DCDB_METJA
ID DCDB_METJA Reviewed; 204 AA.
AC Q57872;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 153.
DE RecName: Full=dCTP deaminase, dUMP-forming {ECO:0000255|HAMAP-Rule:MF_00146, ECO:0000305};
DE EC=3.5.4.30 {ECO:0000255|HAMAP-Rule:MF_00146, ECO:0000269|PubMed:12538648, ECO:0000269|PubMed:12670946};
DE AltName: Full=Bifunctional dCTP deaminase:dUTPase {ECO:0000255|HAMAP-Rule:MF_00146, ECO:0000305};
DE AltName: Full=DCD-DUT {ECO:0000255|HAMAP-Rule:MF_00146, ECO:0000303|PubMed:12909016};
DE AltName: Full=MjDCD-DUT {ECO:0000303|PubMed:12538648};
GN Name=dcd {ECO:0000255|HAMAP-Rule:MF_00146}; OrderedLocusNames=MJ0430;
OS Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM
OS 10045 / NBRC 100440) (Methanococcus jannaschii).
OC Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC Methanocaldococcaceae; Methanocaldococcus.
OX NCBI_TaxID=243232;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=8688087; DOI=10.1126/science.273.5278.1058;
RA Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G.,
RA Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R.,
RA Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R.,
RA Kirkness E.F., Weinstock K.G., Merrick J.M., Glodek A., Scott J.L.,
RA Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D., Utterback T.R.,
RA Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C., Cotton M.D.,
RA Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M., Klenk H.-P.,
RA Fraser C.M., Smith H.O., Woese C.R., Venter J.C.;
RT "Complete genome sequence of the methanogenic archaeon, Methanococcus
RT jannaschii.";
RL Science 273:1058-1073(1996).
RN [2]
RP PROTEIN SEQUENCE OF 1-10, FUNCTION, CATALYTIC ACTIVITY, AND COFACTOR.
RX PubMed=12670946; DOI=10.1074/jbc.m213010200;
RA Bjoernberg O., Neuhard J., Nyman P.O.;
RT "A bifunctional dCTP deaminase-dUTP nucleotidohydrolase from the
RT hyperthermophilic archaeon Methanocaldococcus jannaschii.";
RL J. Biol. Chem. 278:20667-20672(2003).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ACTIVITY REGULATION,
RP BIOPHYSICOCHEMICAL PROPERTIES, MASS SPECTROMETRY, AND MUTAGENESIS OF
RP ASP-135 AND GLU-145.
RX PubMed=12538648; DOI=10.1074/jbc.m212460200;
RA Li H., Xu H., Graham D.E., White R.H.;
RT "The Methanococcus jannaschii dCTP deaminase is a bifunctional deaminase
RT and diphosphatase.";
RL J. Biol. Chem. 278:11100-11106(2003).
RN [4] {ECO:0007744|PDB:1OGH}
RP X-RAY CRYSTALLOGRAPHY (1.88 ANGSTROMS), AND SUBUNIT.
RX PubMed=12756253; DOI=10.1074/jbc.m304361200;
RA Johansson E., Bjoernberg O., Nyman P.O., Larsen S.;
RT "Structure of the bifunctional dCTP deaminase-dUTPase from
RT Methanocaldococcus jannaschii and its relation to other homotrimeric
RT dUTPases.";
RL J. Biol. Chem. 278:27916-27922(2003).
RN [5] {ECO:0007744|PDB:1PKH, ECO:0007744|PDB:1PKJ, ECO:0007744|PDB:1PKK}
RP X-RAY CRYSTALLOGRAPHY (1.42 ANGSTROMS) OF APOENZYME AND IN COMPLEXES WITH
RP DCTP AND DUTP, AND SUBUNIT.
RX PubMed=12909016; DOI=10.1016/s0022-2836(03)00789-7;
RA Huffman J.L., Li H., White R.H., Tainer J.A.;
RT "Structural basis for recognition and catalysis by the bifunctional dCTP
RT deaminase and dUTPase from Methanococcus jannaschii.";
RL J. Mol. Biol. 331:885-896(2003).
RN [6] {ECO:0007744|PDB:2HXB, ECO:0007744|PDB:2HXD}
RP X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF WILD-TYPE AND OF MUTANT ALA-145
RP IN COMPLEX WITH DUTP.
RA Bynck J.H., Willemoes M., Larsen S., Johansson E.;
RT "Structural evidence for a concerted bifunctionality in dCTP deaminase-
RT dUTPase from Methanocaldococcus jannaschii.";
RL Submitted (AUG-2006) to the PDB data bank.
RN [7] {ECO:0007744|PDB:3GF0}
RP X-RAY CRYSTALLOGRAPHY (2.62 ANGSTROMS).
RA Siggaard J.H.B., Johansson E., Vognsen T., Helt S.S., Harris P., Larsen S.,
RA Willemoes M.;
RT "Pre-steady state kinetic and structural evidence for a concerted
RT biofunctionality in dCTP deaminase-dUTPase from Methanocaldococcus
RT jannaschii.";
RL Submitted (FEB-2009) to the PDB data bank.
