ID   DUT_ECOLI               Reviewed;         152 AA.
AC   P06968; Q2M7V4;
DT   01-APR-1988, integrated into UniProtKB/Swiss-Prot.
DT   08-MAY-2019, sequence version 2.
DT   27-MAR-2024, entry version 202.
DE   RecName: Full=Deoxyuridine 5'-triphosphate nucleotidohydrolase;
DE            Short=dUTPase;
DE            EC=3.6.1.23 {ECO:0000269|PubMed:9261872};
DE   AltName: Full=dUTP pyrophosphatase;
GN   Name=dut; Synonyms=dnaS, sof; OrderedLocusNames=b3640, JW3615;
OS   Escherichia coli (strain K12).
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC   Enterobacteriaceae; Escherichia.
OX   NCBI_TaxID=83333;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=K12;
RX   PubMed=6139280; DOI=10.1002/j.1460-2075.1983.tb01529.x;
RA   Lundberg L.G., Thoresson H.-O., Karlstroem O.H., Nyman P.O.;
RT   "Nucleotide sequence of the structural gene for dUTPase of Escherichia coli
RT   K-12.";
RL   EMBO J. 2:967-971(1983).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   PubMed=7686882; DOI=10.1006/geno.1993.1230;
RA   Burland V.D., Plunkett G. III, Daniels D.L., Blattner F.R.;
RT   "DNA sequence and analysis of 136 kilobases of the Escherichia coli genome:
RT   organizational symmetry around the origin of replication.";
RL   Genomics 16:551-561(1993).
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]
RP   PROTEIN SEQUENCE OF 1-5, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
RP   PROPERTIES, SUBCELLULAR LOCATION, SUBUNIT, DOMAIN, AND MASS SPECTROMETRY.
RX   PubMed=9261872;
RX   DOI=10.1002/(sici)1097-0134(199708)28:4<568::aid-prot10>3.3.co;2-d;
RA   Vertessy B.G.;
RT   "Flexible glycine rich motif of Escherichia coli deoxyuridine triphosphate
RT   nucleotidohydrolase is important for functional but not for structural
RT   integrity of the enzyme.";
RL   Proteins 28:568-579(1997).
RN   [6]
RP   IDENTIFICATION BY 2D-GEL.
RX   PubMed=9298644; DOI=10.1002/elps.1150180805;
RA   VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.;
RT   "Escherichia coli proteome analysis using the gene-protein database.";
RL   Electrophoresis 18:1243-1251(1997).
RN   [7] {ECO:0007744|PDB:1DUP}
RP   X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS), SUBUNIT, AND SUBCELLULAR LOCATION.
RX   PubMed=1311056; DOI=10.1038/355740a0;
RA   Cedergren-Zeppezauer E.S., Larsson G., Nyman P.O., Dauter Z., Wilson K.S.;
RT   "Crystal structure of a dUTPase.";
RL   Nature 355:740-743(1992).
RN   [8] {ECO:0007744|PDB:1DUD}
RP   X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
RX   PubMed=8646539; DOI=10.1038/nsb0696-532;
RA   Larsson G., Svensson L.A., Nyman P.O.;
RT   "Crystal structure of the Escherichia coli dUTPase in complex with a
RT   substrate analogue (dUDP).";
RL   Nat. Struct. Biol. 3:532-538(1996).
RN   [9]
RP   X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
RX   PubMed=9757088; DOI=10.1107/s0907444997016223;
RA   Dauter Z., Wilson K.S., Larsson G., Nyman P.O., Cedergren-Zeppezauer E.S.;
RT   "The refined structure of dUTPase from Escherichia coli.";
RL   Acta Crystallogr. D 54:735-749(1998).
RN   [10] {ECO:0007744|PDB:1EU5, ECO:0007744|PDB:1EUW}
RP   X-RAY CRYSTALLOGRAPHY (1.05 ANGSTROMS).
RX   PubMed=11375495; DOI=10.1107/s0907444901004255;
RA   Gonzalez A., Larsson G., Persson R., Cedergren-Zeppezauer E.S.;
RT   "Atomic resolution structure of Escherichia coli dUTPase determined ab
RT   initio.";
RL   Acta Crystallogr. D 57:767-774(2001).
RN   [11] {ECO:0007744|PDB:1RN8, ECO:0007744|PDB:1RNJ, ECO:0007744|PDB:1SEH, ECO:0007744|PDB:1SYL}
RP   X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH MAGNESIUM IONS AND
RP   SUBSTRATE, COFACTOR, MUTAGENESIS OF ASP-90, AND SUBUNIT.
