Bacterial beta-aryl ether cleavage of lignin-derived dimers

A three-stage glutathione-dependent route converts lignin-derived beta-O-4 dimers into aromatic monomers. NAD+-dependent Calpha oxidation produces MPHPV; stereospecific ether cleavage releases guaiacol and an inverted GS-HPV conjugate; reductive deglutathionylation consumes a second glutathione to yield HPV and GSSG. The complete SYK-6 implementation requires coverage of both alpha and beta configurations. F199 provides an independently assayed downstream subroute with a BaeAB heterodimer alternative, and E. coli YghU provides a bounded isolated-activity comparator. Polymer depolymerization, uptake, downstream monomer assimilation and cofactor regeneration lie outside the boundary.

MODULE:bacterial_beta_aryl_ether_dimer_cleavageCOMPLETECONCRETEMetabolic Pathwaymodules/bacterial_beta_aryl_ether_dimer_cleavage.yaml

glutathione-dependent catabolism of lignin-derived beta-O-4 dimers

PMID:41705825

Biochemical parallels between catabolic pathways for lignin-associated aromatic dimers.

The review distinguishes established beta-O-4 dimer catabolism from the pathways for other lignin interunit linkages.

Extensive prior work has established core pathways for catabolism of guaiacylglycerol-β-guaiacyl ether (GGE), a model aromatic dimer with a β-O-4 linkage, and dehydrodivanillate (DDVA), a model dimer with a 5-5 linkage

Specific reaction descriptors are intentionally free text where no precise GO identifier was established. GO:0004364 specifies halide release, GO:0016846 describes elimination of substituted hydrogen sulfide, and GO:0046274 describes polymer catabolism; these are not used as substitutes for the represented aryl-ether substitution, reductive deglutathionylation or bounded dimer process. Exact target selectors coexist with independently verified family metadata; a shared family id does not imply identical stereochemistry or subunit roles. The source-analysis checks document Boolean capacity assumptions and stereochemical continuity. Current and archived source records remain unmodified. Official complete UniParc cross-reference lookups on 2026-11-03 found no active UniProtKB replacement for archived LigN C0SUK1, LigP E1CJ68 or LigQ G2IKM4. Their exact archived sequences match UniParc; active RefSeq/EMBL links and raw responses are recorded in the gene record-evidence files. These selectors identify version-pinned experimental sequences, not currently active UniProtKB records.

30Nodes

19Parts

5Variant Sets

10Variants

17Annotons

9Connections

Derived QC

Recommended-field compliance

42.9% recommended fields populated

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Module deep research

✗ none found

No MODULE:bacterial_beta_aryl_ether_dimer_cleavage 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) · 31 evidence or coverage gap(s) (33 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.

Annoton	Participant	Function	Assessment
syk_ligD_oxidation	ligD (SPHSK) UniProtKB:Q01198 Gene	arylglycerol-beta-aryl ether Calpha-dehydrogenase (NAD+) 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.
syk_ligO_oxidation	ligO (SPHSK) UniProtKB:C0SUK3 Gene	arylglycerol-beta-aryl ether Calpha-dehydrogenase (NAD+) 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.
syk_ligL_oxidation	ligL (SPHSK) UniProtKB:C0SUJ9 Gene	arylglycerol-beta-aryl ether Calpha-dehydrogenase (NAD+) 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.
syk_ligN_oxidation	ligN (SPHSK) UniProtKB:C0SUK1 Gene	arylglycerol-beta-aryl ether Calpha-dehydrogenase (NAD+) 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.
syk_ligE_etherase	ligE (SPHSK) UniProtKB:P27457 Gene	glutathione-dependent beta-aryl etherase 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.
syk_ligP_etherase	ligP (SPHSK) UniProtKB:E1CJ68 Gene	glutathione-dependent beta-aryl etherase 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.
syk_ligF_etherase	ligF (SPHSK) UniProtKB:P30347 Gene	glutathione-dependent beta-aryl etherase 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.
syk_ligG_release_R	ligG (SPHPI) UniProtKB:Q9WXJ9 Gene	GS-HPV glutathione-dependent deglutathionylase 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.
syk_ligQ_release_R	ligQ (SPHSK) UniProtKB:G2IKM4 Gene	GS-HPV glutathione-dependent deglutathionylase 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.
syk_ligQ_release_S	ligQ (SPHSK) UniProtKB:G2IKM4 Gene	GS-HPV glutathione-dependent deglutathionylase 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.
f199_Saro_2405_etherase	Saro_2405 (NOVAD) UniProtKB:Q2G5N2 Gene	glutathione-dependent beta-aryl etherase 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.
f199_baeab_etherase	PROTEIN_COMPLEX Gene	glutathione-dependent beta-aryl etherase 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.
f199_Saro_2091_etherase	Saro_2091 (NOVAD) UniProtKB:Q2G6J3 Gene	glutathione-dependent beta-aryl etherase 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.
f199_Saro_2595_release_R	Saro_2595 (NOVAD) UniProtKB:Q2G542 Gene	GS-HPV glutathione-dependent deglutathionylase 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.
f199_Saro_2595_release_S	Saro_2595 (NOVAD) UniProtKB:Q2G542 Gene	GS-HPV glutathione-dependent deglutathionylase 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.
f199_Saro_2865_analogue_etherase	Saro_2865 (NOVAD) UniProtKB:Q2G4C2 Gene	glutathione-dependent beta-aryl etherase 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.
ecoli_yghU_disulfide_reduction	yghU (ECOLI) UniProtKB:Q46845 Gene	disulfide oxidoreductase activity GO:0015036	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
syk_ligD_oxidation	Experimentally assessed ligD lineage; classification is not reaction-specific PANTHER:PTHR43391:SF12 Family	arylglycerol-beta-aryl ether Calpha-dehydrogenase (NAD+) activity No function ID	No Function Id The family function has no GO identifier for comparison; prose is not matched.
syk_ligO_oxidation	Experimentally assessed ligO lineage; classification is not reaction-specific PANTHER:PTHR43391:SF14 Family	arylglycerol-beta-aryl ether Calpha-dehydrogenase (NAD+) activity No function ID	No Function Id The family function has no GO identifier for comparison; prose is not matched.
syk_ligL_oxidation	Experimentally assessed ligL lineage; classification is not reaction-specific PANTHER:PTHR43391:SF14 Family	arylglycerol-beta-aryl ether Calpha-dehydrogenase (NAD+) activity No function ID	No Function Id The family function has no GO identifier for comparison; prose is not matched.
syk_ligN_oxidation	Experimentally assessed ligN lineage; classification is not reaction-specific PANTHER:PTHR43391:SF26 Family	arylglycerol-beta-aryl ether Calpha-dehydrogenase (NAD+) activity No function ID	No Function Id The family function has no GO identifier for comparison; prose is not matched.
syk_ligE_etherase	Experimentally assessed ligE lineage; classification is not reaction-specific Family	glutathione-dependent beta-aryl etherase activity No function ID	No Function Id The family function has no GO identifier for comparison; prose is not matched.
syk_ligP_etherase	Experimentally assessed ligP lineage; classification is not reaction-specific Family	glutathione-dependent beta-aryl etherase activity No function ID	No Function Id The family function has no GO identifier for comparison; prose is not matched.
syk_ligF_etherase	Experimentally assessed ligF lineage; classification is not reaction-specific PANTHER:PTHR44051:SF8 Family	glutathione-dependent beta-aryl etherase activity No function ID	No Function Id The family function has no GO identifier for comparison; prose is not matched.
syk_ligG_release_R	Experimentally assessed ligG lineage; classification is not reaction-specific PANTHER:PTHR43968:SF6 Family	GS-HPV glutathione-dependent deglutathionylase activity No function ID	No Function Id The family function has no GO identifier for comparison; prose is not matched.
syk_ligQ_release_R	Experimentally assessed ligQ lineage; classification is not reaction-specific PANTHER:PTHR44051:SF22 Family	GS-HPV glutathione-dependent deglutathionylase activity No function ID	No Function Id The family function has no GO identifier for comparison; prose is not matched.
syk_ligQ_release_S	Experimentally assessed ligQ lineage; classification is not reaction-specific PANTHER:PTHR44051:SF22 Family	GS-HPV glutathione-dependent deglutathionylase activity No function ID	No Function Id The family function has no GO identifier for comparison; prose is not matched.
f199_Saro_2405_etherase	Experimentally assessed Saro_2405 lineage; classification is not reaction-specific Family	glutathione-dependent beta-aryl etherase activity No function ID	No Function Id The family function has no GO identifier for comparison; prose is not matched.
f199_Saro_2091_etherase	Experimentally assessed Saro_2091 lineage; classification is not reaction-specific PANTHER:PTHR44051:SF8 Family	glutathione-dependent beta-aryl etherase activity No function ID	No Function Id The family function has no GO identifier for comparison; prose is not matched.
f199_Saro_2595_release_R	Experimentally assessed Saro_2595 lineage; classification is not reaction-specific PANTHER:PTHR44051:SF22 Family	GS-HPV glutathione-dependent deglutathionylase activity No function ID	No Function Id The family function has no GO identifier for comparison; prose is not matched.
f199_Saro_2595_release_S	Experimentally assessed Saro_2595 lineage; classification is not reaction-specific PANTHER:PTHR44051:SF22 Family	GS-HPV glutathione-dependent deglutathionylase activity No function ID	No Function Id The family function has no GO identifier for comparison; prose is not matched.
f199_Saro_2865_analogue_etherase	Experimentally assessed Saro_2865 lineage; classification is not reaction-specific PANTHER:PTHR44051:SF8 Family	glutathione-dependent beta-aryl etherase activity No function ID	No Function Id The family function has no GO identifier for comparison; prose is not matched.
ecoli_yghU_disulfide_reduction	Experimentally assessed yghU lineage; classification is not reaction-specific PANTHER:PTHR44051:SF22 Family	disulfide oxidoreductase activity GO:0015036	Family Review Missing No supported structured family review is available for PANTHER:PTHR44051:SF22.

