Genome Property Definition Page

Namepyrimidine utilization operon, RutABCDEFGR
DescriptionThis seven-gene operon described in E. coli K-12 [1] is responsible for the degradation of uracil, and to a lesser extent, thymine. This has been determined by growth and mutation experiments. The operon contains a luciferase family member (RutA) which likely catalyzes the FMN-dependent critical oxidation for the ring opening as well as RutF which may be involved in recycling the FMN cofactor. Other seemingly essential components are an isochorismate mutase family protein (RutB), a hydrolase (RutD) and a member of the L-PSP endoribonuclease family (RutC) and a regulatory protein (RutR). The transporter RutG found in E. coli is not found in all genomes harboring the rest of the operon and may be replaced by other non-homologous transporters located elsewhere in the genomes. This property appears to be limited to the alpha and gamma proteobacteria.
Parent PropertyGenProp0142: catabolism
GenProp0817: nucleotide catabolism/utilization pathways
Literature References
[ 1 ] Loh KD, Gyaneshwar P, Markenscoff Papadimitriou E, Fong R, Kim KS, Parales R, Zhou Z, Inwood W, Kustu S   A previously undescribed pathway for pyrimidine catabolism.   Proc Natl Acad Sci U S A. 2006 Mar 28;103(13):5114-9. Epub 2006 Mar 15.  PMID 16540542

Step NameStep NumRequiredEvidence (Method)Evidence Go Terms
FMN-dependent luciferase family monoxygenase RutARutAYESTIGR03612 (HMM): pyrimidine utilization protein A
isochorismate mutase family protein RutBRutBYESTIGR03614 (HMM): pyrimidine utilization protein B
L-PSP endoribonuclease family protein RutCRutCYESTIGR03610 (HMM): pyrimidine utilization protein C
hydrolase protein RutDRutDYESTIGR03611 (HMM): pyrimidine utilization protein D
nitroreductase family protein RutERutENOPF00881 (HMM-CLUST): nitroreductase family protein
flavin reductase RutFRutFYESTIGR03615 (HMM): pyrimidine utilization flavin reductase protein F
uracil-xanthine permease family protein RutGRutGNOTIGR03616 (HMM): pyrimidine utilization transport protein G
clustered regulatory proteinRutRNOTIGR03613 (HMM): pyrimidine utilization regulatory protein R

Parent Properties
GenProp0817nucleotide catabolism/utilization pathways

Sibling Properties
GenProp0055polyhydroxyalkanoic acids
GenProp0141galactose-6-phosphate degradation via tagatose-6-phosphate
GenProp0156cyanophycin-like storage polymers
GenProp0168glycogen system
GenProp0210phenylacetic acid catabolism
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
GenProp0902quinohemoprotein amine dehydrogenase
GenProp1071myo-inositol catabolism
GenProp1072cyanase system
GenProp1076choline TMA-lyase system
GenProp0640xanthine dehydrogenase
GenProp0696xanthine utilization as a source of guanine-monophosphate (GMP)
GenProp0705xanthine dehydrogenase, bacillus type (pucABCDE)