ID   RUTD_ECOLI              Reviewed;         266 AA.
AC   P75895;
DT   16-APR-2002, integrated into UniProtKB/Swiss-Prot.
DT   01-FEB-1997, sequence version 1.
DT   03-AUG-2022, entry version 136.
DE   RecName: Full=Putative carbamate hydrolase RutD {ECO:0000305};
DE            EC=3.5.1.- {ECO:0000305|PubMed:33839153};
DE   AltName: Full=Aminohydrolase;
GN   Name=rutD; Synonyms=ycdJ; OrderedLocusNames=b1009, JW0994;
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, AND DISRUPTION PHENOTYPE.
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). May
CC       facilitate the hydrolysis of carbamate, a reaction that can also occur
CC       spontaneously (Probable). {ECO:0000269|PubMed:16540542,
CC       ECO:0000305|PubMed:33839153}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=carbamate + 2 H(+) = CO2 + NH4(+); Xref=Rhea:RHEA:15649,
CC         ChEBI:CHEBI:13941, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526,
CC         ChEBI:CHEBI:28938; Evidence={ECO:0000305|PubMed:33839153};
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 form less than the normal
CC       amount of malonic semialdehyde because a portion of the 3-carbon
CC       intermediate is diverted out of the Rut pathway (PubMed:20400551). It
CC       was shown later that defects could be due to polarity of the lesion on
CC       one or more of the downstream genes (PubMed:33839153).
CC       {ECO:0000269|PubMed:20400551, 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 AB hydrolase superfamily. Hydrolase RutD
CC       family. {ECO:0000255|HAMAP-Rule:MF_00832, ECO:0000305}.
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DR   EMBL; U00096; AAC74094.1; -; Genomic_DNA.
DR   EMBL; AP009048; BAA35776.1; -; Genomic_DNA.
DR   PIR; G64842; G64842.
DR   RefSeq; NP_415529.1; NC_000913.3.
DR   RefSeq; WP_000777653.1; NZ_SSZK01000002.1.
DR   AlphaFoldDB; P75895; -.
DR   SMR; P75895; -.
DR   BioGRID; 4262210; 24.
DR   STRING; 511145.b1009; -.
DR   ESTHER; ecoli-rutD; RutD.
DR   PaxDb; P75895; -.
DR   PRIDE; P75895; -.
DR   EnsemblBacteria; AAC74094; AAC74094; b1009.
DR   EnsemblBacteria; BAA35776; BAA35776; BAA35776.
DR   GeneID; 946586; -.
DR   KEGG; ecj:JW0994; -.
DR   KEGG; eco:b1009; -.
DR   PATRIC; fig|1411691.4.peg.1262; -.
DR   EchoBASE; EB3616; -.
DR   eggNOG; COG2021; Bacteria.
DR   HOGENOM; CLU_020336_50_1_6; -.
DR   InParanoid; P75895; -.
DR   OMA; HAMSVTD; -.
DR   PhylomeDB; P75895; -.
DR   BioCyc; EcoCyc:G6520-MON; -.
DR   PRO; PR:P75895; -.
DR   Proteomes; UP000000318; Chromosome.
DR   Proteomes; UP000000625; Chromosome.
DR   GO; GO:0016787; F:hydrolase activity; IBA:GO_Central.
DR   GO; GO:0016811; F:hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides; IEA:InterPro.
DR   GO; GO:0019740; P:nitrogen utilization; IMP:UniProtKB.
DR   GO; GO:0006208; P:pyrimidine nucleobase catabolic process; IMP:EcoCyc.
DR   GO; GO:0006212; P:uracil catabolic process; IMP:UniProtKB.
DR   Gene3D; 3.40.50.1820; -; 1.
DR   HAMAP; MF_00832; RutD; 1.
DR   InterPro; IPR029058; AB_hydrolase.
DR   InterPro; IPR000073; AB_hydrolase_1.
DR   InterPro; IPR019913; Pyrimidine_utilisation_RutD.
DR   Pfam; PF12697; Abhydrolase_6; 1.
DR   PRINTS; PR00111; ABHYDROLASE.
DR   SUPFAM; SSF53474; SSF53474; 1.
DR   TIGRFAMs; TIGR03611; RutD; 1.
PE   1: Evidence at protein level;
KW   Hydrolase; Reference proteome.
FT   CHAIN           1..266
FT                   /note="Putative carbamate hydrolase RutD"
FT                   /id="PRO_0000168800"
SQ   SEQUENCE   266 AA;  28898 MW;  378E13994425E9E2 CRC64;
     MKLSLSPPPY ADAPVVVLIS GLGGSGSYWL PQLAVLEQEY QVVCYDQRGT GNNPDTLAED
     YSIAQMAAEL HQALVAAGIE HYAVVGHALG ALVGMQLALD YPASVTVLIS VNGWLRINAH
     TRRCFQVRER LLYSGGAQAW VEAQPLFLYP ADWMAARAPR LEAEDALALA HFQGKNNLLR
     RLNALKRADF SHHADRIRCP VQIICASDDL LVPTACSSEL HAALPDSQKM VMPYGGHACN
     VTDPETFNAL LLNGLASLLH HREAAL