RUTC_ECOLI
ID RUTC_ECOLI Reviewed; 128 AA.
AC P0AFQ5; P75896;
DT 20-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT 20-DEC-2005, sequence version 1.
DT 03-AUG-2022, entry version 105.
DE RecName: Full=3-aminoacrylate deaminase RutC {ECO:0000303|PubMed:33839153};
DE Short=3-AA deaminase {ECO:0000303|PubMed:33839153};
DE EC=3.5.-.- {ECO:0000269|PubMed:33839153};
GN Name=rutC; Synonyms=ycdK; OrderedLocusNames=b1010, JW0995;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP INDUCTION.
RX PubMed=11121068; DOI=10.1073/pnas.97.26.14674;
RA Zimmer D.P., Soupene E., Lee H.L., Wendisch V.F., Khodursky A.B.,
RA Peter B.J., Bender R.A., Kustu S.;
RT "Nitrogen regulatory protein C-controlled genes of Escherichia coli:
RT scavenging as a defense against nitrogen limitation.";
RL Proc. Natl. Acad. Sci. U.S.A. 97:14674-14679(2000).
RN [5]
RP FUNCTION IN PYRIMIDINE CATABOLISM, AND NOMENCLATURE.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=16540542; DOI=10.1073/pnas.0600521103;
RA Loh K.D., Gyaneshwar P., Markenscoff Papadimitriou E., Fong R., Kim K.-S.,
RA Parales R., Zhou Z., Inwood W., Kustu S.;
RT "A previously undescribed pathway for pyrimidine catabolism.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:5114-5119(2006).
RN [6]
RP INDUCTION.
RX PubMed=17919280; DOI=10.1111/j.1365-2958.2007.05954.x;
RA Shimada T., Hirao K., Kori A., Yamamoto K., Ishihama A.;
RT "RutR is the uracil/thymine-sensing master regulator of a set of genes for
RT synthesis and degradation of pyrimidines.";
RL Mol. Microbiol. 66:744-757(2007).
RN [7]
RP DISRUPTION PHENOTYPE.
RX PubMed=20400551; DOI=10.1128/jb.00201-10;
RA Kim K.S., Pelton J.G., Inwood W.B., Andersen U., Kustu S., Wemmer D.E.;
RT "The Rut pathway for pyrimidine degradation: novel chemistry and toxicity
RT problems.";
RL J. Bacteriol. 192:4089-4102(2010).
RN [8]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, DISRUPTION
RP PHENOTYPE, AND MUTAGENESIS OF ARG-104.
RC STRAIN=K12;
RX PubMed=33839153; DOI=10.1016/j.jbc.2021.100651;
RA Buckner B.A., Lato A.M., Campagna S.R., Downs D.M.;
RT "The Rid family member RutC of Escherichia coli is a 3-aminoacrylate
RT deaminase.";
RL J. Biol. Chem. 296:100651-100651(2021).
CC -!- FUNCTION: Involved in pyrimidine catabolism (PubMed:16540542).
CC Catalyzes the deamination of 3-aminoacrylate to malonic semialdehyde, a
CC reaction that can also occur spontaneously (PubMed:33839153). RutC may
CC facilitate the reaction and modulate the metabolic fitness, rather than
CC catalyzing essential functions (PubMed:33839153). In vitro, can also
CC deaminate 2-aminoacrylate (PubMed:33839153).
CC {ECO:0000269|PubMed:16540542, ECO:0000269|PubMed:33839153}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(Z)-3-aminoacrylate + H(+) + H2O = 3-oxopropanoate + NH4(+);
CC Xref=Rhea:RHEA:34947, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:28938, ChEBI:CHEBI:33190, ChEBI:CHEBI:59894;
CC Evidence={ECO:0000269|PubMed:33839153};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=9.1 mM for 3-aminoacrylate {ECO:0000269|PubMed:33839153};
CC Note=kcat is 52 min(-1) with 3-aminoacrylate as substrate.
CC {ECO:0000269|PubMed:33839153};
CC -!- SUBUNIT: Homotrimer. {ECO:0000255|HAMAP-Rule:MF_00831}.
CC -!- INDUCTION: Up-regulated by the nitrogen regulatory protein C (NtrC also
CC called GlnG) and repressed by RutR. {ECO:0000269|PubMed:11121068,
CC ECO:0000269|PubMed:17919280}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene fail to grow on uridine
CC as the sole source of nitrogen at room temperature (PubMed:20400551,
CC PubMed:33839153). Expression of rutC in trans did not restore growth
CC (PubMed:33839153). However, a plasmid carrying the complete rutCDEFG
CC operon restored growth of the deletion mutant with uridine as sole
CC nitrogen source, suggesting that the lesion in rutC was polar on
CC downstream gene(s) required for rut pathway function (PubMed:33839153).
