DCD_ECOLI
ID DCD_ECOLI Reviewed; 193 AA.
AC P28248;
DT 01-DEC-1992, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-1992, sequence version 1.
DT 03-AUG-2022, entry version 163.
DE RecName: Full=dCTP deaminase {ECO:0000255|HAMAP-Rule:MF_00146, ECO:0000303|PubMed:1324907};
DE EC=3.5.4.13 {ECO:0000255|HAMAP-Rule:MF_00146, ECO:0000269|PubMed:1324907};
DE AltName: Full=Deoxycytidine triphosphate deaminase {ECO:0000255|HAMAP-Rule:MF_00146};
GN Name=dcd {ECO:0000255|HAMAP-Rule:MF_00146, ECO:0000303|PubMed:1324907};
GN Synonyms=dus {ECO:0000303|PubMed:1324907}, paxA;
GN OrderedLocusNames=b2065, JW2050;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-10, FUNCTION,
RP CATALYTIC ACTIVITY, PATHWAY, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12;
RX PubMed=1324907; DOI=10.1128/jb.174.17.5647-5653.1992;
RA Wang L., Weiss B.;
RT "dcd (dCTP deaminase) gene of Escherichia coli: mapping, cloning,
RT sequencing, and identification as a locus of suppressors of lethal dut
RT (dUTPase) mutations.";
RL J. Bacteriol. 174:5647-5653(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9097040; DOI=10.1093/dnares/3.6.379;
RA Itoh T., Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K.,
RA Kasai H., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T.,
RA Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S., Nakamura Y.,
RA Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y.,
RA Sivasundaram S., Tagami H., Takeda J., Takemoto K., Wada C., Yamamoto Y.,
RA Horiuchi T.;
RT "A 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 40.1-50.0 min region on the linkage map.";
RL DNA Res. 3:379-392(1996).
RN [3]
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 [4]
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 [5] {ECO:0007744|PDB:1XS1, ECO:0007744|PDB:1XS4, ECO:0007744|PDB:1XS6}
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF WILD-TYPE IN COMPLEX WITH DUTP
RP AND OF MUTANT ALA-138 IN COMPLEXES WITH DCTP AND DUTP, FUNCTION, CATALYTIC
RP ACTIVITY, ACTIVITY REGULATION, SUBUNIT, ACTIVE SITE, AND MUTAGENESIS OF
RP ARG-115 AND GLU-138.
RX PubMed=15539408; DOI=10.1074/jbc.m409534200;
RA Johansson E., Fano M., Bynck J.H., Neuhard J., Larsen S., Sigurskjold B.W.,
RA Christensen U., Willemoes M.;
RT "Structures of dCTP deaminase from Escherichia coli with bound substrate
RT and product: reaction mechanism and determinants of mono- and
RT bifunctionality for a family of enzymes.";
RL J. Biol. Chem. 280:3051-3059(2005).
RN [6] {ECO:0007744|PDB:2J4H, ECO:0007744|PDB:2J4Q}
RP X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) OF MUTANT ALA-121 IN COMPLEX WITH
RP DCTP AND OF MUTANT ALA-138 IN COMPLEX WITH DTTP, FUNCTION, CATALYTIC
RP ACTIVITY, ACTIVITY REGULATION, SUBUNIT, AND MUTAGENESIS OF HIS-121 AND
RP VAL-122.
RX PubMed=17651436; DOI=10.1111/j.1742-4658.2007.05945.x;
RA Johansson E., Thymark M., Bynck J.H., Fano M., Larsen S., Willemoes M.;
RT "Regulation of dCTP deaminase from Escherichia coli by nonallosteric dTTP
RT binding to an inactive form of the enzyme.";
RL FEBS J. 274:4188-4198(2007).
RN [7] {ECO:0007744|PDB:2V9X}
RP X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) OF MUTANT ASP-138 IN COMPLEX WITH
RP DUTP, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT,
RP ACTIVE SITE, AND MUTAGENESIS OF SER-111; ARG-115 AND GLU-138.
