metadata
PTHR10061 is the S-formylglutathione hydrolase family used for the FrmC selector.
file:modules/glutathione_dependent_formaldehyde_detoxification-deep-research-openscientist.md
OpenScientist review of glutathione-dependent formaldehyde detoxification
Supports the reusable three-step boundary, spontaneous first step, NAD+-biased FrmA oxidation, FrmC-family hydrolysis, and separation from glutathione-independent formaldehyde oxidation routes.
file:projects/P_PUTIDA/deep-research/PSEPK__glutathione_dependent_formaldehyde_detoxification__ppu00680-deep-research-openscientist.md
OpenScientist PSEPK pathway satisfiability review
Finds the branch satisfiable through adjacent frmA and frmC candidates while emphasizing that their exact KT2440 chemistry lacks direct enzymology and that PP_3970 belongs outside this defined branch.
PANTHER:PTN000191653
PAINT FrmA-function ancestral node
Local PTHR43880 PAINT data place GO:0051903 by IBD at PTN000191653, seeded in part by reviewed Escherichia coli FrmA P25437.
PANTHER:PTN000006872
PAINT S-formylglutathione-hydrolase ancestral node
Local PTHR10061 PAINT data place GO:0018738 by IBD at PTN000006872, seeded in part by reviewed E. coli FrmB P51025 and YeiG P33018.
YeastPathways:PWY-1801-1
formaldehyde oxidation II (glutathione-dependent) (S. cerevisiae, SGD YeastPathways)
YeastCyc lists spontaneous RXN-2961, RXN-2962 (SFA1), S-FORMYLGLUTATHIONE-HYDROLASE-RXN (YJL068C) and 1.2.1.2-RXN (FDH1). All assignments were retained; FDH1 is modelled as an optional downstream formate-oxidation part.
PMID:8483449
Molecular structure and genetic regulation of SFA, a gene responsible for resistance to formaldehyde in Saccharomyces cerevisiae, and characterization of its protein product.
SFA1 encodes the yeast glutathione-dependent formaldehyde dehydrogenase.
PMID:10427036
Purification and properties of an esterase from the yeast Saccharomyces cerevisiae and identification of the encoding gene.
YJL068C encodes an S-formylglutathione hydrolase.
We purified an intracellular esterase that can function as an S-formylglutathione hydrolase from the yeast Saccharomyces cerevisiae.
PMID:11921099
Functional analysis of structural genes for NAD(+)-dependent formate dehydrogenase in Saccharomyces cerevisiae.
FDH1 and FDH2 encode NAD-dependent formate dehydrogenase; in S288C FDH2 is split into two ORFs, and fdh1 fdh2 mutants lack activity.
PMID:8625422
Overexpression of ADH1 confers hyper-resistance to formaldehyde in Saccharomyces cerevisiae.
Sfa1 (Adh5) detoxification needs glutathione, whereas ADH1 provides a glutathione-independent reductive route outside this module.
file:yeast/YJL068C/YJL068C-ai-review.yaml
YJL068C gene review (S. cerevisiae)
Core function GO:0018738.
file:yeast/FDH1/FDH1-ai-review.yaml
FDH1 gene review (S. cerevisiae)
Core function GO:0008863 in formate catabolism.

The boundary begins with glutathione capture of formaldehyde and ends at formate plus regenerated glutathione. Formate oxidation to carbon dioxide, formaldehyde efflux, DNA repair, protein-quality control, and nitrosothiol reduction are distinct downstream or parallel functions. Organisms can carry additional formaldehyde oxidation routes, so this module represents the glutathione-dependent branch rather than the entire cellular response. In KT2440, PP_3970 has genetic evidence for a contribution to formaldehyde mineralization, but that does not place it in the defined FrmA-FrmC reaction sequence. The literature uses conflicting names and glutathione-dependence assignments for PP_3970, while UniProtKB:Q88FV8 currently assigns only a generic zinc-dependent, NAD(P)-binding oxidoreductase function. Its precise chemistry therefore remains unresolved. The exact contribution of PP_1616/FrmA and PP_1617/FrmC to this branch remains based on homology and should be tested directly. ALIGN (YeastPathways project, 2026-10): the bacterial module was widened to bacteria and eukaryotes. S. cerevisiae SFA1 (P32771) shares PANTHER PTHR43880:SF12 with E. coli FrmA, and YJL068C (P40363) and human ESD share PTHR10061 with FrmB/YeiG. Human ADH5 is in PTHR43880:SF4 and is therefore not listed under the SF12 selector. SFA1 is also the yeast S-nitrosoglutathione reductase; that activity is outside this module. The YeastCyc formate dehydrogenase step (FDH1) was added as an optional part 4, because formate oxidation is not required for formaldehyde detoxification. FDH2 is a pseudogene split into YPL275W/YPL276W in S288C. GO-CAM disagreement: the SGD model attaches SFA1 only to the root molecular_function term in cytoplasm, while GO:0051903 is directly supported. No PomBase model is linked for this group. The KT2440 PP_3970 gap was reclassified as BIOLOGY because its substrate and glutathione dependence need direct enzymology.

