The eLignin Microbial Database

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

brinkdp/eLignin 0 0

Fission pathway: protocatechuate 4,5-cleavage

Full Name
protocatechuate 4,5-cleavage
Funneling Branch
beta-ketoadipate branch
Synonyms
protocatechuate 4,5-cleavage pathway
protocatechuate <i>meta</i>-cleavage pathway

Pathway Network Visualization 📥 Export BioPAX JSON-LD

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

📥 Download as TSV
Organism Strain Reference(s)
Sphingobium sp. SYK-6 Peng et al (2005)
Comamonas sp. E6 Kamimura et al (2010)
Comamonas testosteroni CNB-1 Ni et al (2012)
Pseudomonas ochraceae NGJ1 MARUYAMA et al (2004)
Comamonas testosteroni BR6020 Providenti et al (2001)
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 →
Predicted sections are hidden. Show them

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?

📥 Download as TSV
Predicted organism Strain Inferred via substrate Reference
Acetobacterium woodii NZva16 protocatechuic acid Bache et al (1981)
Achromobacter denitrificans SP1 protocatechuic acid Benjamin et al (2016)
Acinetobacter baylyi ADP1 protocatechuic acid Fischer et al (2008)
Acinetobacter calcoaceticus DSM 586 protocatechuic acid Delneri et al (1995)
Aeromonas sp. L17 protocatechuic acid Deschamps et al (1980)
Amycolatopsis sp. 75iv2 (ATCC 39116) protocatechuic acid Davis et al (2012), Pometto III et al (1981)
Burkholderia cepacia Song isolate 1 protocatechuic acid Song (2009)
Candida orthopsilosis MCO457 protocatechuic acid Gérecová et al (2015)
Candida parapsilosis CBS604 protocatechuic acid Middelhoven (1993), Gérecová et al (2015)
Corynebacterium glutamicum ATCC13032 protocatechuic acid Qi et al (2007)
Cupriavidus necator JMP134 protocatechuic acid Pérez-Pantoja et al (2008)
Cupriavidus pinatubonensis 1245 protocatechuic acid Sato et al (2006)
Desulfobacterium catecholicum NZva20 protocatechuic acid Szewzyk et al (1987)
Enterobacter aerogenes L7 protocatechuic acid Deschamps et al (1980)
Enterobacter cloacae P241 protocatechuic acid Yoshida et al (2010)
Exophiala jeanselmei CBS 658.76 protocatechuic acid Middelhoven (1993)
Flavimonas oryzihabitans Song isolate 4 protocatechuic acid Song (2009)
Klebsiella pneumoniae M5a1 protocatechuic acid Jones et al (1990)
Microbacterium esteraromaticum Song isolate 5 protocatechuic acid Song (2009)
Oceanimonas doudoroffii JCM21046T protocatechuic acid Numata et al (2015)
Paenibacillus sp. JJ-1b protocatechuic acid Kasai et al (2009)
Pantoea dispersa Song isolate 2 protocatechuic acid Song (2009)
Pelobacter acidigallici Ma Gal2 (DSM 2377) protocatechuic acid Schink et al (1982)
Phialophora mutabilis 203-E-15-y-l protocatechuic acid Eriksson et al (1984)
Pseudomonas fluorescens AN103 protocatechuic acid Paulsen et al (2005)
Pseudomonas putida KT2440 protocatechuic acid Jiménez et al (2002)
Pseudomonas putida Perestelo isolate 3 protocatechuic acid Perestelo et al (1996)
Pseudomonas sp. HR199 protocatechuic acid Overhage et al (1999)
Rhodococcus erythropolis TA421 protocatechuic acid Chung et al (1994)
Rhodococcus fascians AY730713 protocatechuic acid Song (2009)
Rhodococcus fascians Song isolate 3 protocatechuic acid Song (2009)
Rhodococcus rhodochrous 116 protocatechuic acid Karlson et al (1993)
Rhodococcus sp. UKMP-5M protocatechuic acid Azman (2015)
Rhodopseudomonas palustris CGA001 protocatechuic acid Harwood et al (1988)
Rhodotorula graminis WP1 protocatechuic acid Durham et al (1984)
Rhodotorula mucilaginosa CBS17 protocatechuic acid Sampaio (1999)
Rhodotorula rubra IFO 889 protocatechuic acid Huang et al (1993)
Sinorhizobium meliloti Rm1021 protocatechuic acid MacLean et al (2006)
Streptomyces coelicolor A3(2) M600 protocatechuic acid Davis et al (2009)
Streptomyces viridosporus T7A protocatechuic acid Davis et al (2013)
Thauera aromatica K172 protocatechuic acid Mechichi et al (2002)
Thauera sp. Cin3,4 protocatechuic acid Mechichi et al (2005)
Treponema primitia ZAS-1 protocatechuic acid Lucey et al (2013)
Trichosporon cutaneum CBS2466 protocatechuic acid Middelhoven (1993)