RX PubMed=17996716; DOI=10.1016/j.abb.2007.10.013;
RA Thymark M., Johansson E., Larsen S., Willemoes M.;
RT "Mutational analysis of the nucleotide binding site of Escherichia coli
RT dCTP deaminase.";
RL Arch. Biochem. Biophys. 470:20-26(2008).
CC -!- FUNCTION: Catalyzes the deamination of dCTP to dUTP.
CC {ECO:0000255|HAMAP-Rule:MF_00146, ECO:0000269|PubMed:1324907,
CC ECO:0000269|PubMed:15539408, ECO:0000269|PubMed:17651436,
CC ECO:0000269|PubMed:17996716}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=dCTP + H(+) + H2O = dUTP + NH4(+); Xref=Rhea:RHEA:22680,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:28938,
CC ChEBI:CHEBI:61481, ChEBI:CHEBI:61555; EC=3.5.4.13;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00146,
CC ECO:0000269|PubMed:1324907, ECO:0000269|PubMed:15539408,
CC ECO:0000269|PubMed:17651436, ECO:0000269|PubMed:17996716};
CC -!- ACTIVITY REGULATION: Inhibited by dTTP, which binds to the active site
CC and stabilizes the inactive form of the enzyme (PubMed:17651436).
CC Inhibited by inorganic phosphate (PubMed:15539408).
CC {ECO:0000269|PubMed:15539408, ECO:0000269|PubMed:17651436}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC Note=kcat is 1.24 sec(-1). {ECO:0000269|PubMed:17996716};
CC -!- PATHWAY: Pyrimidine metabolism; dUMP biosynthesis; dUMP from dCTP (dUTP
CC route): step 1/2. {ECO:0000255|HAMAP-Rule:MF_00146,
CC ECO:0000269|PubMed:1324907}.
CC -!- SUBUNIT: Homotrimer. {ECO:0000255|HAMAP-Rule:MF_00146,
CC ECO:0000269|PubMed:15539408, ECO:0000269|PubMed:17651436,
CC ECO:0000269|PubMed:17996716}.
CC -!- DISRUPTION PHENOTYPE: Mutant accumulates dCTP.
CC {ECO:0000269|PubMed:1324907}.
CC -!- SIMILARITY: Belongs to the dCTP deaminase family. {ECO:0000255|HAMAP-
CC Rule:MF_00146, ECO:0000305}.
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DR EMBL; M90069; AAA23669.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75126.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA15918.1; -; Genomic_DNA.
DR PIR; A42940; A42940.
DR RefSeq; NP_416569.1; NC_000913.3.
DR RefSeq; WP_001234768.1; NZ_LN832404.1.
DR PDB; 1XS1; X-ray; 1.80 A; A/B/C/D/E/F=1-193.
DR PDB; 1XS4; X-ray; 2.53 A; A/B/C/D/E/F=1-193.
DR PDB; 1XS6; X-ray; 2.00 A; A/B/C/D/E/F=1-193.
DR PDB; 2J4H; X-ray; 2.70 A; A/B=1-193.
DR PDB; 2J4Q; X-ray; 2.60 A; A/B=1-193.
DR PDB; 2V9X; X-ray; 2.20 A; A/B/C/D/E/F/G/H/I/J/K/L=1-193.
DR PDBsum; 1XS1; -.
DR PDBsum; 1XS4; -.
DR PDBsum; 1XS6; -.
DR PDBsum; 2J4H; -.
DR PDBsum; 2J4Q; -.
DR PDBsum; 2V9X; -.
DR AlphaFoldDB; P28248; -.
DR SMR; P28248; -.
DR BioGRID; 4259684; 5.
DR IntAct; P28248; 2.
DR STRING; 511145.b2065; -.
