Genome Property Definition Page
Accession | GenProp0210 | |
Name | phenylacetic acid catabolism | |
Type | PATHWAY | |
Description | The degradation of phenylacetic acid via phenylacetyl-CoA to TCA intermediates is the core of an extended catabolon [1] for the degradation of various monosubstituted phenyl compounds and polymers including styrene, tropic acid, ethylbenzene, 2-phenylethylamine, phenylacetyl amide, phenyl alkanoates, poly-hydroxyphenylalkanoates, and trans-styrylacetic acid. The pathway consists of four major stages: ligation of phenylacetic acid with CoA, hydroxylation of the phenyl ring at the 2-position, oxidative ring opening and fatty-acid beta-oxidation like steps on the acyclic compound. The precise nature of the intermediates following 2-hydroxyphenylacetyl-CoA are not known. The gene symbol nomenclature for the enzymes in this pathway has been standardized in [1] due to the heterogeneity among the various organisms studied. This new standard is different from all of the old gene symbols, and may add somewhat to the confusion. A key is reproduced below as an aid to the bewildered. The genes of this pathway are typically organized into a single divergon. Some of the genes involved in the final fatty-acid-like degradation (paaABCDE) are occasionally absent and presumably substituted with genes of similar function found elsewhere in the genome. paaA and paaB both code for genes having the same general function (enoyl-CoA hydratases), but often paaA is absent (possibly paaB in these organisms provides both activities). paaD is the most reliable marker of this part of the pathway, nearly always detectable as a distinct homolog within the gene clusters. paaN, which codes for the ring-opening enzyme, is generally related to aldehyde dehydrogenases, but at least three different homology families appear to have evolved members into the specific paaN role. Pseudomonas putida appears to include a transport system (paaLM), but as this has not been reported in any other organism it has not been included in this Genome Property at this time. Gene Name Gene-sym (E.coli/P.putida/A.evansii) ------------------------------------- Phenylacetyl-CoA ligase paaF (paaK/phaE/pacD) Ring-hydroxylating complex. Protein 1 paaG (paaA/phaF/pacE) Ring-hydroxylating complex. Protein 2 paaH (paaB/phaO/pacF) Ring-hydroxylating complex. Protein 3 paaI (paaC/phaG/pacG) Ring-hydroxylating complex. Protein 4 paaJ (paaD/phaH/pacH) Ring-hydroxylating complex. Protein 5 paaK (paaE/phaI/pacI) Ring-opening enzyme paaN (paaZ/phaL/pacL) Enoyl-CoA hydratase 1 paaA (paaF/phaA/----) Enoyl-CoA hydratase 2 paaB (paaG/phaB/pacA) 3-OH-acyl-CoA dehydrogenase paaC (paaH/phaC/pacB) Putative thioesterase paaD (paaI/----/pacC) Ketothiolase paaE (paaJ/phaD/----) Permease paaL (----/phaJ/----) Porine paaM (----/phaK/----) Repressor protein paaX (paaX/phaN/----) Putative regulator paaY (paaY/phaM/pacM) | |
JCVI Role | Other | |
Parent Property | GenProp0142: catabolism | |
Literature References |
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Web References | The Ecocyc Database: phenylacetate degradation I | |
Gene Ontology Term | GO:0010124: phenylacetate catabolic process (biological_process) |
Components
Step Name | Step Num | Required | Evidence (Method) | Evidence Go Terms |
---|---|---|---|---|
enoyl-CoA hydratase | paaA | NO | GENE_CLUSTER (MANUAL) | GO:0010124: phenylacetate catabolic process |
enoyl-CoA hydratase/isomerase, PaaB | paaB | NO | TIGR02280 (HMM): phenylacetate degradation probable enoyl-CoA hydratase PaaB | GO:0010124: phenylacetate catabolic process |
3-hydroxyacyl-CoA dehydrogenase, PaaC | paaC | NO | TIGR02279 (HMM): 3-hydroxyacyl-CoA dehydrogenase PaaC | GO:0010124: phenylacetate catabolic process |
putative thioesterase, PaaD | paaD | YES | TIGR02286 (HMM): phenylacetic acid degradation protein PaaD | GO:0010124: phenylacetate catabolic process |
beta-ketothiolase, PaaE | paaE | NO | GENE_CLUSTER (MANUAL) | GO:0010124: phenylacetate catabolic process |
phenylacetate-CoA ligase | paaF | YES | TIGR02155 (HMM): phenylacetate-CoA ligase | GO:0010124: phenylacetate catabolic process |