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
Comamonas sp. E6 2-hydroxy-4-carboxymuconate semialdehyde hemiacetal dehydrogenase Kamimura et al (2010)
Comamonas testosteroni CNB-1 2-hydroxy-4-carboxymuconate semialdehyde hemiacetal dehydrogenase Ni et al (2012)
Pseudomonas ochraceae NGJ1 2-hydroxy-4-carboxymuconate semialdehyde hemiacetal dehydrogenase MARUYAMA et al (2004)
Comamonas testosteroni BR6020 2-hydroxy-4-carboxymuconate semialdehyde hemiacetal dehydrogenase Providenti et al (2001)
Comamonas sp. E6 2-pyrone-4,6-dicarboxylate hydrolase Kamimura et al (2010)
Comamonas testosteroni CNB-1 2-pyrone-4,6-dicarboxylate hydrolase Ni et al (2012)
Pseudomonas ochraceae NGJ1 2-pyrone-4,6-dicarboxylate hydrolase MARUYAMA et al (2004)
Comamonas testosteroni BR6020 2-pyrone-4,6-dicarboxylate hydrolase Providenti et al (2001)
Comamonas sp. E6 2-pyrone-4,6-dicarboxylate lactonase Kamimura et al (2010)
Comamonas testosteroni CNB-1 2-pyrone-4,6-dicarboxylate lactonase Ni et al (2012)
Pseudomonas ochraceae NGJ1 2-pyrone-4,6-dicarboxylate lactonase MARUYAMA et al (2004)
Comamonas testosteroni BR6020 2-pyrone-4,6-dicarboxylate lactonase Providenti et al (2001)
Sphingobium sp. SYK-6 4-oxalmesaconate hydratase Peng et al (2005)
Comamonas sp. E6 4-oxalmesaconate hydratase Kamimura et al (2010)
Comamonas testosteroni CNB-1 4-oxalmesaconate hydratase Ni et al (2012)
Pseudomonas ochraceae NGJ1 4-oxalmesaconate hydratase MARUYAMA et al (2004)
Comamonas testosteroni BR6020 4-oxalmesaconate hydratase Providenti et al (2001)
Sphingobium sp. SYK-6 4-oxalomesaconate tautomerase Peng et al (2005)
Comamonas sp. E6 4-oxalomesaconate tautomerase Kamimura et al (2010)
Comamonas testosteroni CNB-1 4-oxalomesaconate tautomerase Ni et al (2012)
Pseudomonas ochraceae NGJ1 4-oxalomesaconate tautomerase MARUYAMA et al (2004)
Comamonas testosteroni BR6020 4-oxalomesaconate tautomerase Providenti et al (2001)
Sphingobium sp. SYK-6 HMG aldolase Peng et al (2005)
Comamonas sp. E6 HMG aldolase Kamimura et al (2010)
Comamonas testosteroni CNB-1 HMG aldolase Ni et al (2012)
Pseudomonas ochraceae NGJ1 HMG aldolase MARUYAMA et al (2004)
Comamonas testosteroni BR6020 HMG aldolase Providenti et al (2001)
Comamonas sp. E6 oxaloacetate decarboxylase Kamimura et al (2010)
Comamonas testosteroni CNB-1 oxaloacetate decarboxylase Ni et al (2012)
Pseudomonas ochraceae NGJ1 oxaloacetate decarboxylase MARUYAMA et al (2004)
Comamonas testosteroni BR6020 oxaloacetate decarboxylase Providenti et al (2001)
Comamonas sp. E6 protocatechuate 4,5-dioxygenase Kamimura et al (2010)
Comamonas testosteroni CNB-1 protocatechuate 4,5-dioxygenase Ni et al (2012)
Pseudomonas ochraceae NGJ1 protocatechuate 4,5-dioxygenase MARUYAMA et al (2004)
Comamonas testosteroni BR6020 protocatechuate 4,5-dioxygenase Providenti et al (2001)