CC {ECO:0000269|PubMed:20400551, ECO:0000269|PubMed:33839153}.
CC -!- MISCELLANEOUS: This reaction can occur spontaneously. Under standard
CC laboratory conditions, a Rut pathway lacking RutC generates sufficient
CC nitrogen from uracil for growth of E.coli.
CC {ECO:0000269|PubMed:33839153}.
CC -!- MISCELLANEOUS: The Rut pathway degrades exogenous pyrimidines as the
CC sole nitrogen source at room temperature but not at 37 degrees Celsius,
CC a restriction that is apparently a consequence of an inadequate ability
CC to remove toxic malonic semialdehyde at the higher temperature
CC (RutE/YdfG function).
CC -!- SIMILARITY: Belongs to the RutC family. {ECO:0000255|HAMAP-
CC Rule:MF_00831, ECO:0000305}.
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DR EMBL; U00096; AAC74095.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35777.1; -; Genomic_DNA.
DR PIR; H64842; H64842.
DR RefSeq; NP_415530.1; NC_000913.3.
DR RefSeq; WP_001126780.1; NZ_SSZK01000002.1.
DR AlphaFoldDB; P0AFQ5; -.
DR SMR; P0AFQ5; -.
DR BioGRID; 4260036; 13.
DR IntAct; P0AFQ5; 7.
DR STRING; 511145.b1010; -.
DR PaxDb; P0AFQ5; -.
DR PRIDE; P0AFQ5; -.
DR EnsemblBacteria; AAC74095; AAC74095; b1010.
DR EnsemblBacteria; BAA35777; BAA35777; BAA35777.
DR GeneID; 66670712; -.
DR GeneID; 945599; -.
DR KEGG; ecj:JW0995; -.
DR KEGG; eco:b1010; -.
DR PATRIC; fig|1411691.4.peg.1261; -.
DR EchoBASE; EB3617; -.
DR eggNOG; COG0251; Bacteria.
DR HOGENOM; CLU_100715_7_3_6; -.
DR InParanoid; P0AFQ5; -.
DR OMA; MPKTIIT; -.
DR PhylomeDB; P0AFQ5; -.
DR BioCyc; EcoCyc:G6521-MON; -.
DR BioCyc; MetaCyc:G6521-MON; -.
DR PRO; PR:P0AFQ5; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0019239; F:deaminase activity; IBA:GO_Central.
DR GO; GO:0016491; F:oxidoreductase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0019740; P:nitrogen utilization; IMP:UniProtKB.
DR GO; GO:1901565; P:organonitrogen compound catabolic process; IBA:GO_Central.
DR GO; GO:0006208; P:pyrimidine nucleobase catabolic process; IMP:EcoCyc.
DR GO; GO:0006212; P:uracil catabolic process; IMP:UniProtKB.
DR Gene3D; 3.30.1330.40; -; 1.
DR HAMAP; MF_00831; RutC; 1.
DR InterPro; IPR019897; RidA_CS.
DR InterPro; IPR019898; RutC.
DR InterPro; IPR035959; RutC-like_sf.
DR InterPro; IPR006175; YjgF/YER057c/UK114.
DR PANTHER; PTHR11803; PTHR11803; 1.
DR Pfam; PF01042; Ribonuc_L-PSP; 1.
DR SUPFAM; SSF55298; SSF55298; 1.
DR TIGRFAMs; TIGR03610; RutC; 1.
DR PROSITE; PS01094; UPF0076; 1.
PE 1: Evidence at protein level;
KW Hydrolase; Reference proteome.
FT CHAIN 1..128
FT /note="3-aminoacrylate deaminase RutC"
FT /id="PRO_0000170319"
FT MUTAGEN 104
FT /note="R->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:33839153"
SQ SEQUENCE 128 AA; 13763 MW; 7D5FC2374597D907 CRC64;
MPKSVIIPAG SSAPLAPFVP GTLADGVVYV SGTLAFDQHN NVLFADDPKA QTRHVLETIR
KVIETAGGTM ADVTFNSIFI TDWKNYAAIN EIYAEFFPGD KPARFCIQCG LVKPDALVEI
ATIAHIAK