5Nodes
4Parts
0Variant Sets
0Variants
3Annotons
3Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✓ present

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

Leaf nodes lacking representative members

1 leaf node(s) with no concrete protein grounding:

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Reaction chaining (advisory)

✓ every PRECEDES step chains, or its break is acknowledged via chaining_status.

  • formaldehyde_glutathione_capture → frma_hemithioacetal_oxidation [NOT_CHECKED]
    Glutathione-bound one-carbon intermediates link the steps; no CoA carrier is involved.
  • frma_hemithioacetal_oxidation → frmc_formylglutathione_hydrolysis [NOT_CHECKED]
    Glutathione-bound one-carbon intermediates link the steps; no CoA carrier is involved.
  • frmc_formylglutathione_hydrolysis → formate_oxidation [NOT_CHECKED]
    Formate links the steps; no CoA carrier is involved.

Function consistency and core coverage

5 gene-function check(s) reflected in core functions · 0 conflict(s) · 4 evidence or coverage gap(s) (12 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
frma_formaldehyde_dehydrogenase frmA (Pseudomonas putida KT2440)
UniProtKB:Q88MF5
Family Representative 		S-(hydroxymethyl)glutathione dehydrogenase [NAD(P)+] activity
GO:0051903 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
frma_formaldehyde_dehydrogenase frmA (Escherichia coli; characterized)
UniProtKB:P25437
Family Representative 		S-(hydroxymethyl)glutathione dehydrogenase [NAD(P)+] activity
GO:0051903 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
frma_formaldehyde_dehydrogenase SFA1 (Saccharomyces cerevisiae)
UniProtKB:P32771
Family Representative 		S-(hydroxymethyl)glutathione dehydrogenase [NAD(P)+] activity
GO:0051903 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
frmc_formylglutathione_hydrolase frmC (Pseudomonas putida KT2440)
UniProtKB:Q88MF4
Family Representative 		S-formylglutathione hydrolase activity
GO:0018738 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
frmc_formylglutathione_hydrolase frmB (Escherichia coli; characterized)
UniProtKB:P51025
Family Representative 		S-formylglutathione hydrolase activity
GO:0018738 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
frmc_formylglutathione_hydrolase yeiG (Escherichia coli; characterized)
UniProtKB:P33018
Family Representative 		S-formylglutathione hydrolase activity
GO:0018738 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
frmc_formylglutathione_hydrolase YJL068C (Saccharomyces cerevisiae)
UniProtKB:P40363
Family Representative 		S-formylglutathione hydrolase activity
GO:0018738 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
frmc_formylglutathione_hydrolase ESD (human)
UniProtKB:P10768
Family Representative 		S-formylglutathione hydrolase activity
GO:0018738 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
fdh_activity FDH1 (Saccharomyces cerevisiae)
UniProtKB:Q08911
Family Representative 		formate dehydrogenase (NAD+) activity
GO:0008863 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
frma_formaldehyde_dehydrogenase zinc-containing alcohol dehydrogenase family, class-3 lineage
PANTHER:PTHR43880:SF12
Family 		S-(hydroxymethyl)glutathione dehydrogenase [NAD(P)+] activity
GO:0051903 		Family Supported
Family review supports GO:0051903 for PANTHER:PTHR43880:SF12. Safe for the class III subfamilies: SF12 (bacterial and fungal, incl. SFA1, FrmA), SF4 (mammalian ADH5), SF21 (fish) and SF58 (plant HOT5). Not safe for the plant class P or vertebrate class I, II, IV and V subfamilies, which are ethanol/retinol-active derivatives. The glutathione-dependent formaldehyde detoxification module selects SF12, which is safe; it does not capture human ADH5 (SF4), as the module notes already state.
frmc_formylglutathione_hydrolase FrmC family
PANTHER:PTHR10061
Family 		S-formylglutathione hydrolase activity
GO:0018738 		Family Supported
Family review supports GO:0018738 FAMILY_WIDE. Asserted by glutathione_dependent_formaldehyde_detoxification for the family. Accepted by reviewed members in both subfamilies (YJL068C in SF0, P. putida frmC in SF1).
fdh_activity NAD-dependent formate dehydrogenase family
PANTHER:PTHR42938:SF9
Family 		formate dehydrogenase (NAD+) activity
GO:0008863 		Family Supported
Family review supports GO:0008863 for PANTHER:PTHR42938:SF9. Eukaryotic formate dehydrogenases in SF9, as glutathione_dependent_formaldehyde_detoxification selects; the PdxB lineage of SF9 is excepted.