Gene-review completeness (16/16 grounded genes reviewed)

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

Gene	Review	Complete	Deep research
ligD Q01198	✓	✓	✗
ligE P27457	✓	0/1	✗
ligF P30347	✓	0/0	✗
ligG Q9WXJ9	✓	✓	✗
ligL C0SUJ9	✓	✓	✗
ligN C0SUK1	✓	0/0	✗
ligO C0SUK3	✓	✓	✗
ligP E1CJ68	✓	0/0	✗
ligQ G2IKM4	✓	0/0	✗
Saro_2091 Q2G6J3	✓	0/0	✗
Saro_2405 Q2G5N2	✓	0/0	✗
Saro_2595 Q2G542	✓	0/0	✗
Saro_2865 Q2G4C2	✓	0/0	✗
Saro_2872 Q2G4B5	✓	0/0	✗
Saro_2873 Q2G4B4	✓	0/0	✗
yghU Q46845	✓	✓	✗

Tree

Complete stereochemical capacity for beta-O-4 dimer cleavageMetabolic Pathwaybacterial_beta_aryl_ether_dimer_cleavage

Parts
1. SYK-6 capacity for all four GGE stereoisomers
2. SYK-6 capacity for all four GGE stereoisomersMetabolic Pathwaysyk_complete_capacity
  
  Parts
  1. 1. Oxidation capacity for both alpha configurations
  2. Oxidation capacity for both alpha configurationsMetabolic Pathwaysyk_oxidation
    
    Parts
    
    SYK-6 alphaR GGE oxidation
    
    SYK-6 alphaR GGE oxidationReactionsyk_alphaR_oxidation
    
    Variants
    
    Alternative assayed carriers [Realizer] (One Or More)
    
    ligD: arylglycerol-beta-aryl ether Calpha-dehydrogenase (NAD+) activityReactionsyk_ligD_oxidation_node
    
    Annotons
    
    ligD: arylglycerol-beta-aryl ether Calpha-dehydrogenase (NAD+) activity Gene Product: ligD (SPHSK)
    
    ligO: arylglycerol-beta-aryl ether Calpha-dehydrogenase (NAD+) activityReactionsyk_ligO_oxidation_node
    
    Annotons
    
    ligO: arylglycerol-beta-aryl ether Calpha-dehydrogenase (NAD+) activity Gene Product: ligO (SPHSK)
    
    SYK-6 alphaS GGE oxidation
    
    SYK-6 alphaS GGE oxidationReactionsyk_alphaS_oxidation
    
    Variants
    
    Alternative assayed carriers [Realizer] (One Or More)
    
    ligL: arylglycerol-beta-aryl ether Calpha-dehydrogenase (NAD+) activityReactionsyk_ligL_oxidation_node
    
    Annotons
    
    ligL: arylglycerol-beta-aryl ether Calpha-dehydrogenase (NAD+) activity Gene Product: ligL (SPHSK)
    
    ligN: arylglycerol-beta-aryl ether Calpha-dehydrogenase (NAD+) activityReactionsyk_ligN_oxidation_node
    
    Annotons
    
    ligN: arylglycerol-beta-aryl ether Calpha-dehydrogenase (NAD+) activity Gene Product: ligN (SPHSK)
  3. 2. Ether cleavage for both MPHPV enantiomers
  4. Ether cleavage for both MPHPV enantiomersMetabolic Pathwaysyk_etherase
    
    Parts
    
    syk betaR MPHPV cleavage
    
    syk betaR MPHPV cleavageReactionsyk_betaR_etherase
    
    Variants
    
    Alternative assayed carriers [Realizer] (One Or More)
    
    ligE: glutathione-dependent beta-aryl etherase activityReactionsyk_ligE_etherase_node
    
    Annotons
    
    ligE: glutathione-dependent beta-aryl etherase activity Gene Product: ligE (SPHSK)
    
    ligP: glutathione-dependent beta-aryl etherase activityReactionsyk_ligP_etherase_node
    
    Annotons
    
    ligP: glutathione-dependent beta-aryl etherase activity Gene Product: ligP (SPHSK)
    
    syk betaS MPHPV cleavage
    
    syk betaS MPHPV cleavageReactionsyk_betaS_etherase
    
    Annotons
    
    ligF: glutathione-dependent beta-aryl etherase activity Gene Product: ligF (SPHSK)
  5. 3. Reductive deglutathionylation of both conjugate stereoisomers
  6. Reductive deglutathionylation of both conjugate stereoisomersMetabolic Pathwaysyk_release
    
    Parts
    
    syk betaR conjugate reduction
    
    syk betaR conjugate reductionReactionsyk_GSR_release
    
    Variants
    
    Alternative assayed carriers [Realizer] (One Or More)
    
    ligG: GS-HPV glutathione-dependent deglutathionylase activityReactionsyk_ligG_release_R_node
    
    Annotons
    
    ligG: GS-HPV glutathione-dependent deglutathionylase activity Gene Product: ligG (SPHPI)
    
    ligQ: GS-HPV glutathione-dependent deglutathionylase activityReactionsyk_ligQ_release_R_node
    
    Annotons
    
    ligQ: GS-HPV glutathione-dependent deglutathionylase activity Gene Product: ligQ (SPHSK)
    
    syk betaS conjugate reduction
    
    syk betaS conjugate reductionReactionsyk_GSS_release
    
    Annotons
    
    ligQ: GS-HPV glutathione-dependent deglutathionylase activity Gene Product: ligQ (SPHSK)
3. F199 experimentally grounded MPHPV-to-monomer subroute optional
4. F199 experimentally grounded MPHPV-to-monomer subrouteMetabolic Pathwayf199_mphpv_to_monomers
  
  Parts
  1. 1. Ether cleavage for both MPHPV enantiomers
  2. Ether cleavage for both MPHPV enantiomersMetabolic Pathwayf199_etherase
    
    Parts
    
    f199 betaR MPHPV cleavage
    
    f199 betaR MPHPV cleavageReactionf199_betaR_etherase
    
    Variants
    
    Alternative assayed carriers [Realizer] (One Or More)
    
    Saro_2405: glutathione-dependent beta-aryl etherase activityReactionf199_Saro_2405_etherase_node
    
    Annotons
    
    Saro_2405: glutathione-dependent beta-aryl etherase activity Gene Product: Saro_2405 (NOVAD)
    