CC -!- FUNCTION: Bifunctional enzyme that catalyzes both the deamination of
CC dCTP to dUTP and the hydrolysis of dUTP to dUMP without releasing the
CC toxic dUTP intermediate. It also acts as a dUTP diphosphatase with a
CC lower affinity for dUTP than for dCTP. {ECO:0000269|PubMed:12538648,
CC ECO:0000269|PubMed:12670946}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=dCTP + 2 H2O = diphosphate + dUMP + NH4(+);
CC Xref=Rhea:RHEA:19205, ChEBI:CHEBI:15377, ChEBI:CHEBI:28938,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:61481, ChEBI:CHEBI:246422;
CC EC=3.5.4.30; Evidence={ECO:0000255|HAMAP-Rule:MF_00146,
CC ECO:0000269|PubMed:12538648, ECO:0000269|PubMed:12670946};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:12538648, ECO:0000269|PubMed:12670946};
CC -!- ACTIVITY REGULATION: Inhibited by dTTP. {ECO:0000269|PubMed:12538648}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=17.6 uM for dCTP (at 60 degrees Celsius)
CC {ECO:0000269|PubMed:12538648};
CC KM=263 uM for dUTP (at 60 degrees Celsius)
CC {ECO:0000269|PubMed:12538648};
CC Vmax=14.7 umol/min/mg enzyme with dCTP as substrate (at 60 degrees
CC Celsius) {ECO:0000269|PubMed:12538648};
CC Vmax=23.9 umol/min/mg enzyme with dUTP as substrate (at 60 degrees
CC Celsius) {ECO:0000269|PubMed:12538648};
CC pH dependence:
CC Optimum pH is 7.5. {ECO:0000269|PubMed:12538648};
CC Temperature dependence:
CC Retains over 70% of its activity after heating at 90 degrees Celsius
CC for 10 min. {ECO:0000269|PubMed:12538648};
CC -!- PATHWAY: Pyrimidine metabolism; dUMP biosynthesis; dUMP from dCTP: step
CC 1/1. {ECO:0000255|HAMAP-Rule:MF_00146}.
CC -!- SUBUNIT: Homotrimer (PubMed:12756253, PubMed:12909016). Two trimers
CC assemble into a hexamer by stacking on top of each other
CC (PubMed:12909016). {ECO:0000269|PubMed:12756253,
CC ECO:0000269|PubMed:12909016}.
CC -!- MASS SPECTROMETRY: Mass=23619; Mass_error=94; Method=MALDI;
CC Evidence={ECO:0000269|PubMed:12538648};
CC -!- SIMILARITY: Belongs to the dCTP deaminase family. {ECO:0000255|HAMAP-
CC Rule:MF_00146, ECO:0000305}.
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DR EMBL; L77117; AAB98415.1; -; Genomic_DNA.
DR PIR; F64353; F64353.
DR RefSeq; WP_010869929.1; NC_000909.1.
DR PDB; 1OGH; X-ray; 1.88 A; A/B=1-204.
DR PDB; 1PKH; X-ray; 1.42 A; A/B=1-204.
DR PDB; 1PKJ; X-ray; 2.10 A; A/B=1-204.
DR PDB; 1PKK; X-ray; 1.77 A; A/B=1-204.
DR PDB; 2HXB; X-ray; 2.55 A; A=1-204.
DR PDB; 2HXD; X-ray; 2.30 A; A=1-204.
DR PDB; 3GF0; X-ray; 2.62 A; A=1-204.
DR PDBsum; 1OGH; -.
DR PDBsum; 1PKH; -.
DR PDBsum; 1PKJ; -.
DR PDBsum; 1PKK; -.
DR PDBsum; 2HXB; -.
DR PDBsum; 2HXD; -.
DR PDBsum; 3GF0; -.
DR AlphaFoldDB; Q57872; -.
DR SMR; Q57872; -.
DR STRING; 243232.MJ_0430; -.
DR MoonProt; Q57872; -.
DR EnsemblBacteria; AAB98415; AAB98415; MJ_0430.
DR GeneID; 1451290; -.
DR KEGG; mja:MJ_0430; -.
DR eggNOG; arCOG04048; Archaea.
DR HOGENOM; CLU_087476_2_1_2; -.
DR InParanoid; Q57872; -.
DR OMA; PPIERIN; -.
DR OrthoDB; 91282at2157; -.
DR PhylomeDB; Q57872; -.
DR BioCyc; MetaCyc:MON-17894; -.
DR BRENDA; 3.5.4.13; 3260.
DR BRENDA; 3.5.4.30; 3260.
DR BRENDA; 3.6.1.23; 3260.
DR SABIO-RK; Q57872; -.
DR UniPathway; UPA00610; UER00667.
DR EvolutionaryTrace; Q57872; -.
DR Proteomes; UP000000805; Chromosome.
DR GO; GO:0033973; F:dCTP deaminase (dUMP-forming) activity; IEA:UniProtKB-UniRule.