Reactions in this Pathway

📥 Download as TSV
Order Substrates Products Enzyme(s) Reaction
1 protocatechuic acid → 2-hydroxy-4-carboxymuconate-6-semialdehyde protocatechuate 4,5-dioxygenase R00007
2 2-hydroxy-4-carboxymuconate-6-semialdehyde → 2-hydroxy-4-carboxymuconate semialdehyde hemiacetal - R00008
3 2-hydroxy-4-carboxymuconate semialdehyde hemiacetal → 2-pyrone-4,6-dicarboxylate 2-hydroxy-4-carboxymuconate semialdehyde hemiacetal dehydrogenase R00009
4 2-pyrone-4,6-dicarboxylate → (1E)-4-oxobut-1-ene-1,2,4-tricarboxylate 2-pyrone-4,6-dicarboxylate lactonase R00010
5 (1E)-4-oxobut-1-ene-1,2,4-tricarboxylate → (1E,3E)-4-hydroxybuta-1,3-diene-1,2,4-tricarboxylate 4-oxalomesaconate tautomerase R00011
6 (1E,3E)-4-hydroxybuta-1,3-diene-1,2,4-tricarboxylate → 2-hydroxy-4-oxobutane-1,2,4-tricarboxylate 4-oxalmesaconate hydratase R00012
7 2-hydroxy-4-oxobutane-1,2,4-tricarboxylate → pyruvate + oxaloacetic acid oxaloacetate decarboxylase , HMG aldolase R00013
8 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
protocatechuic acid C7H6O4 C1=CC(=C(C=C1C(=O)O)O)O 72 substrate
2-hydroxy-4-carboxymuconate-6-semialdehyde (intermediate) C7H4O62- C(=C[O-])C(=CC(=O)C(=O)O)C(=O)[O-] 25244909 product, substrate
2-hydroxy-4-carboxymuconate semialdehyde hemiacetal (intermediate) C7H4O62- C1=C(C=C(OC1O)C(=O)[O-])C(=O)[O-] 25203591 product, substrate
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
Funneling pathway: vanillin I protocatechuic acid
Funneling pathway: vanillin II protocatechuic acid

Incoming Connections (Pathways connecting to this one:)

Source Pathway Connecting Compound
Funneling pathway: m-cresol protocatechuic acid
Fission pathway: syringic acid II -
Funneling pathway: p-cresol protocatechuic acid
Funneling pathway: caffeic acid protocatechuic acid
Funneling pathway: p-coumaric acid protocatechuic acid

Genes

Gene Enzyme
Pp_galA protocatechuate 4,5-dioxygenase
Sph_ligA protocatechuate 4,5-dioxygenase
Sph_ligB protocatechuate 4,5-dioxygenase
Sph_ligC 2-hydroxy-4-carboxymuconate semialdehyde hemiacetal dehydrogenase
Sph_ligI 2-pyrone-4,6-dicarboxylate lactonase
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

← Back to Pathways List