    F199 BaeAB betaR etherase heterodimerReactionf199_baeab_etherase_node
    
    Annotons
    
    F199 BaeAB betaR etherase heterodimer Protein Complex: BaeAB heterodimer
    
    f199 betaS MPHPV cleavage
    
    f199 betaS MPHPV cleavageReactionf199_betaS_etherase
    
    Annotons
    
    Saro_2091: glutathione-dependent beta-aryl etherase activity Gene Product: Saro_2091 (NOVAD)
  3. 2. Reductive deglutathionylation of both conjugate stereoisomers
  4. Reductive deglutathionylation of both conjugate stereoisomersMetabolic Pathwayf199_release
    
    Parts
    
    f199 betaR conjugate reduction
    
    f199 betaR conjugate reductionReactionf199_GSR_release
    
    Annotons
    
    Saro_2595: GS-HPV glutathione-dependent deglutathionylase activity Gene Product: Saro_2595 (NOVAD)
    
    f199 betaS conjugate reduction
    
    f199 betaS conjugate reductionReactionf199_GSS_release
    
    Annotons
    
    Saro_2595: GS-HPV glutathione-dependent deglutathionylase activity Gene Product: Saro_2595 (NOVAD)
  5. Isolated NaLigF2 substituted-dimer reaction; does not supply the MPHPV step optional
  6. Saro_2865: glutathione-dependent beta-aryl etherase activityReactionf199_analogue_comparator
    
    Annotons
    
    Saro_2865: glutathione-dependent beta-aryl etherase activity Gene Product: Saro_2865 (NOVAD)
5. Isolated E. coli Nu-class comparator, not a complete pathway optional
6. E. coli YghU: a related disulfide reductase and heterologous capacity comparatorReactionecoli_nu_comparator
  
  Annotons
  - K-12 YghU disulfide oxidoreductase Gene Product: yghU (ECOLI)

Details

Context

BacteriaNCBITaxon:2

Demonstrated native dimer-catabolic implementations sampled here are Sphingomonadales. Current SYK-6 and F199 lineages are in different families; family-wide or order-wide pathway presence is not asserted. The E. coli branch is an explicitly isolated assay comparator.

Complete stereochemical capacity for beta-O-4 dimer cleavageMetabolic Pathwaybacterial_beta_aryl_ether_dimer_cleavage

glutathione-dependent catabolism of lignin-derived beta-O-4 dimers

Context

BacteriaNCBITaxon:2

Part: SYK-6 capacity for all four GGE stereoisomers

SYK-6 capacity for all four GGE stereoisomersMetabolic Pathwaysyk_complete_capacity

Context

Sphingobium sp. SYK-6NCBITaxon:627192

Historical strain identity is fixed by the experiments; source-record taxon identifiers are retained independently.

Conjunctive stereochemical coverage is required at each stage. This is capacity under enzyme-expression/resource assumptions, not a quantitative knockout or growth model. LigO has alphaR activity but negligible native contribution under the published ligD-mutant conditions; LigG has low betaS activity, which does not replace the established native LigQ betaS role. Each converted GGE consumes NAD+ and two GSH equivalents; cofactor regeneration and transport are external.

Connections

syk_alphaR_oxidation -> syk_betaR_etherase Provides Input For

alphaR GGE with betaR configuration produces betaR-MPHPV; the oxidation erases alpha stereochemistry and retains beta configuration.

PMID:19542348

Identification of three alcohol dehydrogenase genes involved in the stereospecific catabolism of arylglycerol-beta-aryl ether by Sphingobium sp. strain SYK-6.

LigD accepts both alphaR substrate configurations; the beta stereocenter is retained.

These results clearly indicated that LigD converted (α R ,β S )-GGE and (α R ,β R )-GGE into (β S )-MPHPV and (β R )-MPHPV, respectively.

PMID:24509858

Stereochemical features of glutathione-dependent enzymes in the Sphingobium sp. strain SYK-6 β-aryl etherase pathway.

Glutathione substitution inverts beta configuration; etherase substrate and conjugate stereochemistry must not be conflated.

Thus, β-etherase catalysis causes stereochemical inversion of the chiral center, converting a β(R)-substrate to a β(S)-product (LigE and LigP), and a β(S)-substrate to a β(R)-product (LigF).

syk_alphaR_oxidation -> syk_betaS_etherase Provides Input For

alphaR GGE with betaS configuration produces betaS-MPHPV; the oxidation erases alpha stereochemistry and retains beta configuration.

PMID:19542348

Identification of three alcohol dehydrogenase genes involved in the stereospecific catabolism of arylglycerol-beta-aryl ether by Sphingobium sp. strain SYK-6.

LigD accepts both alphaR substrate configurations; the beta stereocenter is retained.

These results clearly indicated that LigD converted (α R ,β S )-GGE and (α R ,β R )-GGE into (β S )-MPHPV and (β R )-MPHPV, respectively.

PMID:24509858

Stereochemical features of glutathione-dependent enzymes in the Sphingobium sp. strain SYK-6 β-aryl etherase pathway.

Glutathione substitution inverts beta configuration; etherase substrate and conjugate stereochemistry must not be conflated.

Thus, β-etherase catalysis causes stereochemical inversion of the chiral center, converting a β(R)-substrate to a β(S)-product (LigE and LigP), and a β(S)-substrate to a β(R)-product (LigF).

syk_alphaS_oxidation -> syk_betaR_etherase Provides Input For

alphaS GGE with betaR configuration produces betaR-MPHPV; the oxidation erases alpha stereochemistry and retains beta configuration.

PMID:19542348

Identification of three alcohol dehydrogenase genes involved in the stereospecific catabolism of arylglycerol-beta-aryl ether by Sphingobium sp. strain SYK-6.

Both LigL and LigN oxidize both alphaS configurations, retaining beta stereochemistry.

LigL and LigN have the same stereospecificity and transformed (α S ,β R )-GGE and (α S ,β S )-GGE to (β R )-MPHPV and (β S )-MPHPV, respectively

PMID:24509858

Stereochemical features of glutathione-dependent enzymes in the Sphingobium sp. strain SYK-6 β-aryl etherase pathway.

Glutathione substitution inverts beta configuration; etherase substrate and conjugate stereochemistry must not be conflated.

Thus, β-etherase catalysis causes stereochemical inversion of the chiral center, converting a β(R)-substrate to a β(S)-product (LigE and LigP), and a β(S)-substrate to a β(R)-product (LigF).

syk_alphaS_oxidation -> syk_betaS_etherase Provides Input For

alphaS GGE with betaS configuration produces betaS-MPHPV; the oxidation erases alpha stereochemistry and retains beta configuration.

PMID:19542348

Identification of three alcohol dehydrogenase genes involved in the stereospecific catabolism of arylglycerol-beta-aryl ether by Sphingobium sp. strain SYK-6.

Both LigL and LigN oxidize both alphaS configurations, retaining beta stereochemistry.

LigL and LigN have the same stereospecificity and transformed (α S ,β R )-GGE and (α S ,β S )-GGE to (β R )-MPHPV and (β S )-MPHPV, respectively

PMID:24509858

Stereochemical features of glutathione-dependent enzymes in the Sphingobium sp. strain SYK-6 β-aryl etherase pathway.

Glutathione substitution inverts beta configuration; etherase substrate and conjugate stereochemistry must not be conflated.

Thus, β-etherase catalysis causes stereochemical inversion of the chiral center, converting a β(R)-substrate to a β(S)-product (LigE and LigP), and a β(S)-substrate to a β(R)-product (LigF).

syk_betaR_etherase -> syk_GSS_release Provides Input For

betaR-MPHPV undergoes inversion to the betaS-GS-HPV substrate of the terminal step.

PMID:24509858

Stereochemical features of glutathione-dependent enzymes in the Sphingobium sp. strain SYK-6 β-aryl etherase pathway.

Glutathione substitution inverts beta configuration; etherase substrate and conjugate stereochemistry must not be conflated.

Thus, β-etherase catalysis causes stereochemical inversion of the chiral center, converting a β(R)-substrate to a β(S)-product (LigE and LigP), and a β(S)-substrate to a β(R)-product (LigF).

PMID:33244017

Roles of two glutathione S-transferases in the final step of the β-aryl ether cleavage pathway in Sphingobium sp. strain SYK-6.

Native mutants assign betaR-conjugate conversion to LigG and LigQ, and betaS-conjugate conversion to LigQ.

