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|
Expected Taxonomic Range:
Gallate, gallate esters, and compounds structurally related to them 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 (in [Kasai04]). Fission of the benzene nucleus of gallate and its esters is catalyzed by bacterial dioxygenases. Several distinct pathways of aerobic aromatic catabolixm can be initiated by these dioxygenases, and their distribution among bacteria is complex [Gottschalk86]. Examples of these oxidative pathways are MetaCyc pathways gallate degradation II, gallate degradation I, 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).
Cell suspensions of Comamonas testosteroni grown with 4-hydroxybenzoate contain induced protocatechuate 4,5-dioxygenase. This enzyme cleaves the benzene nucleus of 3-O-methylgallate by meta fission to produce 2-pyrone-4,6-dicarboxylate and methanol. Methanol was shown to be eliminated by the cells during pyrone formation, and a mechanism for this reaction was proposed. The 2-pyrone-4,6-dicarboxylate product of the dioxygenase is then degraded by 2-pyrone-4,6-dicarboxylate hydrolase. The product can spontaneously or enzymatically form the enol tautomer, (1Z,3Z)-4-hydroxybuta-1,3-diene-1,2,4-tricarboxylate. Hydration forms 2-hydroxy-4-oxobutane-1,2,4-tricarboxylate. Finally, an aldolase cleaves this compound to pyruvate and oxaloacetate, which enter central metabolism [Kersten82].
In Sphingomonas sp. SYK6 a dedicated 3-O-methylgallate 3,4-dioxygenase has been found (the product of the desZ gene). This enzyme catalyzes a similar ring fission reaction to the one catalyzed by protocatechuate 4,5-dioxygenase [Kasai04].
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
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
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
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
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
Kasai07: Kasai D, Masai E, Katayama Y, Fukuda M (2007). "Degradation of 3-O-methylgallate in Sphingomonas paucimobilis SYK-6 by pathways involving protocatechuate 4,5-dioxygenase." FEMS Microbiol Lett 274(2);323-8. PMID: 17645527
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
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
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
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
Park86: Park SH, Harris BG, Cook PF (1986). "pH dependence of kinetic parameters for oxalacetate decarboxylation and pyruvate reduction reactions catalyzed by malic enzyme." Biochemistry 25(13);3752-9. PMID: 3741834
Patil92: Patil RV, Dekker EE (1992). "Cloning, nucleotide sequence, overexpression, and inactivation of the Escherichia coli 2-keto-4-hydroxyglutarate aldolase gene." J Bacteriol 1992;174(1);102-7. PMID: 1339418
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