DR GO; GO:0008829; F:dCTP deaminase activity; IEA:InterPro.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0006226; P:dUMP biosynthetic process; IEA:UniProtKB-UniRule.
DR GO; GO:0006229; P:dUTP biosynthetic process; IEA:InterPro.
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; Magnesium;
KW Nucleotide metabolism; Nucleotide-binding; Reference proteome.
FT CHAIN 1..204
FT /note="dCTP deaminase, dUMP-forming"
FT /id="PRO_0000156029"
FT ACT_SITE 145
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250|UniProtKB:P28248, ECO:0000255|HAMAP-
FT Rule:MF_00146"
FT BINDING 117..122
FT /ligand="dCTP"
FT /ligand_id="ChEBI:CHEBI:61481"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00146"
FT BINDING 128
FT /ligand="dCTP"
FT /ligand_id="ChEBI:CHEBI:61481"
FT /evidence="ECO:0000305|PubMed:12909016"
FT BINDING 132
FT /ligand="dCTP"
FT /ligand_id="ChEBI:CHEBI:61481"
FT /evidence="ECO:0000305|Ref.6"
FT BINDING 135
FT /ligand="dCTP"
FT /ligand_id="ChEBI:CHEBI:61481"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00146,
FT ECO:0000305|Ref.6"
FT BINDING 143..145
FT /ligand="dCTP"
FT /ligand_id="ChEBI:CHEBI:61481"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00146,
FT ECO:0000305|PubMed:12909016, ECO:0000305|Ref.6"
FT BINDING 163
FT /ligand="dCTP"
FT /ligand_id="ChEBI:CHEBI:61481"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00146"
FT BINDING 177
FT /ligand="dCTP"
FT /ligand_id="ChEBI:CHEBI:61481"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00146,
FT ECO:0000305|Ref.6"
FT BINDING 184
FT /ligand="dCTP"
FT /ligand_id="ChEBI:CHEBI:61481"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00146,
FT ECO:0000305|Ref.6"
FT BINDING 188
FT /ligand="dCTP"
FT /ligand_id="ChEBI:CHEBI:61481"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00146,
FT ECO:0000305|Ref.6"
FT SITE 132..133
FT /note="Important for bifunctional activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00146"
FT MUTAGEN 135
FT /note="D->N: Loss of activity."
FT /evidence="ECO:0000269|PubMed:12538648"
FT MUTAGEN 145
FT /note="E->Q: Loss of dCTP deaminase activity, but retains
FT 25% dUTP pyrophosphatase activity."
FT /evidence="ECO:0000269|PubMed:12538648"
FT HELIX 5..13
FT /evidence="ECO:0007829|PDB:1PKH"
FT STRAND 16..21
FT /evidence="ECO:0007829|PDB:1PKH"
FT HELIX 24..26
FT /evidence="ECO:0007829|PDB:1PKH"
FT STRAND 32..36
FT /evidence="ECO:0007829|PDB:1PKH"
FT STRAND 38..43
FT /evidence="ECO:0007829|PDB:1PKH"
FT STRAND 45..47
FT /evidence="ECO:0007829|PDB:1OGH"
FT STRAND 56..60
FT /evidence="ECO:0007829|PDB:1PKH"
FT STRAND 62..68
FT /evidence="ECO:0007829|PDB:1PKH"
FT HELIX 76..86
FT /evidence="ECO:0007829|PDB:1PKH"
FT STRAND 89..94
FT /evidence="ECO:0007829|PDB:1PKH"
FT STRAND 96..105
FT /evidence="ECO:0007829|PDB:1PKH"
FT STRAND 110..116
FT /evidence="ECO:0007829|PDB:1PKH"
FT HELIX 118..121
FT /evidence="ECO:0007829|PDB:1PKH"
FT TURN 122..124
FT /evidence="ECO:0007829|PDB:1PKH"
FT STRAND 125..127
FT /evidence="ECO:0007829|PDB:1PKH"
FT STRAND 139..151
FT /evidence="ECO:0007829|PDB:1PKH"
FT STRAND 153..156
FT /evidence="ECO:0007829|PDB:1PKH"
FT STRAND 160..168
FT /evidence="ECO:0007829|PDB:1PKH"
FT STRAND 176..180
FT /evidence="ECO:0007829|PDB:1PKH"
FT HELIX 196..198
FT /evidence="ECO:0007829|PDB:2HXD"
SQ SEQUENCE 204 AA; 23432 MW; 1218368057723371 CRC64;
MILSDKDIID YVTSKRIIIK PFNKDFVGPC SYDVTLGDEF IIYDDEVYDL SKELNYKRIK
IKNSILVCPL NYNLTEEKIN YFKEKYNVDY VVEGGVLGTT NEYIELPNDI SAQYQGRSSL
GRVFLTSHQT AGWIDAGFKG KITLEIVAFD KPVILYKNQR IGQLIFSKLL SPADVGYSER
KTSKYAYQKS VMPSLIHLDN HKKD