Analyses of mutants of ligG, ligQ, and both genes revealed that SYK-6 converted (βR)-GS-HPV using both LigG and LigQ, whereas only LigQ was involved in converting (βS)-GS-HPV.

syk_betaS_etherase -> syk_GSR_release Provides Input For

betaS-MPHPV undergoes inversion to the betaR-GS-HPV substrate of the terminal step.

PMID:24509858

Stereochemical features of glutathione-dependent enzymes in the Sphingobium sp. strain SYK-6 β-aryl etherase pathway.

Glutathione substitution inverts beta configuration; etherase substrate and conjugate stereochemistry must not be conflated.

Thus, β-etherase catalysis causes stereochemical inversion of the chiral center, converting a β(R)-substrate to a β(S)-product (LigE and LigP), and a β(S)-substrate to a β(R)-product (LigF).

PMID:33244017

Roles of two glutathione S-transferases in the final step of the β-aryl ether cleavage pathway in Sphingobium sp. strain SYK-6.

Native mutants assign betaR-conjugate conversion to LigG and LigQ, and betaS-conjugate conversion to LigQ.

Analyses of mutants of ligG, ligQ, and both genes revealed that SYK-6 converted (βR)-GS-HPV using both LigG and LigQ, whereas only LigQ was involved in converting (βS)-GS-HPV.

Part 1: Oxidation capacity for both alpha configurations

Oxidation capacity for both alpha configurationsMetabolic Pathwaysyk_oxidation

Part: SYK-6 alphaR GGE oxidation

SYK-6 alphaR GGE oxidationReactionsyk_alphaR_oxidation

Variant set: Alternative assayed carriers [Realizer] (One Or More)

ligD: arylglycerol-beta-aryl ether Calpha-dehydrogenase (NAD+) activityReactionsyk_ligD_oxidation_node

Annotons

ligD: arylglycerol-beta-aryl ether Calpha-dehydrogenase (NAD+) activity

syk_ligD_oxidation

Participant: Gene Product: ligD (SPHSK)

Gene Product:

ligD (SPHSK)UniProtKB:Q01198

Family:

Experimentally assessed ligD lineage; classification is not reaction-specificPANTHER:PTHR43391:SF12

Representative Members: ligD (SPHSK)UniProtKB:Q01198

Taxon:

Sphingobium sp. SYK-6NCBITaxon:627192

Function

arylglycerol-beta-aryl ether Calpha-dehydrogenase (NAD+) activity

Substrates: alphaR-GGE (either beta configuration) NAD+

Products: MPHPV (beta configuration retained) NADH H+

Oxidizes either beta configuration within the stated alpha class. This is assayed enzyme capacity; LigO does not rescue native ligD loss under the published conditions.

PMID:26940872

Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6.

The first reaction oxidizes the benzylic alcohol using NAD+; NADH and a solvent proton are formed.

The conversion from GGE to MPHPV during the Cα-dehydrogenase reaction is achieved by the loss of a proton and a hydride ion from the substrate, creating NADH from NAD+, and transfer of the proton to the bulk solvent

PMID:19542348

Identification of three alcohol dehydrogenase genes involved in the stereospecific catabolism of arylglycerol-beta-aryl ether by Sphingobium sp. strain SYK-6.

LigD accepts both alphaR substrate configurations; the beta stereocenter is retained.

These results clearly indicated that LigD converted (α R ,β S )-GGE and (α R ,β R )-GGE into (β S )-MPHPV and (β R )-MPHPV, respectively.

ligO: arylglycerol-beta-aryl ether Calpha-dehydrogenase (NAD+) activityReactionsyk_ligO_oxidation_node

Annotons

ligO: arylglycerol-beta-aryl ether Calpha-dehydrogenase (NAD+) activity

syk_ligO_oxidation

Participant: Gene Product: ligO (SPHSK)

Gene Product:

ligO (SPHSK)UniProtKB:C0SUK3

Family:

Experimentally assessed ligO lineage; classification is not reaction-specificPANTHER:PTHR43391:SF14

Representative Members: ligO (SPHSK)UniProtKB:C0SUK3

Taxon:

Sphingobium sp. SYK-6NCBITaxon:627192

Function

arylglycerol-beta-aryl ether Calpha-dehydrogenase (NAD+) activity

Substrates: alphaR-GGE (either beta configuration) NAD+

Products: MPHPV (beta configuration retained) NADH H+

Oxidizes either beta configuration within the stated alpha class. This is assayed enzyme capacity; LigO does not rescue native ligD loss under the published conditions.

PMID:26940872

Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6.

The first reaction oxidizes the benzylic alcohol using NAD+; NADH and a solvent proton are formed.

PMID:19542348

Identification of three alcohol dehydrogenase genes involved in the stereospecific catabolism of arylglycerol-beta-aryl ether by Sphingobium sp. strain SYK-6.

LigO has the same alphaR specificity as LigD, not complementary beta specificity. Its contribution in the tested native cells was negligible.

These results indicated that LigO has the same stereospecificity as LigD. However, ligO 's contribution to the degradation of (α R ,β S )-GGE and (α R ,β R )-GGE appeared to be negligible

Part: SYK-6 alphaS GGE oxidation

SYK-6 alphaS GGE oxidationReactionsyk_alphaS_oxidation

Variant set: Alternative assayed carriers [Realizer] (One Or More)

ligL: arylglycerol-beta-aryl ether Calpha-dehydrogenase (NAD+) activityReactionsyk_ligL_oxidation_node

Annotons

ligL: arylglycerol-beta-aryl ether Calpha-dehydrogenase (NAD+) activity

syk_ligL_oxidation

Participant: Gene Product: ligL (SPHSK)

Gene Product:

ligL (SPHSK)UniProtKB:C0SUJ9

Family:

Experimentally assessed ligL lineage; classification is not reaction-specificPANTHER:PTHR43391:SF14

Representative Members: ligL (SPHSK)UniProtKB:C0SUJ9

Taxon:

Sphingobium sp. SYK-6NCBITaxon:627192

Function

arylglycerol-beta-aryl ether Calpha-dehydrogenase (NAD+) activity

Substrates: alphaS-GGE (either beta configuration) NAD+

Products: MPHPV (beta configuration retained) NADH H+

Oxidizes either beta configuration within the alphaS substrate class. This represents assayed enzyme capacity under the stated resource assumptions.

PMID:26940872

Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6.

The first reaction oxidizes the benzylic alcohol using NAD+; NADH and a solvent proton are formed.

PMID:19542348

Identification of three alcohol dehydrogenase genes involved in the stereospecific catabolism of arylglycerol-beta-aryl ether by Sphingobium sp. strain SYK-6.

Both LigL and LigN oxidize both alphaS configurations, retaining beta stereochemistry.

LigL and LigN have the same stereospecificity and transformed (α S ,β R )-GGE and (α S ,β S )-GGE to (β R )-MPHPV and (β S )-MPHPV, respectively

ligN: arylglycerol-beta-aryl ether Calpha-dehydrogenase (NAD+) activityReactionsyk_ligN_oxidation_node

Annotons

ligN: arylglycerol-beta-aryl ether Calpha-dehydrogenase (NAD+) activity

syk_ligN_oxidation

Participant: Gene Product: ligN (SPHSK)

Gene Product:

ligN (SPHSK)UniProtKB:C0SUK1

Family:

Experimentally assessed ligN lineage; classification is not reaction-specificPANTHER:PTHR43391:SF26

Representative Members: ligN (SPHSK)UniProtKB:C0SUK1

Taxon:

Sphingobium sp. SYK-6NCBITaxon:627192

Function

arylglycerol-beta-aryl ether Calpha-dehydrogenase (NAD+) activity

Substrates: alphaS-GGE (either beta configuration) NAD+

Products: MPHPV (beta configuration retained) NADH H+

Oxidizes either beta configuration within the alphaS substrate class. This represents assayed enzyme capacity under the stated resource assumptions.

PMID:26940872

Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6.

The first reaction oxidizes the benzylic alcohol using NAD+; NADH and a solvent proton are formed.

PMID:19542348

Identification of three alcohol dehydrogenase genes involved in the stereospecific catabolism of arylglycerol-beta-aryl ether by Sphingobium sp. strain SYK-6.

