The eLignin Microbial Database

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

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Fission pathway: protocatechuate 2,3-cleavage

Full Name
protocatechuate 2,3-cleavage
Funneling Branch
protocatechuate 2,3-cleavage 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)
Paenibacillus sp. JJ-1b Kasai et al (2009)
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 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)
Comamonas testosteroni BR6020 protocatechuic acid Providenti et al (2006)
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)
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
Paenibacillus sp. JJ-1b 2-oxopent-4-enoate hydratase Kasai et al (2009)
Paenibacillus sp. JJ-1b 4-hydroxy-2-oxovalerate aldolase Kasai et al (2009)

Reactions in this Pathway

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Order Substrates Products Enzyme(s) Reaction
1 protocatechuic acid → (2Z,4Z)-2-hydroxy-5-carboxymuconate-6-semialdehyde protocatechuate 2,3-dioxygenase R00032
2 (2Z,4Z)-2-hydroxy-5-carboxymuconate-6-semialdehyde → (2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate - R00033
3 (2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate → (2Z,4E)-2-hydroxyhexa-2,4-dienedioate 2-hydroxymuconate-6-semialdehyde dehydrogenase R00034
4 (2Z,4E)-2-hydroxyhexa-2,4-dienedioate → (3E)-2-oxohex-3-enedioate 4-oxalocrotonate tautomerase R00059
5 (3E)-2-oxohex-3-enedioate → (2Z)-2-hydroxypenta-2,4-dienoate 2-oxo-3-hexenedioate decarboxylase R00060
6 2-oxopent-4-enoate → 4-hydroxy-2-oxopentanoate 2-oxopent-4-enoate hydratase R00029
7 4-hydroxy-2-oxopentanoate → acetaldehyde + pyruvate 4-hydroxy-2-oxovalerate aldolase R00030
8 acetaldehyde → acetyl-CoA - R00031

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
(2Z,4Z)-2-hydroxy-5-carboxymuconate-6-semialdehyde (intermediate) C7H4O62- C(=CC(=O)C(=O)O)C(=C[O-])C(=O)[O-] 90657979 product, substrate
(2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate (intermediate) C6H5O4- C(=CC(=O)C(=O)O)C=C[O-] 70678568 product, substrate
(2Z,4E)-2-hydroxyhexa-2,4-dienedioate (intermediate) C6H4O52- C(=CC(=O)O)C=C(C(=O)[O-])[O-] 54711929 product, substrate
(3E)-2-oxohex-3-enedioate (intermediate) C6H4O52- C(C=CC(=O)C(=O)[O-])C(=O)[O-] 25245156 product, substrate
(2Z)-2-hydroxypenta-2,4-dienoate (intermediate) C5H5O3- C=CC=C(C(=O)O)[O-] 54713710 product
2-oxopent-4-enoate (intermediate) C5H5O3- C=CCC(=O)C(=O)[O-] 9543147 substrate
4-hydroxy-2-oxopentanoate (intermediate) C5H7O4- CC(CC(=O)C(=O)[O-])O 9543038 product, substrate
acetaldehyde (intermediate) C2H4O CC=O 177 product, substrate
pyruvate (intermediate) C3H3O3- CC(=O)C(=O)[O-] 107735 product
acetyl-CoA (intermediate) C23H38N7O17P3S CC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)N2C=NC3=C(N=CN=C32)N)O)OP(=O)(O)O)O 444493 product

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: caffeic acid protocatechuic acid
Funneling pathway: m-cresol protocatechuic acid
Funneling pathway: p-cresol protocatechuic acid
Funneling pathway: p-coumaric acid protocatechuic acid

Genes

Gene Enzyme
Pae_praA protocatechuate 2,3-dioxygenase
Pae_praB 2-hydroxymuconate-6-semialdehyde dehydrogenase
Pp_xylG 2-hydroxymuconate-6-semialdehyde dehydrogenase
Pae_praC 4-oxalocrotonate tautomerase
Ppmt2_xylH 4-oxalocrotonate tautomerase
Pae_praD 2-oxo-3-hexenedioate decarboxylase
CNE_BB1p11950 4-hydroxy-2-oxovalerate aldolase
CNE_BB1p13240 4-hydroxy-2-oxovalerate aldolase
CNE_1c17880 4-hydroxy-2-oxovalerate aldolase
Cn_mhpE 4-hydroxy-2-oxovalerate aldolase
Cn_bpHI 4-hydroxy-2-oxovalerate aldolase

Other Databases

Database Comment
MetaCyc Metabolic pathway database

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