phenylacetate-CoA oxygenase, PaaG subunit | paaG | YES | TIGR02156 (HMM): phenylacetate-CoA oxygenase, PaaG subunit | GO:0010124: phenylacetate catabolic process |
phenylacetate-CoA oxygenase, PaaH subunit | paaH | YES | TIGR02157 (HMM): phenylacetate-CoA oxygenase, PaaH subunit | GO:0010124: phenylacetate catabolic process |
phenylacetate-CoA oxygenase, PaaI subunit | paaI | YES | TIGR02158 (HMM): phenylacetate-CoA oxygenase, PaaI subunit | GO:0010124: phenylacetate catabolic process |
phenylacetate-CoA oxygenase, PaaJ subunit | paaJ | YES | TIGR02159 (HMM): phenylacetate-CoA oxygenase, PaaJ subunit | GO:0010124: phenylacetate catabolic process |
phenylacetate-CoA oxygenase/reductase, PaaK subunit | paaK | YES | TIGR02160 (HMM): phenylacetate-CoA oxygenase/reductase, PaaK subunit | GO:0010124: phenylacetate catabolic process |
putative ring-opening aldehyde dehydrogenase, PaaN | paaN | YES | TIGR02278 (HMM): phenylacetic acid degradation protein paaN TIGR02288 (HMM): phenylacetic acid degradation protein paaN | GO:0010124: phenylacetate catabolic process GO:0010124: phenylacetate catabolic process |
negative transcriptional regulator | paaX | NO | TIGR02277 (HMM): phenylacetic acid degradation operon negative regulatory protein PaaX | GO:0010124: phenylacetate catabolic process |
putative regulator (?) | paaY | NO | TIGR02287 (HMM): phenylacetic acid degradation protein PaaY | GO:0010124: phenylacetate catabolic process |
Parent Properties
Accession | Name |
---|---|
GenProp0142 | catabolism |
Sibling Properties
Accession | Name |
---|---|
GenProp0055 | polyhydroxyalkanoic acids |
GenProp0141 | galactose-6-phosphate degradation via tagatose-6-phosphate |
GenProp0156 | cyanophycin-like storage polymers |
GenProp0168 | glycogen system |
GenProp0231 | 4-hydroxyphenylacetate degradation |
GenProp0233 | GABA utilization |
GenProp0238 | 2-aminoethylphosphonate catabolism to acetaldehyde |
GenProp0239 | propionyl-CoA catabolism |
GenProp0241 | phosphonate catabolism |
GenProp0271 | trehalose utilization |
GenProp0272 | pyruvate fermentation to acetoin |
GenProp0273 | protocatechuate degradation to beta-ketoadipate |
GenProp0283 | beta-ketoadipate degradation to succinyl-CoA and acetyl-CoA |
GenProp0294 | ethanolamine degradation proteinaceous organelle |
GenProp0457 | rhamnose catabolism |
GenProp0458 | fucose catabolism |
GenProp0461 | utilization of deoxynucleosides |
GenProp0653 | ectoine catabolism |
GenProp0674 | malonate decarboxylase |
GenProp0686 | allantoin catabolism to glyoxalate and urea |
GenProp0687 | allantoin catabolism to oxamate and carbamoyl-phosphate |
GenProp0688 | urate catabolism to allantoin |
GenProp0691 | glycolysis |
GenProp0693 | fructose utilization as fructose-1,6-bisphosphate |
GenProp0694 | glucose utilization as fructose-1,6-bisphosphate |
GenProp0700 | purine catabolism via urate, xanthine and allantoin |
GenProp0702 | benzoyl-CoA reductase |
GenProp0703 | 4-hydroxybenzoyl-CoA reductase |
GenProp0706 | cyclohexa-1,5-diene-1-carbonyl-CoA to 3-hydroxypimelyl-CoA, dch/had/oah pathway |
GenProp0708 | catechol meta-cleavage pathway |
GenProp0709 | benzoate catabolism BoxABC pathway |
GenProp0711 | catechol ortho-cleavage upper pathway |
GenProp0714 | galactarate utilization via tartronate semi-aldehyde |
GenProp0715 | galactarate utilization via 2-oxoglutarate semialdehyde |
GenProp0716 | glucarate utilization via tartronate semi-aldehyde |
GenProp0717 | glucarate utilization via 2-oxoglutarate semialdehyde |
GenProp0718 | oxalate degradation |
GenProp0734 | amino acid catabolism |
GenProp0749 | choline sulfate utilization |
GenProp0760 | putrescine degradation to GABA via gamma-glutamylation |
GenProp0763 | nicotinate fermentation to pyruvate and propionate |
GenProp0810 | encapsulin proteinaceous organelle |
GenProp0813 | pyrimidine utilization operon, RutABCDEFGR |
GenProp0902 | quinohemoprotein amine dehydrogenase |
GenProp1071 | myo-inositol catabolism |
GenProp1072 | cyanase system |
GenProp1076 | choline TMA-lyase system |