Both LigL and LigN oxidize both alphaS configurations, retaining beta stereochemistry.

LigL and LigN have the same stereospecificity and transformed (α S ,β R )-GGE and (α S ,β S )-GGE to (β R )-MPHPV and (β S )-MPHPV, respectively

Part 2: Ether cleavage for both MPHPV enantiomers

Ether cleavage for both MPHPV enantiomersMetabolic Pathwaysyk_etherase

Part: syk betaR MPHPV cleavage

syk betaR MPHPV cleavageReactionsyk_betaR_etherase

Variant set: Alternative assayed carriers [Realizer] (One Or More)

ligE: glutathione-dependent beta-aryl etherase activityReactionsyk_ligE_etherase_node

Annotons

ligE: glutathione-dependent beta-aryl etherase activity

syk_ligE_etherase

Participant: Gene Product: ligE (SPHSK)

Gene Product:

ligE (SPHSK)UniProtKB:P27457

Family:

Experimentally assessed ligE lineage; classification is not reaction-specific

Representative Members: ligE (SPHSK)UniProtKB:P27457

Taxon:

Sphingobium sp. SYK-6NCBITaxon:627192

Function

glutathione-dependent beta-aryl etherase activity

Substrates: betaR-MPHPV glutathione

Products: betaS-GS-HPV guaiacol

A directly characterized reaction capacity within the stated substrate boundary.

PMID:24509858

Stereochemical features of glutathione-dependent enzymes in the Sphingobium sp. strain SYK-6 β-aryl etherase pathway.

Glutathione substitution inverts beta configuration; etherase substrate and conjugate stereochemistry must not be conflated.

Thus, β-etherase catalysis causes stereochemical inversion of the chiral center, converting a β(R)-substrate to a β(S)-product (LigE and LigP), and a β(S)-substrate to a β(R)-product (LigF).

PMID:12618439

Roles of the enantioselective glutathione S-transferases in cleavage of beta-aryl ether.

Direct product identification links LigF/LigE MPHPV cleavage to guaiacol and the glutathione conjugate.

a model compound of beta-aryl ether, alpha-(2-methoxyphenoxy)-beta-hydroxypropiovanillone (MPHPV), was transformed by LigF or LigE to guaiacol and alpha-glutathionyl-beta-hydroxypropiovanillone (GS-HPV).

ligP: glutathione-dependent beta-aryl etherase activityReactionsyk_ligP_etherase_node

Annotons

ligP: glutathione-dependent beta-aryl etherase activity

syk_ligP_etherase

Participant: Gene Product: ligP (SPHSK)

Gene Product:

ligP (SPHSK)UniProtKB:E1CJ68

Family:

Experimentally assessed ligP lineage; classification is not reaction-specific

Representative Members: ligP (SPHSK)UniProtKB:E1CJ68

Taxon:

Sphingobium sp. SYK-6NCBITaxon:627192

Function

glutathione-dependent beta-aryl etherase activity

Substrates: betaR-MPHPV glutathione

Products: betaS-GS-HPV guaiacol

A directly characterized reaction capacity within the stated substrate boundary.

PMID:24509858

Stereochemical features of glutathione-dependent enzymes in the Sphingobium sp. strain SYK-6 β-aryl etherase pathway.

Glutathione substitution inverts beta configuration; etherase substrate and conjugate stereochemistry must not be conflated.

Thus, β-etherase catalysis causes stereochemical inversion of the chiral center, converting a β(R)-substrate to a β(S)-product (LigE and LigP), and a β(S)-substrate to a β(R)-product (LigF).

PMID:22146726

Characterization of the third glutathione S-transferase gene involved in enantioselective cleavage of the β-aryl ether by Sphingobium sp. strain SYK-6.

LigP directly acts on betaR-MPHPV and overlaps LigE in the native strain; the accessible abstract establishes this bounded result.

LigP produced in Escherichia coli revealed enantioselectivity for (-)-(βR)-MPHPV, and ligE and ligP alone contributed to the degradation of (-)-(βR)-MPHPV in SYK-6.

Part: syk betaS MPHPV cleavage

syk betaS MPHPV cleavageReactionsyk_betaS_etherase

Annotons

ligF: glutathione-dependent beta-aryl etherase activity

syk_ligF_etherase

Participant: Gene Product: ligF (SPHSK)

Gene Product:

ligF (SPHSK)UniProtKB:P30347

Family:

Experimentally assessed ligF lineage; classification is not reaction-specificPANTHER:PTHR44051:SF8

Representative Members: ligF (SPHSK)UniProtKB:P30347

Taxon:

Sphingobium sp. SYK-6NCBITaxon:627192

Function

glutathione-dependent beta-aryl etherase activity

Substrates: betaS-MPHPV glutathione

Products: betaR-GS-HPV guaiacol

A directly characterized reaction capacity within the stated substrate boundary.

PMID:24509858

Stereochemical features of glutathione-dependent enzymes in the Sphingobium sp. strain SYK-6 β-aryl etherase pathway.

Glutathione substitution inverts beta configuration; etherase substrate and conjugate stereochemistry must not be conflated.

Thus, β-etherase catalysis causes stereochemical inversion of the chiral center, converting a β(R)-substrate to a β(S)-product (LigE and LigP), and a β(S)-substrate to a β(R)-product (LigF).

PMID:12618439

Roles of the enantioselective glutathione S-transferases in cleavage of beta-aryl ether.

Direct product identification links LigF/LigE MPHPV cleavage to guaiacol and the glutathione conjugate.

Part 3: Reductive deglutathionylation of both conjugate stereoisomers

Reductive deglutathionylation of both conjugate stereoisomersMetabolic Pathwaysyk_release

Part: syk betaR conjugate reduction

syk betaR conjugate reductionReactionsyk_GSR_release

Variant set: Alternative assayed carriers [Realizer] (One Or More)

ligG: GS-HPV glutathione-dependent deglutathionylase activityReactionsyk_ligG_release_R_node

Annotons

ligG: GS-HPV glutathione-dependent deglutathionylase activity

syk_ligG_release_R

Participant: Gene Product: ligG (SPHPI)

Gene Product:

ligG (SPHPI)UniProtKB:Q9WXJ9

Family:

Experimentally assessed ligG lineage; classification is not reaction-specificPANTHER:PTHR43968:SF6

Representative Members: ligG (SPHPI)UniProtKB:Q9WXJ9

Taxon:

Sphingomonas paucimobilisNCBITaxon:13689

Function

GS-HPV glutathione-dependent deglutathionylase activity

Substrates: betaR-GS-HPV glutathione

Products: HPV glutathione disulfide

Effective conversion of the stated GS-HPV stereoisomer; the two stereo classes need not have equal catalytic efficiencies.

PMID:29449375

Novosphingobium aromaticivorans uses a Nu-class glutathione S-transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin.

Deglutathionylation consumes a second GSH, yields GSSG and releases HPV. Glutathione recycling lies outside this reaction boundary.

Finally, the glutathione moiety is removed from GS-HPV and combined with another GSH, producing hydroxypropiovanillone (HPV) and glutathione disulfide (GSSG).

PMID:33244017

Roles of two glutathione S-transferases in the final step of the β-aryl ether cleavage pathway in Sphingobium sp. strain SYK-6.

Native mutants assign betaR-conjugate conversion to LigG and LigQ, and betaS-conjugate conversion to LigQ.

Analyses of mutants of ligG, ligQ, and both genes revealed that SYK-6 converted (βR)-GS-HPV using both LigG and LigQ, whereas only LigQ was involved in converting (βS)-GS-HPV.

PMID:33244017

Roles of two glutathione S-transferases in the final step of the β-aryl ether cleavage pathway in Sphingobium sp. strain SYK-6.

Both enzymes are kinetically biased; dual-substrate activity does not mean equal efficiency, and LigG is not absolutely inactive on betaS conjugate.

Purified LigG showed an approximately 300-fold higher specific activity for (βR)-GS-HPV than that for (βS)-GS-HPV, whereas purified LigQ showed an approximately six-fold higher specific activity for (βS)-GS-HPV than that for (βR)-GS-HPV.

