title: The Rut pathway for pyrimidine degradation: novel chemistry and toxicity problems.
abstract: The Rut pathway is composed of seven proteins, all of which are required by Escherichia coli K-12 to grow on uracil as the sole nitrogen source. The RutA and RutB proteins are central: no spontaneous suppressors arise in strains lacking them. RutA works in conjunction with a flavin reductase (RutF or a substitute) to catalyze a novel reaction. It directly cleaves the uracil ring between N-3 and C-4 to yield ureidoacrylate, as established by both nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry. Although ureidoacrylate appears to arise by hydrolysis, the requirements for the reaction and the incorporation of (18)O at C-4 from molecular oxygen indicate otherwise. Mass spectrometry revealed the presence of a small amount of product with the mass of ureidoacrylate peracid in reaction mixtures, and we infer that this is the direct product of RutA. In vitro RutB cleaves ureidoacrylate hydrolytically to release 2 mol of ammonium, malonic semialdehyde, and carbon dioxide. Presumably the direct products are aminoacrylate and carbamate, both of which hydrolyze spontaneously. Together with bioinformatic predictions and published crystal structures, genetic and physiological studies allow us to predict functions for RutC, -D, and -E. In vivo we postulate that RutB hydrolyzes the peracid of ureidoacrylate to yield the peracid of aminoacrylate. We speculate that RutC reduces aminoacrylate peracid to aminoacrylate and RutD increases the rate of spontaneous hydrolysis of aminoacrylate. The function of RutE appears to be the same as that of YdfG, which reduces malonic semialdehyde to 3-hydroxypropionic acid. RutG appears to be a uracil transporter.
authors.affiliation: Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720-3102, USA.
authors.forename: Kwang-Seo
authors.initials: KS
authors.lastname: Kim
authors.forename: Jeffrey G
authors.initials: JG
authors.lastname: Pelton
authors.forename: William B
authors.initials: WB
authors.lastname: Inwood
authors.forename: Ulla
authors.initials: U
authors.lastname: Andersen
authors.forename: Sydney
authors.initials: S
authors.lastname: Kustu
authors.forename: David E
authors.initials: DE
authors.lastname: Wemmer
mesh_terms: D002245:Carbon Dioxide / Q000378:metabolism; D048168:Escherichia coli K12 / Q000254:growth & development / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D017353:Gene Deletion; D009682:Magnetic Resonance Spectroscopy; D008315:Malondialdehyde / Q000031:analogs & derivatives / Q000378:metabolism; D013058:Mass Spectrometry; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D009584:Nitrogen / Q000378:metabolism*; D010088:Oxidoreductases / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D000644:Quaternary Ammonium Compounds / Q000378:metabolism; D014498:Uracil / Q000378:metabolism*
chemical_list: D029968:Escherichia coli Proteins; D000644:Quaternary Ammonium Compounds; D002245:Carbon Dioxide; D008315:Malondialdehyde; D014498:Uracil; C039786:malonic semialdehyde; D010088:Oxidoreductases; C580879:RutC protein, E coli; D009584:Nitrogen
references.citation: Proc Natl Acad Sci U S A. 2006 May 16;103(20):7601-6
references.pmid: 16682646
references.citation: J Bacteriol. 2000 Feb;182(3):627-36
references.pmid: 10633095
references.citation: Z Naturforsch C Biosci. 1978 Nov-Dec;33(11-12):1006-8
references.pmid: 154218
references.citation: Biochemistry. 1982 May 25;21(11):2644-55
references.pmid: 7093214
references.citation: J Am Chem Soc. 2010 Apr 28;132(16):5550-1
references.pmid: 20369853
references.citation: Int J Biochem. 1981;13(5):615-9
references.pmid: 6113173
references.citation: J Bacteriol. 2008 Sep;190(17):5890-7
references.pmid: 18567656
references.citation: Nat Chem Biol. 2009 Aug;5(8):593-9
references.pmid: 19561621
references.citation: J Biol Chem. 1999 Jul 16;274(29):20688-92
references.pmid: 10400702
references.citation: J Bacteriol. 2001 Dec;183(23):6943-6
references.pmid: 11698384
references.citation: Mol Syst Biol. 2006;2:2006.0008
