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MetaCyc Pathway: gallate degradation II

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 ? : Pseudomonas putida , Pseudomonas putida PDC

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

Fluorescent pseudomonads such as Pseudomonas putida can cleave gallate using the inducible ortho fission enzyme, protocatechuate 3,4-dioxygenase. However, the product 2-pyrone-4,6-dicarboxylate (PDC) is usually not degraded further due to the lack of an enzyme that can process PDC. A strain that contains a 2-pyrone-4,6-dicarboxylate hydrolase enzyme was isolated from soil by selection for growth on PDC as the sole carbon source, and named Pseudomonas putida PDC. Extracts of cells grown with PDC contained the hydrolase and high levels of gallate dioxygenase, but demonstrated only low activity against protocatechuate. Cells adapted to gallate expressed the hydrolase while cells adapted to protocatechuate did not. Thin layer chromatography of derivatized catabolites produced by cells grown with PDC revealed 4-carboxy-2-oxo-3-hexenedioate, pyruvate, and oxaloacetate. The time of the appearance of these compounds was used to propose the catabolic pathway [Kersten82].

In this pathway, the lactone, 2-pyrone-4,6-dicarboxylate, is hydrolyzed to the open chain keto form of the ring fission product. The enol tautomer, (1Z,3Z)-4-hydroxybuta-1,3-diene-1,2,4-tricarboxylate, can form spontaneously or enzymatically [Nogales10]. Hydration by a hydratase forms 4-carboxy-4-hydroxy-2-oxoadipate. This is cleaved to pyruvate and oxaloacetate by the aldolase. These 2 metabolites enter central metabolism, as indicated by the pathway link. These results demonstrated that Pseudomonas putida PDC can use enzymes of the meta fission pathway to degrade gallate [Kersten82, Tack72].

It should be noted that a second route of gallate degradation exists in Pseudomonas putida, which involves a highly specific gallate dioxygenases (see gallate degradation I).

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

Unification Links: KEGG:MAP00360

Credits:
Created 17-Jun-1998 by Ying HC , SRI International
Revised 22-Nov-2010 by Caspi R , SRI International


References

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

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

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

Tack72: Tack BF, Chapman PJ, Dagley S (1972). "Metabolism of gallic acid and syringic acid by Pseudomonas putida." J Biol Chem 247(20);6438-43. PMID: 4342601

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

Bull81: Bull C, Ballou DP (1981). "Purification and properties of protocatechuate 3,4-dioxygenase from Pseudomonas putida. A new iron to subunit stoichiometry." J Biol Chem 256(24);12673-80. PMID: 6273403

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

Frazee93: Frazee RW, Livingston DM, LaPorte DC, Lipscomb JD (1993). "Cloning, sequencing, and expression of the Pseudomonas putida protocatechuate 3,4-dioxygenase genes." J Bacteriol 175(19);6194-202. PMID: 8407791

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

Harwood96: Harwood CS, Parales RE (1996). "The beta-ketoadipate pathway and the biology of self-identity." Annu Rev Microbiol 50;553-90. PMID: 8905091

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

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

Maruyama83: Maruyama K (1983). "Purification and properties of 2-pyrone-4,6-dicarboxylate hydrolase." J Biochem (Tokyo) 93(2);557-65. PMID: 6841353

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

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

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

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

Ohlendorf94: Ohlendorf DH, Orville AM, Lipscomb JD (1994). "Structure of protocatechuate 3,4-dioxygenase from Pseudomonas aeruginosa at 2.15 A resolution." J Mol Biol 244(5);586-608. PMID: 7990141

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

Sparnins75: Sparnins VL, Dagley S (1975). "Alternative routes of aromatic catabolism in Pseudomonas acidovorans and Pseudomonas putida: gallic acid as a substrate and inhibitor of dioxygenases." J Bacteriol 124(3);1374-81. PMID: 1194238

Tack72a: 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 Wed Nov 26, 2014, biocyc13.