The live record retains legacy S. paucimobilis taxon13689; the cited experiments identify this exact ligG as SYK-6. Do not infer a second strain implementation from the record taxonomy.

ligQ: GS-HPV glutathione-dependent deglutathionylase activityReactionsyk_ligQ_release_R_node

Annotons

ligQ: GS-HPV glutathione-dependent deglutathionylase activity

syk_ligQ_release_R

Participant: Gene Product: ligQ (SPHSK)

Gene Product:

ligQ (SPHSK)UniProtKB:G2IKM4

Family:

Experimentally assessed ligQ lineage; classification is not reaction-specificPANTHER:PTHR44051:SF22

Representative Members: ligQ (SPHSK)UniProtKB:G2IKM4

Taxon:

Sphingobium sp. SYK-6NCBITaxon:627192

Function

GS-HPV glutathione-dependent deglutathionylase activity

Substrates: betaR-GS-HPV glutathione

Products: HPV glutathione disulfide

Effective conversion of the stated GS-HPV stereoisomer; the two stereo classes need not have equal catalytic efficiencies.

PMID:29449375

Novosphingobium aromaticivorans uses a Nu-class glutathione S-transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin.

Deglutathionylation consumes a second GSH, yields GSSG and releases HPV. Glutathione recycling lies outside this reaction boundary.

Finally, the glutathione moiety is removed from GS-HPV and combined with another GSH, producing hydroxypropiovanillone (HPV) and glutathione disulfide (GSSG).

PMID:33244017

Roles of two glutathione S-transferases in the final step of the β-aryl ether cleavage pathway in Sphingobium sp. strain SYK-6.

Native mutants assign betaR-conjugate conversion to LigG and LigQ, and betaS-conjugate conversion to LigQ.

Analyses of mutants of ligG, ligQ, and both genes revealed that SYK-6 converted (βR)-GS-HPV using both LigG and LigQ, whereas only LigQ was involved in converting (βS)-GS-HPV.

PMID:33244017

Roles of two glutathione S-transferases in the final step of the β-aryl ether cleavage pathway in Sphingobium sp. strain SYK-6.

Both enzymes are kinetically biased; dual-substrate activity does not mean equal efficiency, and LigG is not absolutely inactive on betaS conjugate.

Part: syk betaS conjugate reduction

syk betaS conjugate reductionReactionsyk_GSS_release

Annotons

ligQ: GS-HPV glutathione-dependent deglutathionylase activity

syk_ligQ_release_S

Participant: Gene Product: ligQ (SPHSK)

Gene Product:

ligQ (SPHSK)UniProtKB:G2IKM4

Family:

Experimentally assessed ligQ lineage; classification is not reaction-specificPANTHER:PTHR44051:SF22

Representative Members: ligQ (SPHSK)UniProtKB:G2IKM4

Taxon:

Sphingobium sp. SYK-6NCBITaxon:627192

Function

GS-HPV glutathione-dependent deglutathionylase activity

Substrates: betaS-GS-HPV glutathione

Products: HPV glutathione disulfide

Effective conversion of the stated GS-HPV stereoisomer; the two stereo classes need not have equal catalytic efficiencies.

PMID:29449375

Novosphingobium aromaticivorans uses a Nu-class glutathione S-transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin.

Deglutathionylation consumes a second GSH, yields GSSG and releases HPV. Glutathione recycling lies outside this reaction boundary.

Finally, the glutathione moiety is removed from GS-HPV and combined with another GSH, producing hydroxypropiovanillone (HPV) and glutathione disulfide (GSSG).

PMID:33244017

Roles of two glutathione S-transferases in the final step of the β-aryl ether cleavage pathway in Sphingobium sp. strain SYK-6.

Native mutants assign betaR-conjugate conversion to LigG and LigQ, and betaS-conjugate conversion to LigQ.

Analyses of mutants of ligG, ligQ, and both genes revealed that SYK-6 converted (βR)-GS-HPV using both LigG and LigQ, whereas only LigQ was involved in converting (βS)-GS-HPV.

PMID:33244017

Roles of two glutathione S-transferases in the final step of the β-aryl ether cleavage pathway in Sphingobium sp. strain SYK-6.

Both enzymes are kinetically biased; dual-substrate activity does not mean equal efficiency, and LigG is not absolutely inactive on betaS conjugate.

Part: F199 experimentally grounded MPHPV-to-monomer subroute (optional)

F199 experimentally grounded MPHPV-to-monomer subrouteMetabolic Pathwayf199_mphpv_to_monomers

Context

Novosphingobium aromaticivorans DSM 12444NCBITaxon:279238

PMID:30541921

A heterodimeric glutathione S-transferase that stereospecifically breaks lignin's β(R)-aryl ether bond reveals the diversity of bacterial β-etherases.

F199 downstream etherases and Nu enzyme have direct assays, unlike the predicted upstream dehydrogenases.

NaLigF1, NaLigF2, NaLigE, and NaGSTNu have been characterized in vitro

PMID:30541921

A heterodimeric glutathione S-transferase that stereospecifically breaks lignin's β(R)-aryl ether bond reveals the diversity of bacterial β-etherases.

The F199 dehydrogenase identities in this pathway figure are homology/expression predictions, not individually assayed identities.

The dehydrogenases NaLigD, NaLigO, and NaLigN are predicted to oxidize GGE based on homology to enzymes in Sphingobium sp. SYK-6

The represented boundary begins with oxidized MPHPV. Native F199 GGE metabolism is established, but its proposed first-step dehydrogenase identities are not converted here into directly assayed gene assignments. This optional subroute cannot satisfy the required complete GGE route.

Connections

f199_Saro_2405_etherase -> f199_GSS_release Provides Input For

NaLigE supplies GS-HPV. Its betaS configuration is inferred from established LigE-class inversion; NaGSTNu accepts both epimers, so downstream continuity does not depend on independent confirmation of that assignment.

PMID:30541921

A heterodimeric glutathione S-transferase that stereospecifically breaks lignin's β(R)-aryl ether bond reveals the diversity of bacterial β-etherases.

NaLigE and NaLigF1 directly cleave the betaR and betaS MPHPV enantiomers, respectively; NaLigF1 is linked explicitly to Saro_2091.

recombinant NaLigE or NaLigF1 (encoded by Saro_2091), which are known to stereospecifically cleave the β(R) or β(S) isomers of MPHPV, respectively

PMID:29449375

Novosphingobium aromaticivorans uses a Nu-class glutathione S-transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin.

F199 NaGSTNu supports both GS-HPV stereoisomers in the native late step.

NaGSTNu is the only enzyme needed to remove glutathione from both (R)- and (S)-GS-HPV in N. aromaticivorans

f199_baeab_etherase -> f199_release Provides Input For

BaeAB supplies GS-HPV without a directly assigned product epimer. NaGSTNu accepts both epimers, so continuity does not require an unmeasured configuration assignment.

PMID:30541921

A heterodimeric glutathione S-transferase that stereospecifically breaks lignin's β(R)-aryl ether bond reveals the diversity of bacterial β-etherases.

BaeAB is a heterodimeric F199 betaR etherase, not two independent full-activity enzymes.

a heterodimeric β-etherase (BaeAB) from the sphingomonad Novosphingobium aromaticivorans that stereospecifically cleaves the β(R)-aryl ether bond

PMID:29449375

Novosphingobium aromaticivorans uses a Nu-class glutathione S-transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin.

F199 NaGSTNu supports both GS-HPV stereoisomers in the native late step.

NaGSTNu is the only enzyme needed to remove glutathione from both (R)- and (S)-GS-HPV in N. aromaticivorans

f199_betaS_etherase -> f199_GSR_release Provides Input For

NaLigF1 supplies GS-HPV. Its betaR configuration is inferred from established LigF-class inversion; NaGSTNu accepts both epimers, so downstream continuity does not depend on independent confirmation of that assignment.

PMID:30541921

A heterodimeric glutathione S-transferase that stereospecifically breaks lignin's β(R)-aryl ether bond reveals the diversity of bacterial β-etherases.

NaLigE and NaLigF1 directly cleave the betaR and betaS MPHPV enantiomers, respectively; NaLigF1 is linked explicitly to Saro_2091.

recombinant NaLigE or NaLigF1 (encoded by Saro_2091), which are known to stereospecifically cleave the β(R) or β(S) isomers of MPHPV, respectively

PMID:29449375

Novosphingobium aromaticivorans uses a Nu-class glutathione S-transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin.