DR DrugBank; DB03258; 2'-Deoxycytidine 5'-triphosphate.
DR DrugBank; DB02333; Deoxyuridine-5'-Triphosphate.
DR jPOST; P28248; -.
DR PaxDb; P28248; -.
DR PRIDE; P28248; -.
DR EnsemblBacteria; AAC75126; AAC75126; b2065.
DR EnsemblBacteria; BAA15918; BAA15918; BAA15918.
DR GeneID; 946593; -.
DR KEGG; ecj:JW2050; -.
DR KEGG; eco:b2065; -.
DR PATRIC; fig|1411691.4.peg.186; -.
DR EchoBASE; EB1389; -.
DR eggNOG; COG0717; Bacteria.
DR HOGENOM; CLU_087476_2_0_6; -.
DR InParanoid; P28248; -.
DR OMA; PPIERIN; -.
DR PhylomeDB; P28248; -.
DR BioCyc; EcoCyc:DCTP-DEAM-MON; -.
DR BioCyc; MetaCyc:DCTP-DEAM-MON; -.
DR BRENDA; 3.5.4.13; 2026.
DR UniPathway; UPA00610; UER00665.
DR EvolutionaryTrace; P28248; -.
DR PRO; PR:P28248; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0032991; C:protein-containing complex; IDA:EcoCyc.
DR GO; GO:0008829; F:dCTP deaminase activity; IDA:EcoCyc.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0006235; P:dTTP biosynthetic process; IMP:EcoCyc.
DR GO; GO:0006226; P:dUMP biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0006229; P:dUTP biosynthetic process; IDA:EcoCyc.
DR GO; GO:0015949; P:nucleobase-containing small molecule interconversion; IMP:EcoCyc.
DR GO; GO:0009314; P:response to radiation; IMP:EcoCyc.
DR CDD; cd07557; trimeric_dUTPase; 1.
DR Gene3D; 2.70.40.10; -; 1.
DR HAMAP; MF_00146; dCTP_deaminase; 1.
DR InterPro; IPR011962; dCTP_deaminase.
DR InterPro; IPR029054; dUTPase-like.
DR InterPro; IPR036157; dUTPase-like_sf.
DR InterPro; IPR033704; dUTPase_trimeric.
DR Pfam; PF00692; dUTPase; 1.
DR SUPFAM; SSF51283; SSF51283; 1.
DR TIGRFAMs; TIGR02274; dCTP_deam; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Hydrolase; Nucleotide metabolism;
KW Nucleotide-binding; Reference proteome.
FT CHAIN 1..193
FT /note="dCTP deaminase"
FT /id="PRO_0000155984"
FT ACT_SITE 138
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00146,
FT ECO:0000305|PubMed:15539408, ECO:0000305|PubMed:17996716"
FT BINDING 110..115
FT /ligand="dCTP"
FT /ligand_id="ChEBI:CHEBI:61481"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00146,
FT ECO:0000305|PubMed:15539408, ECO:0000305|PubMed:17651436,
FT ECO:0000305|PubMed:17996716"
FT BINDING 124..128
FT /ligand="dCTP"
FT /ligand_id="ChEBI:CHEBI:61481"
FT /evidence="ECO:0000305|PubMed:15539408,
FT ECO:0000305|PubMed:17651436, ECO:0000305|PubMed:17996716"
FT BINDING 136..138
FT /ligand="dCTP"
FT /ligand_id="ChEBI:CHEBI:61481"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00146,
FT ECO:0000305|PubMed:15539408, ECO:0000305|PubMed:17651436,
FT ECO:0000305|PubMed:17996716"
FT BINDING 171..174
FT /ligand="dCTP"
FT /ligand_id="ChEBI:CHEBI:61481"
FT /evidence="ECO:0000305|PubMed:15539408,
FT ECO:0000305|PubMed:17996716"
FT BINDING 178
FT /ligand="dCTP"
FT /ligand_id="ChEBI:CHEBI:61481"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00146,
FT ECO:0000305|PubMed:15539408, ECO:0000305|PubMed:17996716"
FT BINDING 182
FT /ligand="dCTP"
FT /ligand_id="ChEBI:CHEBI:61481"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00146,
FT ECO:0000305|PubMed:15539408, ECO:0000305|PubMed:17996716"
FT MUTAGEN 111
FT /note="S->C: Loss of activity."