Gene-review completeness (5/9 grounded genes reviewed)

4 complete review(s) · 5 with deep research · 4 missing review · 0 reviewed but lacking deep research

Gene Review Complete Deep research
FDH1 Q08911 ✓ ✓ ✓
frmA Q88MF5 ✓ ✓ ✓
frmC Q88MF4 ✓ ✓ ✓
ESD (human) P10768 ✗ — —
frmA (Escherichia coli; characterized) P25437 ✗ — —
yeiG (Escherichia coli; characterized) P33018 ✗ — —
frmB (Escherichia coli; characterized) P51025 ✗ — —
SFA1 P32771 ✓ 48/50 ✓
YJL068C P40363 ✓ ✓ ✓

Details

Context
bacteriaNCBITaxon:2 eukaryotesNCBITaxon:2759
Glutathione-dependent formaldehyde detoxificationBiological Processglutathione_dependent_formaldehyde_detoxification
formaldehyde catabolic processGO:0046294
Context
bacteriaNCBITaxon:2 eukaryotesNCBITaxon:2759

Connections

Part 1: Glutathione capture of formaldehyde
S-(hydroxymethyl)glutathione formationReactionformaldehyde_glutathione_capture

Formaldehyde reacts with glutathione to form the hemithioacetal S-(hydroxymethyl)glutathione, which feeds the subsequent dehydrogenase step. This capture is spontaneous and has no gene participant.

Part 2: Hemithioacetal oxidation
S-(hydroxymethyl)glutathione oxidationReactionfrma_hemithioacetal_oxidation

A class-3 alcohol dehydrogenase oxidizes S-(hydroxymethyl)glutathione to S-formylglutathione. The GO term permits NAD(P)+, whereas characterized family members are NAD+-biased.

Annotons

FrmA S-(hydroxymethyl)glutathione dehydrogenase
frma_formaldehyde_dehydrogenase
Participant: Family: zinc-containing alcohol dehydrogenase family, class-3 lineage
Family:
zinc-containing alcohol dehydrogenase family, class-3 lineagePANTHER:PTHR43880:SF12
Representative Members: frmA (Pseudomonas putida KT2440)UniProtKB:Q88MF5 frmA (Escherichia coli; characterized)UniProtKB:P25437 SFA1 (Saccharomyces cerevisiae)UniProtKB:P32771
Required Function:
S-(hydroxymethyl)glutathione dehydrogenase [NAD(P)+] activityGO:0051903

Function

S-(hydroxymethyl)glutathione dehydrogenase [NAD(P)+] activityGO:0051903
Substrates: S-(hydroxymethyl)glutathione NAD+
Products: S-formylglutathione NADH
Cofactors: zinc ion

Processes

formaldehyde catabolic processGO:0046294

Locations

cytosolGO:0005829

Oxidizes the glutathione-bound formaldehyde intermediate.

Part 3: S-formylglutathione hydrolysis and glutathione regeneration
S-formylglutathione hydrolysisReactionfrmc_formylglutathione_hydrolysis

A serine hydrolase converts S-formylglutathione to formate and glutathione, completing detoxification and regenerating the carrier.

Annotons

FrmC S-formylglutathione hydrolase
frmc_formylglutathione_hydrolase
Participant: Family: FrmC family
Family:
FrmC familyPANTHER:PTHR10061
Representative Members: frmC (Pseudomonas putida KT2440)UniProtKB:Q88MF4 frmB (Escherichia coli; characterized)UniProtKB:P51025 yeiG (Escherichia coli; characterized)UniProtKB:P33018 YJL068C (Saccharomyces cerevisiae)UniProtKB:P40363 ESD (human)UniProtKB:P10768
Required Function:
S-formylglutathione hydrolase activityGO:0018738

Function

S-formylglutathione hydrolase activityGO:0018738
Substrates: S-formylglutathione water
Products: formate glutathione

Processes

formaldehyde catabolic processGO:0046294

Locations

cytosolGO:0005829

Releases formate and regenerates glutathione.

Part 4: Formate oxidation to CO2 (optional downstream step) (optional)

Present in yeast and many other organisms but not required to detoxify formaldehyde; formate can also enter one-carbon metabolism.

NAD-dependent formate dehydrogenaseReactionformate_oxidation

Annotons

NAD-dependent formate dehydrogenase (FDH1)
fdh_activity
Participant: Family: NAD-dependent formate dehydrogenase family
Family:
NAD-dependent formate dehydrogenase family
Representative Members: FDH1 (Saccharomyces cerevisiae)UniProtKB:Q08911

Function

formate dehydrogenase (NAD+) activityGO:0008863
Substrates: formate NAD+
Products: CO2 NADH

Processes

formate catabolic processGO:0042183

Locations

cytosolGO:0005829

Oxidizes the formate released by S-formylglutathione hydrolase to CO2.