The eLignin Microbial Database

A curated resource for microbial metabolism of lignin-derived aromatic compounds

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Fission pathway: syringic acid II

Full Name
syringic acid II
Funneling Branch
sinapyl branch

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Interactive metabolic pathway map showing compounds (text labels) connected by reaction arrows. Click arrows to view reaction details, click compounds to view substrate details. Zoom with mouse wheel, pan by dragging.

Empirical Data

Organisms with this Pathway Empirical

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Organism Strain Reference(s)
Sphingobium sp. SYK-6 MASAI et al (2007)
Predicted Relationships Hide predicted
The sections below contain relationships inferred from the empirical data above. They are computationally predicted and have not been independently verified. Learn more about data assumptions →
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Organisms predicted for this pathway Predicted

Inferred from reported substrate utilization: organisms that can utilise a compound entering this pathway as a reactant are predicted to carry the pathway, unless already confirmed. The reference confirming substrate use is shown. Not experimentally verified. What does this mean?

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Predicted organism Strain Inferred via substrate Reference
Acetobacterium dehalogenans MC syringic acid Kaufmann et al (1998)
Acetobacterium woodii NZva16 syringic acid Bache et al (1981)
Clostridium methoxybenzovorans SR3 syringic acid Mechichi et al (1999), Mechichi et al (2005)
Clostridium thermoaceticum ATCC 39073 syringic acid Daniel et al (1988)
Enterobacter sp. DG-6 syringic acid Grbić-Galić (1985)
Exophiala jeanselmei CBS 658.76 syringic acid Middelhoven (1993)
Holophaga foetida TMBS4 syringic acid Bak et al (1993)
Oceanimonas doudoroffii JCM21046T syringic acid Numata et al (2015)
Pandoraea norimbergensis LD001 syringic acid Bandounas et al (2011)
Petriellidium boydii SP 31-4 syringic acid Eriksson et al (1984)
Phialophora mutabilis 203-E-15-y-l syringic acid Eriksson et al (1984)
Pseudomonas chlororaphis subsp. aureofaciens PT02 syringic acid Tian et al (2016)
Rhizobium sp. YS-1r syringic acid Jackson et al (2017)
Serratia liquefaciens sp. PT01 syringic acid Tian et al (2016)
Serratia sp. JHT01 syringic acid Tian et al (2016)
Stenotrophomonas sp. PT03 syringic acid Tian et al (2016)

Predicted enzyme assignments for confirmed organisms Predicted

Inferred from confirmed pathway membership: if an organism is confirmed to carry this pathway, enzymes known to catalyse reactions within it are predicted to be present. The reference confirming the organism’s membership of this pathway is shown. Not experimentally verified. What does this mean?

Organism Strain Predicted enzyme Reference confirming pathway
Sphingobium sp. SYK-6 4-oxalmesaconate hydratase MASAI et al (2007)
Sphingobium sp. SYK-6 4-oxalomesaconate tautomerase MASAI et al (2007)
Sphingobium sp. SYK-6 HMG aldolase MASAI et al (2007)

Reactions in this Pathway

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Order Substrates Products Enzyme(s) Reaction
1 syringic acid + tetrahydrofolate → 3-O-methylgallate syringate O-demethylase R00055
2 3-O-methylgallate → methanol + 2-pyrone-4,6-dicarboxylate 3-O-methylgallate 3,4-dioxygenase R00067
3 2-pyrone-4,6-dicarboxylate → (1E)-4-oxobut-1-ene-1,2,4-tricarboxylate 2-pyrone-4,6-dicarboxylate hydrolase R00010
4 (1E)-4-oxobut-1-ene-1,2,4-tricarboxylate → (1E,3E)-4-hydroxybuta-1,3-diene-1,2,4-tricarboxylate 4-oxalomesaconate tautomerase R00011
5 (1E,3E)-4-hydroxybuta-1,3-diene-1,2,4-tricarboxylate → 2-hydroxy-4-oxobutane-1,2,4-tricarboxylate 4-oxalmesaconate hydratase R00012
6 2-hydroxy-4-oxobutane-1,2,4-tricarboxylate → pyruvate + oxaloacetic acid oxaloacetate decarboxylase , HMG aldolase R00013
7 oxaloacetate → pyruvate oxaloacetate decarboxylase R00054

Compounds (Substrates & Products)

Intermediate metabolites that are not registered in the Substrate table are shown as plain text without a hyperlink.

Compound Name Formula SMILES PubChem Role
syringic acid C9H10O5 COC1=CC(=CC(=C1O)OC)C(=O)O 10742 substrate
tetrahydrofolate (intermediate) C19H23N7O6 C1C(NC2=C(N1)N=C(NC2=O)N)CNC3=CC=C(C=C3)C(=O)NC(CCC(=O)O)C(=O)O 135444742 substrate
3-O-methylgallate (intermediate) C8H7O5- COC1=CC(=CC(=C1[O-])O)C(=O)O 54707974 product, substrate
methanol (intermediate) CH4O CO 887 product
2-pyrone-4,6-dicarboxylate (intermediate) C7H2O62- C1=C(C=C(OC1=O)C(=O)[O-])C(=O)[O-] 22483467 product, substrate
(1E)-4-oxobut-1-ene-1,2,4-tricarboxylate (intermediate) C7H3O73- C(C(=CC(=O)[O-])C(=O)[O-])C(=O)C(=O)[O-] 21158452 product, substrate
(1E,3E)-4-hydroxybuta-1,3-diene-1,2,4-tricarboxylate (intermediate) C7H3O73- C(=C(C=C(C(=O)[O-])[O-])C(=O)[O-])C(=O)O 54729370 product, substrate
2-hydroxy-4-oxobutane-1,2,4-tricarboxylate (intermediate) C7H5O83- C(C(=O)C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O 23615207 product, substrate
pyruvate (intermediate) C3H3O3- CC(=O)C(=O)[O-] 107735 product
oxaloacetic acid (intermediate) C4H4O5 C(C(=O)C(=O)O)C(=O)O 970 product
oxaloacetate (intermediate) C4H4O5 C(C(=O)C(=O)O)C(=O)O 970 substrate

Connected Pathways

Outgoing Connections (This pathway connects to:)

Connected Pathway Connecting Compound
Fission pathway: protocatechuate 4,5-cleavage -

Genes

Gene Enzyme
Sph_desA syringate O-demethylase
Sph_desZ 3-O-methylgallate 3,4-dioxygenase
Sph_ligI 2-pyrone-4,6-dicarboxylate hydrolase
Pp_galD 4-oxalomesaconate tautomerase
Pp_galB 4-oxalmesaconate hydratase
Sph_ligK oxaloacetate decarboxylase
Pp_galC HMG aldolase

Other Databases

Database Comment
MetaCyc Metabolic pathway database

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