F199 NaGSTNu supports both GS-HPV stereoisomers in the native late step.

NaGSTNu is the only enzyme needed to remove glutathione from both (R)- and (S)-GS-HPV in N. aromaticivorans

Part 1: Ether cleavage for both MPHPV enantiomers

Ether cleavage for both MPHPV enantiomersMetabolic Pathwayf199_etherase

Part: f199 betaR MPHPV cleavage

f199 betaR MPHPV cleavageReactionf199_betaR_etherase

Variant set: Alternative assayed carriers [Realizer] (One Or More)

Saro_2405: glutathione-dependent beta-aryl etherase activityReactionf199_Saro_2405_etherase_node

Annotons

Saro_2405: glutathione-dependent beta-aryl etherase activity

f199_Saro_2405_etherase

Participant: Gene Product: Saro_2405 (NOVAD)

Gene Product:

Saro_2405 (NOVAD)UniProtKB:Q2G5N2

Family:

Experimentally assessed Saro_2405 lineage; classification is not reaction-specific

Representative Members: Saro_2405 (NOVAD)UniProtKB:Q2G5N2

Taxon:

Novosphingobium aromaticivorans DSM 12444NCBITaxon:279238

Function

glutathione-dependent beta-aryl etherase activity

Substrates: betaR-MPHPV glutathione

Products: betaS-GS-HPV guaiacol

A directly characterized reaction capacity within the stated substrate boundary.

PMID:24509858

Stereochemical features of glutathione-dependent enzymes in the Sphingobium sp. strain SYK-6 β-aryl etherase pathway.

Glutathione substitution inverts beta configuration; etherase substrate and conjugate stereochemistry must not be conflated.

Thus, β-etherase catalysis causes stereochemical inversion of the chiral center, converting a β(R)-substrate to a β(S)-product (LigE and LigP), and a β(S)-substrate to a β(R)-product (LigF).

PMID:30541921

A heterodimeric glutathione S-transferase that stereospecifically breaks lignin's β(R)-aryl ether bond reveals the diversity of bacterial β-etherases.

NaLigE and NaLigF1 directly cleave the betaR and betaS MPHPV enantiomers, respectively; NaLigF1 is linked explicitly to Saro_2091.

recombinant NaLigE or NaLigF1 (encoded by Saro_2091), which are known to stereospecifically cleave the β(R) or β(S) isomers of MPHPV, respectively

PMID:25232892

A group of sequence-related sphingomonad enzymes catalyzes cleavage of β-aryl ether linkages in lignin β-guaiacyl and β-syringyl ether dimers.

Assayed etherases cover guaiacyl and syringyl keto-dimer substrates while retaining their beta stereospecificity; this does not establish a complete route for every such dimer.

Although each β-etherase cleaves β-guaiacyl and β-syringyl substrates, we have found that each is stereospecific for a given β-enantiomer in a racemic substrate; LigE and LigP β-etherase homologues exhibited stereospecificity toward β(R)-enantiomers whereas LigF and its homologues exhibited β(S)-stereospecificity.

Substrate enantioselectivity is directly assayed for this F199 enzyme. Reciprocal GS-HPV configuration is the established LigE/LigF-class inversion interpretation, not a separately measured absolute product assignment for this protein. NaGSTNu accepts both product epimers, so full downstream capacity does not depend on this inference.

F199 BaeAB betaR etherase heterodimerReactionf199_baeab_etherase_node

Annotons

F199 BaeAB betaR etherase heterodimer

f199_baeab_etherase

Participant: Protein Complex: BaeAB heterodimer

Protein Complex:

BaeAB heterodimer

Active units:

BaeA1

Participant: Gene Product: Saro_2873 (NOVAD)

Gene Product:

Saro_2873 (NOVAD)UniProtKB:Q2G4B4

Family:

Experimentally assessed Saro_2873 lineage; classification is not reaction-specificPANTHER:PTHR44051:SF8

Representative Members: Saro_2873 (NOVAD)UniProtKB:Q2G4B4

Taxon:

Novosphingobium aromaticivorans DSM 12444NCBITaxon:279238

Role: Catalytic subunit of the BaeAB heterodimer

PMID:30541921

A heterodimeric glutathione S-transferase that stereospecifically breaks lignin's β(R)-aryl ether bond reveals the diversity of bacterial β-etherases.

Separately supplied BaeA or BaeB gave only trace conversion; the modeled substantial activity requires both subunits.

When the Saro_2873 or Saro_2872 polypeptides were individually incubated with racemic (β(R) and β(S)) MPHPV and GSH, only a trace amount of GS-HPV was observed (representing <1% conversion of the MPHPV present in the reaction)

BaeB1

Participant: Gene Product: Saro_2872 (NOVAD)

Gene Product:

Saro_2872 (NOVAD)UniProtKB:Q2G4B5

Family:

Experimentally assessed Saro_2872 lineage; classification is not reaction-specificPANTHER:PTHR44051:SF8

Representative Members: Saro_2872 (NOVAD)UniProtKB:Q2G4B5

Taxon:

Novosphingobium aromaticivorans DSM 12444NCBITaxon:279238

Role: Required partner subunit of the BaeAB heterodimer

PMID:30541921

A heterodimeric glutathione S-transferase that stereospecifically breaks lignin's β(R)-aryl ether bond reveals the diversity of bacterial β-etherases.

Separately supplied BaeA or BaeB gave only trace conversion; the modeled substantial activity requires both subunits.

Taxon:

Novosphingobium aromaticivorans DSM 12444NCBITaxon:279238

Function

glutathione-dependent beta-aryl etherase activity

Substrates: betaR-MPHPV glutathione

Products: GS-HPV (epimer not directly assigned) guaiacol

Product stereoconfiguration is not independently assigned by the BaeAB study. Substantial betaR etherase activity requires one BaeA and one BaeB. Trace isolated-subunit conversion is not modeled as an independently sufficient pathway step.

PMID:30541921

A heterodimeric glutathione S-transferase that stereospecifically breaks lignin's β(R)-aryl ether bond reveals the diversity of bacterial β-etherases.

BaeAB is a heterodimeric F199 betaR etherase, not two independent full-activity enzymes.

a heterodimeric β-etherase (BaeAB) from the sphingomonad Novosphingobium aromaticivorans that stereospecifically cleaves the β(R)-aryl ether bond

PMID:30541921

A heterodimeric glutathione S-transferase that stereospecifically breaks lignin's β(R)-aryl ether bond reveals the diversity of bacterial β-etherases.

Separately supplied BaeA or BaeB gave only trace conversion; the modeled substantial activity requires both subunits.

Part: f199 betaS MPHPV cleavage

f199 betaS MPHPV cleavageReactionf199_betaS_etherase

Annotons

Saro_2091: glutathione-dependent beta-aryl etherase activity

f199_Saro_2091_etherase

Participant: Gene Product: Saro_2091 (NOVAD)

Gene Product:

Saro_2091 (NOVAD)UniProtKB:Q2G6J3

Family:

Experimentally assessed Saro_2091 lineage; classification is not reaction-specificPANTHER:PTHR44051:SF8

Representative Members: Saro_2091 (NOVAD)UniProtKB:Q2G6J3

Taxon:

Novosphingobium aromaticivorans DSM 12444NCBITaxon:279238

Function

glutathione-dependent beta-aryl etherase activity

Substrates: betaS-MPHPV glutathione

Products: betaR-GS-HPV guaiacol

A directly characterized reaction capacity within the stated substrate boundary.

PMID:24509858

Stereochemical features of glutathione-dependent enzymes in the Sphingobium sp. strain SYK-6 β-aryl etherase pathway.

Glutathione substitution inverts beta configuration; etherase substrate and conjugate stereochemistry must not be conflated.

Thus, β-etherase catalysis causes stereochemical inversion of the chiral center, converting a β(R)-substrate to a β(S)-product (LigE and LigP), and a β(S)-substrate to a β(R)-product (LigF).

PMID:30541921

A heterodimeric glutathione S-transferase that stereospecifically breaks lignin's β(R)-aryl ether bond reveals the diversity of bacterial β-etherases.

