Genome Property Definition Page

Namephenylacetic acid catabolism
DescriptionThe 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 RoleOther
Parent PropertyGenProp0142: catabolism
Literature References
[ 1 ]Luengo JM, Garcia JL, Olivera ER  The phenylacetyl-CoA catabolon: a complex catabolic unit with broad biotechnological applications.  Mol Microbiol. 2001 Mar;39(6):1434-42.  PMID 11260461
Web ReferencesThe Ecocyc Database: phenylacetate degradation I
Gene Ontology TermGO:0010124: phenylacetate catabolic process (biological_process)

Step NameStep NumRequiredEvidence (Method)Evidence Go Terms
enoyl-CoA hydratasepaaANOGENE_CLUSTER (MANUAL)
GO:0010124: phenylacetate catabolic process
enoyl-CoA hydratase/isomerase, PaaBpaaBNOTIGR02280 (HMM): phenylacetate degradation probable enoyl-CoA hydratase PaaBGO:0010124: phenylacetate catabolic process
3-hydroxyacyl-CoA dehydrogenase, PaaCpaaCNOTIGR02279 (HMM): 3-hydroxyacyl-CoA dehydrogenase PaaCGO:0010124: phenylacetate catabolic process
putative thioesterase, PaaDpaaDYESTIGR02286 (HMM): phenylacetic acid degradation protein PaaDGO:0010124: phenylacetate catabolic process
beta-ketothiolase, PaaEpaaENOGENE_CLUSTER (MANUAL)
GO:0010124: phenylacetate catabolic process
phenylacetate-CoA ligasepaaFYESTIGR02155 (HMM): phenylacetate-CoA ligaseGO:0010124: phenylacetate catabolic process
phenylacetate-CoA oxygenase, PaaG subunitpaaGYESTIGR02156 (HMM): phenylacetate-CoA oxygenase, PaaG subunitGO:0010124: phenylacetate catabolic process
phenylacetate-CoA oxygenase, PaaH subunitpaaHYESTIGR02157 (HMM): phenylacetate-CoA oxygenase, PaaH subunitGO:0010124: phenylacetate catabolic process
phenylacetate-CoA oxygenase, PaaI subunitpaaIYESTIGR02158 (HMM): phenylacetate-CoA oxygenase, PaaI subunitGO:0010124: phenylacetate catabolic process
phenylacetate-CoA oxygenase, PaaJ subunitpaaJYESTIGR02159 (HMM): phenylacetate-CoA oxygenase, PaaJ subunitGO:0010124: phenylacetate catabolic process
phenylacetate-CoA oxygenase/reductase, PaaK subunitpaaKYESTIGR02160 (HMM): phenylacetate-CoA oxygenase/reductase, PaaK subunitGO:0010124: phenylacetate catabolic process
putative ring-opening aldehyde dehydrogenase, PaaNpaaNYESTIGR02278 (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 regulatorpaaXNOTIGR02277 (HMM): phenylacetic acid degradation operon negative regulatory protein PaaXGO:0010124: phenylacetate catabolic process
putative regulator (?)paaYNOTIGR02287 (HMM): phenylacetic acid degradation protein PaaYGO:0010124: phenylacetate catabolic process

Parent Properties

Sibling Properties
GenProp0055polyhydroxyalkanoic acids
GenProp0141galactose-6-phosphate degradation via tagatose-6-phosphate
GenProp0156cyanophycin-like storage polymers
GenProp0168glycogen system
GenProp02314-hydroxyphenylacetate degradation
GenProp0233GABA utilization
GenProp02382-aminoethylphosphonate catabolism to acetaldehyde
GenProp0239propionyl-CoA catabolism
GenProp0241phosphonate catabolism
GenProp0271trehalose utilization
GenProp0272pyruvate fermentation to acetoin
GenProp0273protocatechuate degradation to beta-ketoadipate
GenProp0283beta-ketoadipate degradation to succinyl-CoA and acetyl-CoA
GenProp0294ethanolamine degradation proteinaceous organelle
GenProp0457rhamnose catabolism
GenProp0458fucose catabolism
GenProp0461utilization of deoxynucleosides
GenProp0653ectoine catabolism
GenProp0674malonate decarboxylase
GenProp0686allantoin catabolism to glyoxalate and urea
GenProp0687allantoin catabolism to oxamate and carbamoyl-phosphate
GenProp0688urate catabolism to allantoin
GenProp0693fructose utilization as fructose-1,6-bisphosphate
GenProp0694glucose utilization as fructose-1,6-bisphosphate
GenProp0700purine catabolism via urate, xanthine and allantoin
GenProp0702benzoyl-CoA reductase
GenProp07034-hydroxybenzoyl-CoA reductase
GenProp0706cyclohexa-1,5-diene-1-carbonyl-CoA to 3-hydroxypimelyl-CoA, dch/had/oah pathway
GenProp0708catechol meta-cleavage pathway
GenProp0709benzoate catabolism BoxABC pathway
GenProp0711catechol ortho-cleavage upper pathway
GenProp0714galactarate utilization via tartronate semi-aldehyde
GenProp0715galactarate utilization via 2-oxoglutarate semialdehyde
GenProp0716glucarate utilization via tartronate semi-aldehyde
GenProp0717glucarate utilization via 2-oxoglutarate semialdehyde
GenProp0718oxalate degradation
GenProp0734amino acid catabolism
GenProp0749choline sulfate utilization
GenProp0760putrescine degradation to GABA via gamma-glutamylation
GenProp0763nicotinate fermentation to pyruvate and propionate
GenProp0810encapsulin proteinaceous organelle
GenProp0813pyrimidine utilization operon, RutABCDEFGR
GenProp0902quinohemoprotein amine dehydrogenase
GenProp1071myo-inositol catabolism
GenProp1072cyanase system
GenProp1076choline TMA-lyase system