references.pmid: 16738554
references.citation: J Biol Chem. 1999 Sep 17;274(38):26639-46
references.pmid: 10480865
references.citation: J Bacteriol. 2003 Sep;185(18):5611-26
references.pmid: 12949114
references.citation: Bacteriol Rev. 1976 Jun;40(2):403-68
references.pmid: 786256
references.citation: BMC Struct Biol. 2007 May 16;7:30
references.pmid: 17506874
references.citation: J Biol Chem. 1952 May;197(2):717-32
references.pmid: 12981104
references.citation: Cell. 2002 Nov 27;111(5):747-56
references.pmid: 12464185
references.citation: J Bacteriol. 2005 Feb;187(3):1074-90
references.pmid: 15659685
references.citation: Biochim Biophys Acta. 1999 Feb 25;1422(1):1-56
references.pmid: 10082980
references.citation: J Mol Biol. 2008 Mar 14;377(1):258-67
references.pmid: 18241886
references.citation: Mol Microbiol. 2007 Nov;66(3):744-57
references.pmid: 17919280
references.citation: IUBMB Life. 2006 May-Jun;58(5-6):253
references.pmid: 16754307
references.citation: J Biol Chem. 1977 Jun 25;252(12):4151-6
references.pmid: 16925
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D205-10
references.pmid: 18984618
references.citation: J Bacteriol. 1998 Dec;180(24):6519-28
references.pmid: 9851994
references.citation: Protein Sci. 1999 Nov;8(11):2428-37
references.pmid: 10595546
references.citation: J Histochem Cytochem. 1985 Aug;33(8):845-53
references.pmid: 3894502
references.citation: J Biomol NMR. 1995 Nov;6(3):277-93
references.pmid: 8520220
references.citation: J Biol Chem. 1986 Sep 5;261(25):11832-9
references.pmid: 3745168
references.citation: DNA Res. 2005;12(5):291-9
references.pmid: 16769691
references.citation: Proc Natl Acad Sci U S A. 2006 Mar 28;103(13):5114-9
references.pmid: 16540542
references.citation: J Bacteriol. 1978 Mar;133(3):1126-9
references.pmid: 417060
references.citation: J Mol Biol. 1992 Aug 20;226(4):1111-30
references.pmid: 1381445
references.citation: Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6640-5
references.pmid: 10829079
references.citation: Biochem J. 2006 Apr 1;395(1):107-15
references.pmid: 16332250
references.citation: J Bacteriol. 2008 Feb;190(3):972-9
references.pmid: 18065551
references.citation: Plant Physiol. 2001 Feb;125(2):1001-11
references.pmid: 11161056
references.citation: Bioessays. 1987 Sep;7(3):125-30
references.pmid: 3318818
references.citation: J Mol Biol. 2008 Jul 18;380(4):656-66
references.pmid: 18550080
references.citation: Nucleic Acids Res. 2008 Jul;36(12):3950-5
references.pmid: 18515344
references.citation: Microbiology (Reading). 2002 Jun;148(Pt 6):1607-1614
references.pmid: 12055282
references.citation: J Bacteriol. 1995 Apr;177(8):2008-13
references.pmid: 7721693
references.citation: Appl Environ Microbiol. 2000 Feb;66(2):481-6
references.pmid: 10653707
references.citation: Proc Natl Acad Sci U S A. 2002 Dec 10;99(25):15908-13
references.pmid: 12456892
references.citation: J Mol Biol. 1998 Jul 10;280(2):259-73
references.pmid: 9654450
references.citation: Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14674-9
references.pmid: 11121068
references.citation: J Biol Chem. 1994 Sep 9;269(36):22459-62
references.pmid: 8077188
references.citation: Proc Natl Acad Sci U S A. 2006 Apr 11;103(15):5637-8
references.pmid: 16595627
references.citation: J Bacteriol. 2008 Jun;190(11):3793-8
references.pmid: 18390652
references.citation: J Biomol NMR. 1995 Sep;6(2):135-40
references.pmid: 8589602
references.citation: J Biol Chem. 2002 Mar 1;277(9):7051-8
references.pmid: 11748240
references.citation: J Biomol NMR. 2006 Oct;36(2):111-22
references.pmid: 17013682
references.citation: J Bacteriol. 2008 Apr;190(8):3057-62
references.pmid: 18296521
references.citation: Biochem Soc Trans. 2000;28(4):283-96
references.pmid: 10961912
references.citation: J Biol Chem. 2000 Oct 13;275(41):32277-80
references.pmid: 10913144
references.citation: J Biomol NMR. 1994 Mar;4(2):301-6
references.pmid: 8019138
references.citation: Genetics. 2009 Dec;183(4):1327-40
references.pmid: 19596908
references.citation: Biochim Biophys Acta. 2003 Jan 31;1645(1):89-94
references.pmid: 12535615