Fission pathway: syringic acid I

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Fission pathway: syringic acid I

Full Name: syringic acid I
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.

Organisms with this Pathway Empirical

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Organism	Strain	Reference(s)
Sphingobium sp.	SYK-6	MASAI et al (2007)

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	gallic acid, 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)
Haloferax sp.	D1227	gallic acid	Emerson et al (1994)
Holophaga foetida	TMBS4	gallic acid, syringic acid	Bak et al (1993)
Leucosporidium scottii	G43	gallic acid	Middelhoven (1993)
Oceanimonas doudoroffii	JCM21046T	gallic acid, syringic acid	Numata et al (2015)
Pandoraea norimbergensis	LD001	syringic acid	Bandounas et al (2011)
Pantoea agglomerans	T71	gallic acid	Zeida et al (1998)
Pelobacter acidigallici	Ma Gal2 (DSM 2377)	gallic acid	Schink et al (1982)
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)
Pseudomonas citronellolis	T8	gallic acid	Chowdhury et al (2004)
Pseudomonas plecoglossicida	G2	gallic acid	Chowdhury et al (2004)
Pseudomonas putida	KT2440	gallic acid	Nogales et al (2010)
Rhizobium sp.	YS-1r	syringic acid	Jackson et al (2017)
Rhodococcus fascians	AY730713	gallic acid	Song (2009)
Rhodococcus fascians	Song isolate 3	gallic acid	Song (2009)
Rhodotorula glutinis	Jain isolate	gallic acid	GUPTA et al (1986)
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 + tetrahydrofolate	→	gallic acid + 5-methyltetrahydrofolate	Vanillate monooxygenase	R00056
3	gallic acid	→	(1E)-4-oxobut-1-ene-1,2,4-tricarboxylate	gallate dioxygenase	R00057
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
gallic acid	C₇H₆O₅	`C1=C(C=C(C(=C1O)O)O)C(=O)O`	370	product, substrate
5-methyltetrahydrofolate (intermediate)	C₂₀H₂₅N₇O₆	`CN1C(CNC2=C1C(=O)NC(=N2)N)CNC3=CC=C(C=C3)C(=O)NC(CCC(=O)O)C(=O)O`	135415868	product
(1E)-4-oxobut-1-ene-1,2,4-tricarboxylate (intermediate)	C₇H₃O₇^3-	`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)	C₇H₃O₇^3-	`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)	C₇H₅O₈^3-	`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

No pathway connections are currently defined.

Genes

Gene	Enzyme
Sph_desA	syringate O-demethylase
Sph_ligM	Vanillate monooxygenase
Sph_desB	gallate dioxygenase
Pp_galA	gallate dioxygenase
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