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MetaCyc Pathway: gallate degradation I

Enzyme View:

This view shows enzymes only for those organisms listed below, in the list of taxa known to possess the pathway. If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Superclasses: Degradation/Utilization/Assimilation Aromatic Compounds Degradation Gallate Degradation

Some taxa known to possess this pathway include ? : Comamonas testosteroni , Pseudomonas putida KT2440 , Sphingomonas sp. SYK6

Expected Taxonomic Range: Bacteria

Summary:
General Background

Gallate and structurally related compounds are widely distributed in nature. Plant lignin and tannins are major sources of these compounds, which are degraded by soil microorganisms as part of the terrestrial carbon cycle. Gallate is also used industrially in inks and paints, and gallate esters are used as food, cosmetics and pharmaceutical antioxidants. Gallate and its derivatives are also of interest in drug development (reviewed in [Ow03].

Gallate and related compounds contain a benzene nucleus and at least 2 phenolic hydroxyl groups. Under aerobic conditions the benzene ring is cleaved by varioius dioxygenases. The benzene nucleus can be cleaved by ortho or meta fission enzymes, leading to different degradation pathways. Several distinct pathways of aerobic aromatic catabolism can be initiated by these dioxygenases, and their distribution among bacteria is complex [Gottschalk86]. Examples of these oxidative pathways are shown in MetaCyc pathways gallate degradation II, methylgallate degradation, protocatechuate degradation I (meta-cleavage pathway), protocatechuate degradation II (ortho-cleavage pathway), and superpathway of aromatic compound degradation via 3-oxoadipate. An anaerobic pathway for gallate degradation is shown in MetaCyc pathway gallate degradation III (anaerobic).

About This Pathway

Gallate dioxygenase is a ring-cleavage dioxygenase found in several gallate-degrading organisms that acts specifically on gallate to produce the keto-tautomer of 4-oxalomesaconate [Nogales05, Nogales10]. The enzyme shares a common ancestor with protocatechuate 4,5-dioxygenase, and has a two-domain architecture that might have evolved from the fusion of the large and small subunits of the latter. In some organisms, such as Comamonas testosteroni, it has been shown that protocatechuate 4,5-dioxygenase can catalyze the same reaction, although with lower efficiency [Zabinski72].

The product of the ring cleavage is the keto tautomer of 4-oxalomesaconate, (1E)-4-oxobut-1-ene-1,2,4-tricarboxylate [Nogales10]. While it can form the enol form, (1Z,3Z)-4-hydroxybuta-1,3-diene-1,2,4-tricarboxylate, spontaneously, it has been shown that in Pseudomonas putida KT2440 a dedicated enzyme, 4-oxalomesaconate tautomerase, catalyzes this conversion [Nogales10].

The enol form is the substrate for 4-oxalomesaconate hydratase [Hara00], and the product of this enzyme, 2-hydroxy-4-oxobutane-1,2,4-tricarboxylate, is cleaved by an aldolase to oxaloacetate and pyruvate, which enter central metabolism [Hara03].

Fluorescent pseudomonads, such as Pseudomonas putida, can also cleave gallate by the ortho cleavage enzyme protocatechuate 3,4-dioxygenase, resulting in formation of the lactone 2-pyrone-4,6-dicarboxylate (see MetaCyc pathway gallate degradation II).

Superpathways: syringate degradation

Variants: gallate degradation II , gallate degradation III (anaerobic)

Credits:
Created 18-Jun-1998 by Ying HC , SRI International
Revised 25-Sep-2009 by Caspi R , SRI International
Revised 29-Nov-2010 by Caspi R , SRI International


References

Gottschalk86: Gottschalk, G "Bacterial Metabolism, Second Edition." Springer-Verlag, New York. 1986.

Hara00: Hara H, Masai E, Katayama Y, Fukuda M (2000). "The 4-oxalomesaconate hydratase gene, involved in the protocatechuate 4,5-cleavage pathway, is essential to vanillate and syringate degradation in Sphingomonas paucimobilis SYK-6." J Bacteriol 182(24);6950-7. PMID: 11092855

Hara03: Hara H, Masai E, Miyauchi K, Katayama Y, Fukuda M (2003). "Characterization of the 4-carboxy-4-hydroxy-2-oxoadipate aldolase gene and operon structure of the protocatechuate 4,5-cleavage pathway genes in Sphingomonas paucimobilis SYK-6." J Bacteriol 185(1);41-50. PMID: 12486039

Kersten82: Kersten PJ, Dagley S, Whittaker JW, Arciero DM, Lipscomb JD (1982). "2-pyrone-4,6-dicarboxylic acid, a catabolite of gallic acids in Pseudomonas species." J Bacteriol 1982;152(3);1154-62. PMID: 7142106

Nogales05: Nogales J, Canales A, Jimenez-Barbero J, Garcia JL, Diaz E (2005). "Molecular characterization of the gallate dioxygenase from Pseudomonas putida KT2440: The prototype of a new subgroup of extradiol dioxygenases." J Biol Chem 280(42):35382-90. PMID: 16030014

Nogales10: Nogales, J., Canales, A., Jimenez-barbero, J., Serra, B., Pingarron, J. M., Garcia, J. L., Diaz, E. (2010). "Unravelling the gallic acid degradation pathway in bacteria: the gal cluster from Pseudomonas putida." Molecular Microbiology, 79:359-374. PMID: 21219457