FT /evidence="ECO:0000269|PubMed:17996716"
FT MUTAGEN 111
FT /note="S->T: 30-fold decrease in kcat. Shows altered dTTP
FT inhibition."
FT /evidence="ECO:0000269|PubMed:17996716"
FT MUTAGEN 115
FT /note="R->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:15539408"
FT MUTAGEN 115
FT /note="R->Q: Loss of activity."
FT /evidence="ECO:0000269|PubMed:17996716"
FT MUTAGEN 121
FT /note="H->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:17651436"
FT MUTAGEN 122
FT /note="V->G: Loss of activity."
FT /evidence="ECO:0000269|PubMed:17651436"
FT MUTAGEN 138
FT /note="E->A,Q: Loss of activity."
FT /evidence="ECO:0000269|PubMed:15539408"
FT MUTAGEN 138
FT /note="E->D: 140-fold decrease in kcat. Shows altered dTTP
FT inhibition."
FT /evidence="ECO:0000269|PubMed:17996716"
FT HELIX 5..14
FT /evidence="ECO:0007829|PDB:1XS1"
FT STRAND 15..21
FT /evidence="ECO:0007829|PDB:1XS1"
FT HELIX 25..27
FT /evidence="ECO:0007829|PDB:1XS1"
FT STRAND 32..37
FT /evidence="ECO:0007829|PDB:1XS1"
FT STRAND 39..42
FT /evidence="ECO:0007829|PDB:1XS1"
FT HELIX 46..48
FT /evidence="ECO:0007829|PDB:1XS1"
FT STRAND 54..56
FT /evidence="ECO:0007829|PDB:2J4Q"
FT HELIX 58..68
FT /evidence="ECO:0007829|PDB:1XS1"
FT STRAND 81..83
FT /evidence="ECO:0007829|PDB:1XS1"
FT STRAND 89..98
FT /evidence="ECO:0007829|PDB:1XS1"
FT STRAND 103..108
FT /evidence="ECO:0007829|PDB:1XS1"
FT HELIX 111..114
FT /evidence="ECO:0007829|PDB:1XS1"
FT TURN 115..117
FT /evidence="ECO:0007829|PDB:1XS1"
FT STRAND 118..120
FT /evidence="ECO:0007829|PDB:1XS1"
FT STRAND 132..141
FT /evidence="ECO:0007829|PDB:1XS1"
FT STRAND 143..145
FT /evidence="ECO:0007829|PDB:1XS1"
FT STRAND 147..149
FT /evidence="ECO:0007829|PDB:1XS1"
FT STRAND 153..162
FT /evidence="ECO:0007829|PDB:1XS1"
FT HELIX 171..173
FT /evidence="ECO:0007829|PDB:1XS1"
FT STRAND 180..182
FT /evidence="ECO:0007829|PDB:1XS1"
FT HELIX 190..192
FT /evidence="ECO:0007829|PDB:1XS1"
SQ SEQUENCE 193 AA; 21249 MW; B0044051ADE7F919 CRC64;
MRLCDRDIEA WLDEGRLSIN PRPPVERING ATVDVRLGNK FRTFRGHTAA FIDLSGPKDE
VSAALDRVMS DEIVLDEGEA FYLHPGELAL AVTLESVTLP ADLVGWLDGR SSLARLGLMV
HVTAHRIDPG WSGCIVLEFY NSGKLPLALR PGMLIGALSF EPLSGPAVRP YNRREDAKYR
NQQGAVASRI DKD