NaLigE and NaLigF1 directly cleave the betaR and betaS MPHPV enantiomers, respectively; NaLigF1 is linked explicitly to Saro_2091.

recombinant NaLigE or NaLigF1 (encoded by Saro_2091), which are known to stereospecifically cleave the β(R) or β(S) isomers of MPHPV, respectively

PMID:25232892

A group of sequence-related sphingomonad enzymes catalyzes cleavage of β-aryl ether linkages in lignin β-guaiacyl and β-syringyl ether dimers.

Assayed etherases cover guaiacyl and syringyl keto-dimer substrates while retaining their beta stereospecificity; this does not establish a complete route for every such dimer.

Part 2: Reductive deglutathionylation of both conjugate stereoisomers

Reductive deglutathionylation of both conjugate stereoisomersMetabolic Pathwayf199_release

Part: f199 betaR conjugate reduction

f199 betaR conjugate reductionReactionf199_GSR_release

Annotons

Saro_2595: GS-HPV glutathione-dependent deglutathionylase activity

f199_Saro_2595_release_R

Participant: Gene Product: Saro_2595 (NOVAD)

Gene Product:

Saro_2595 (NOVAD)UniProtKB:Q2G542

Family:

Experimentally assessed Saro_2595 lineage; classification is not reaction-specificPANTHER:PTHR44051:SF22

Representative Members: Saro_2595 (NOVAD)UniProtKB:Q2G542

Taxon:

Novosphingobium aromaticivorans DSM 12444NCBITaxon:279238

Function

GS-HPV glutathione-dependent deglutathionylase activity

Substrates: betaR-GS-HPV glutathione

Products: HPV glutathione disulfide

Effective conversion of the stated GS-HPV stereoisomer; the two stereo classes need not have equal catalytic efficiencies.

PMID:29449375

Novosphingobium aromaticivorans uses a Nu-class glutathione S-transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin.

Deglutathionylation consumes a second GSH, yields GSSG and releases HPV. Glutathione recycling lies outside this reaction boundary.

Finally, the glutathione moiety is removed from GS-HPV and combined with another GSH, producing hydroxypropiovanillone (HPV) and glutathione disulfide (GSSG).

PMID:29449375

Novosphingobium aromaticivorans uses a Nu-class glutathione S-transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin.

F199 NaGSTNu supports both GS-HPV stereoisomers in the native late step.

NaGSTNu is the only enzyme needed to remove glutathione from both (R)- and (S)-GS-HPV in N. aromaticivorans

Part: f199 betaS conjugate reduction

f199 betaS conjugate reductionReactionf199_GSS_release

Annotons

Saro_2595: GS-HPV glutathione-dependent deglutathionylase activity

f199_Saro_2595_release_S

Participant: Gene Product: Saro_2595 (NOVAD)

Gene Product:

Saro_2595 (NOVAD)UniProtKB:Q2G542

Family:

Experimentally assessed Saro_2595 lineage; classification is not reaction-specificPANTHER:PTHR44051:SF22

Representative Members: Saro_2595 (NOVAD)UniProtKB:Q2G542

Taxon:

Novosphingobium aromaticivorans DSM 12444NCBITaxon:279238

Function

GS-HPV glutathione-dependent deglutathionylase activity

Substrates: betaS-GS-HPV glutathione

Products: HPV glutathione disulfide

Effective conversion of the stated GS-HPV stereoisomer; the two stereo classes need not have equal catalytic efficiencies.

PMID:29449375

Novosphingobium aromaticivorans uses a Nu-class glutathione S-transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin.

Deglutathionylation consumes a second GSH, yields GSSG and releases HPV. Glutathione recycling lies outside this reaction boundary.

Finally, the glutathione moiety is removed from GS-HPV and combined with another GSH, producing hydroxypropiovanillone (HPV) and glutathione disulfide (GSSG).

PMID:29449375

Novosphingobium aromaticivorans uses a Nu-class glutathione S-transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin.

F199 NaGSTNu supports both GS-HPV stereoisomers in the native late step.

NaGSTNu is the only enzyme needed to remove glutathione from both (R)- and (S)-GS-HPV in N. aromaticivorans

Part: Isolated NaLigF2 substituted-dimer reaction; does not supply the MPHPV step (optional)

Saro_2865: glutathione-dependent beta-aryl etherase activityReactionf199_analogue_comparator

Context

Novosphingobium aromaticivorans DSM 12444NCBITaxon:279238

Annotons

Saro_2865: glutathione-dependent beta-aryl etherase activity

f199_Saro_2865_analogue_etherase

Participant: Gene Product: Saro_2865 (NOVAD)

Gene Product:

Saro_2865 (NOVAD)UniProtKB:Q2G4C2

Family:

Experimentally assessed Saro_2865 lineage; classification is not reaction-specificPANTHER:PTHR44051:SF8

Representative Members: Saro_2865 (NOVAD)UniProtKB:Q2G4C2

Taxon:

Novosphingobium aromaticivorans DSM 12444NCBITaxon:279238

Function

glutathione-dependent beta-aryl etherase activity

Substrates: betaS-GβG: alpha-(4-O-Me)-guaiacylglycerone-beta-(1-prime-formyl)-guaiacyl ether glutathione

Products: Gβ-SG: substituted glutathionyl-guaiacyl monomer vanillin

NaLigF2 directly cleaves substituted G/G, G/S, S/G and S/S alpha-keto dimers. This isolated GβG reaction is not treated as demonstrated MPHPV capacity, and no downstream conversion of its distinct conjugate is asserted here.

PMID:25232892

A group of sequence-related sphingomonad enzymes catalyzes cleavage of β-aryl ether linkages in lignin β-guaiacyl and β-syringyl ether dimers.

Assayed etherases cover guaiacyl and syringyl keto-dimer substrates while retaining their beta stereospecificity; this does not establish a complete route for every such dimer.

PMID:25232892

A group of sequence-related sphingomonad enzymes catalyzes cleavage of β-aryl ether linkages in lignin β-guaiacyl and β-syringyl ether dimers.

The substituted GβG substrate is chemically distinct from MPHPV; its aryl product is vanillin, not guaiacol.

α-(4-O-Me)-guaiacylglycerone-β-(1′-formyl)-guaiacyl ether (GβG)

Part: Isolated E. coli Nu-class comparator, not a complete pathway (optional)

E. coli YghU: a related disulfide reductase and heterologous capacity comparatorReactionecoli_nu_comparator

Context

Escherichia coli K-12NCBITaxon:83333

Exact K-12 reductase experiments are distinguished from the DH5alpha-derived YghU used for GS-HPV assays and F199 complementation. No native E. coli dimer-catabolic pathway is asserted.

Annotons

K-12 YghU disulfide oxidoreductase

ecoli_yghU_disulfide_reduction

Participant: Gene Product: yghU (ECOLI)

Gene Product:

yghU (ECOLI)UniProtKB:Q46845

Family:

Experimentally assessed yghU lineage; classification is not reaction-specificPANTHER:PTHR44051:SF22

Representative Members: yghU (ECOLI)UniProtKB:Q46845

Taxon:

Escherichia coli K-12NCBITaxon:83333

Function

disulfide oxidoreductase activityGO:0015036

An isolated family comparator. The specific GS-HPV result belongs to the DH5alpha-derived experimental protein; it is not an asserted native K-12 pathway step.

PMID:21222452

Structure and function of YghU, a nu-class glutathione transferase related to YfcG from Escherichia coli.

K-12 YghU has directly measured disulfide reduction; this comparison does not place a dimer substrate in its native pathway.

the enzyme also exhibits disulfide-bond reductase activity toward 2-hydroxyethyl disulfide

PMID:29449375

Novosphingobium aromaticivorans uses a Nu-class glutathione S-transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin.

The DH5alpha-derived E. coli YghU enzyme can replace F199 NaGSTNu experimentally; this is isolated reaction capacity, not an E. coli lignin pathway.

EcYghU complements growth of an N. aromaticivorans ΔNaGSTNu mutant, showing that it can perform these reactions in vivo.

PMID:29449375

Novosphingobium aromaticivorans uses a Nu-class glutathione S-transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin.

The isolated E. coli activities are less efficient and do not establish a physiological GS-HPV substrate in E. coli.

the lower catalytic efficiencies we find with EcYghU and EcYfcG toward GS-HPV may reflect the fact that this compound is not a natural substrate for E. coli.