Ow03: Ow YY, Stupans I (2003). "Gallic acid and gallic acid derivatives: effects on drug metabolizing enzymes." Curr Drug Metab 4(3);241-8. PMID: 12769668

Zabinski72: Zabinski R, Munck E, Champion PM, Wood JM (1972). "Kinetic and Mossbauer studies on the mechanism of protocatechuic acid 4,5-oxygenase." Biochemistry 11(17);3212-9. PMID: 5048285

Other References Related to Enzymes, Genes, Subpathways, and Substrates of this Pathway

Arciero83: Arciero DM, Lipscomb JD, Huynh BH, Kent TA, Munck E (1983). "EPR and Mossbauer studies of protocatechuate 4,5-dioxygenase. Characterization of a new Fe2+ environment." J Biol Chem 258(24);14981-91. PMID: 6317682

Dagley82: Dagley S (1982). "4-Hydroxy-4-methyl-2-ketoglutarate aldolase from Pseudomonas putida." Methods Enzymol 90 Pt E;272-6. PMID: 7154956

Kasai04: Kasai D, Masai E, Miyauchi K, Katayama Y, Fukuda M (2004). "Characterization of the 3-O-methylgallate dioxygenase gene and evidence of multiple 3-O-methylgallate catabolic pathways in Sphingomonas paucimobilis SYK-6." J Bacteriol 186(15);4951-9. PMID: 15262932

Kasai05: Kasai D, Masai E, Miyauchi K, Katayama Y, Fukuda M (2005). "Characterization of the gallate dioxygenase gene: three distinct ring cleavage dioxygenases are involved in syringate degradation by Sphingomonas paucimobilis SYK-6." J Bacteriol 187(15);5067-74. PMID: 16030198

Kersten85: Kersten PJ, Chapman PJ, Dagley S (1985). "Enzymatic release of halogens or methanol from some substituted protocatechuic acids." J Bacteriol 162(2);693-7. PMID: 3988709

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."

Mampel05: Mampel J, Providenti MA, Cook AM (2005). "Protocatechuate 4,5-dioxygenase from Comamonas testosteroni T-2: biochemical and molecular properties of a new subgroup within class III of extradiol dioxygenases." Arch Microbiol 183(2);130-9. PMID: 15650824

Maruyama01: Maruyama K, Miwa M, Tsujii N, Nagai T, Tomita N, Harada T, Sobajima H, Sugisaki H (2001). "Cloning, sequencing, and expression of the gene encoding 4-hydroxy-4-methyl-2-oxoglutarate aldolase from Pseudomonas ochraceae NGJ1." Biosci Biotechnol Biochem 65(12);2701-9. PMID: 11826967

Maruyama85: Maruyama K (1985). "Purification and properties of gamma-oxalomesaconate hydratase from Pseudomonas ochraceae grown with phthalate." Biochem Biophys Res Commun 128(1);271-7. PMID: 3985968

Maruyama90: Maruyama K (1990). "Purification and properties of 4-hydroxy-4-methyl-2-oxoglutarate aldolase from Pseudomonas ochraceae grown on phthalate." J Biochem (Tokyo) 1990;108(2);327-33. PMID: 2229032

Masai00: Masai E, Momose K, Hara H, Nishikawa S, Katayama Y, Fukuda M (2000). "Genetic and biochemical characterization of 4-carboxy-2-hydroxymuconate-6-semialdehyde dehydrogenase and its role in the protocatechuate 4,5-cleavage pathway in Sphingomonas paucimobilis SYK-6." J Bacteriol 182(23);6651-8. PMID: 11073908

Masai99: Masai E, Shinohara S, Hara H, Nishikawa S, Katayama Y, Fukuda M (1999). "Genetic and biochemical characterization of a 2-pyrone-4, 6-dicarboxylic acid hydrolase involved in the protocatechuate 4, 5-cleavage pathway of Sphingomonas paucimobilis SYK-6." J Bacteriol 181(1);55-62. PMID: 9864312

Noda90: Noda Y, Nishikawa S, Shiozuka K, Kadokura H, Nakajima H, Yoda K, Katayama Y, Morohoshi N, Haraguchi T, Yamasaki M (1990). "Molecular cloning of the protocatechuate 4,5-dioxygenase genes of Pseudomonas paucimobilis." J Bacteriol 172(5);2704-9. PMID: 2185230

Nogales11: Nogales J, Canales A, Jimenez-Barbero J, Serra B, Pingarron JM, Garcia JL, Diaz E (2011). "Unravelling the gallic acid degradation pathway in bacteria: the gal cluster from Pseudomonas putida." Mol Microbiol 79(2);359-74. PMID: 21219457

Providenti01: Providenti MA, Mampel J, MacSween S, Cook AM, Wyndham RC (2001). "Comamonas testosteroni BR6020 possesses a single genetic locus for extradiol cleavage of protocatechuate." Microbiology 147(Pt 8);2157-67. PMID: 11495993

Ritter73: Ritter CS, Chapman PJ, Dagley S (1973). "Absolute configuration of a metabolite in the m-fission pathway of protocatechuate." J Bacteriol 113(2);1064-5. PMID: 4347922

Tack72: Tack BF, Chapman PJ, Dagley S (1972). "Purification and properties of 4-hydroxy-4-methyl-2-oxoglutarate aldolase." J Biol Chem 247(20);6444-9. PMID: 5076765


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Sat Nov 29, 2014, biocyc13.