RX   PubMed=15208312; DOI=10.1074/jbc.m406135200;
RA   Barabas O., Pongracz V., Kovari J., Wilmanns M., Vertessy B.G.;
RT   "Structural insights into the catalytic mechanism of phosphate ester
RT   hydrolysis by dUTPase.";
RL   J. Biol. Chem. 279:42907-42915(2004).
CC   -!- FUNCTION: This enzyme is involved in nucleotide metabolism: it produces
CC       dUMP, the immediate precursor of thymidine nucleotides and it decreases
CC       the intracellular concentration of dUTP so that uracil cannot be
CC       incorporated into DNA. {ECO:0000269|PubMed:9261872}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=dUTP + H2O = diphosphate + dUMP + H(+); Xref=Rhea:RHEA:10248,
CC         ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:33019,
CC         ChEBI:CHEBI:61555, ChEBI:CHEBI:246422; EC=3.6.1.23;
CC         Evidence={ECO:0000269|PubMed:9261872};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000269|PubMed:15208312};
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Kinetic parameters:
CC         KM=0.28 uM for dUTP {ECO:0000269|PubMed:9261872};
CC         Note=kcat is 5.15 sec(-1). {ECO:0000269|PubMed:9261872};
CC   -!- PATHWAY: Pyrimidine metabolism; dUMP biosynthesis; dUMP from dCTP (dUTP
CC       route): step 2/2.
CC   -!- SUBUNIT: Homotrimer. {ECO:0000269|PubMed:1311056,
CC       ECO:0000269|PubMed:15208312, ECO:0000269|PubMed:9261872}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305|PubMed:1311056,
CC       ECO:0000305|PubMed:9261872}.
CC   -!- DOMAIN: The C-terminal 11 residues (motif 5) are important for
CC       function; its removal by trypsin decreases kcat about 40-fold with a
CC       less than 2-fold increase in KM for dUTP. {ECO:0000269|PubMed:9261872}.
CC   -!- MASS SPECTROMETRY: Mass=16296; Method=Electrospray;
CC       Evidence={ECO:0000269|PubMed:9261872};
CC   -!- SIMILARITY: Belongs to the dUTPase family. {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAA61993.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305|PubMed:9261872};
CC       Sequence=BAE77652.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305|PubMed:9261872};
CC       Sequence=CAA24897.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305|PubMed:9261872};
CC       Sequence=CAA25859.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305|PubMed:9261872};
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DR   EMBL; X01714; CAA25859.1; ALT_INIT; Genomic_DNA.
DR   EMBL; V01578; CAA24897.1; ALT_INIT; Genomic_DNA.
DR   EMBL; L10328; AAA61993.1; ALT_INIT; Genomic_DNA.
DR   EMBL; U00096; AAC76664.2; -; Genomic_DNA.
DR   EMBL; AP009048; BAE77652.1; ALT_INIT; Genomic_DNA.
DR   PIR; A30388; WPECDU.
DR   RefSeq; NP_418097.1; NC_000913.3.
DR   RefSeq; WP_000976073.1; NZ_LN832404.1.
DR   PDB; 1DUD; X-ray; 2.30 A; A=1-152.
DR   PDB; 1DUP; X-ray; 1.90 A; A=1-152.
DR   PDB; 1EU5; X-ray; 1.45 A; A=1-152.
DR   PDB; 1EUW; X-ray; 1.05 A; A=1-152.
DR   PDB; 1RN8; X-ray; 1.93 A; A=1-152.
DR   PDB; 1RNJ; X-ray; 1.70 A; A=1-152.
DR   PDB; 1SEH; X-ray; 1.47 A; A=1-152.
DR   PDB; 1SYL; X-ray; 1.95 A; A=1-152.
DR   PDB; 2HR6; X-ray; 1.84 A; A=1-152.
DR   PDB; 2HRM; X-ray; 1.70 A; A=1-152.
DR   PDB; 6HDE; X-ray; 1.82 A; A/B/C=1-152.
DR   PDBsum; 1DUD; -.
DR   PDBsum; 1DUP; -.
DR   PDBsum; 1EU5; -.
DR   PDBsum; 1EUW; -.
DR   PDBsum; 1RN8; -.
DR   PDBsum; 1RNJ; -.
DR   PDBsum; 1SEH; -.
DR   PDBsum; 1SYL; -.
DR   PDBsum; 2HR6; -.
DR   PDBsum; 2HRM; -.
DR   PDBsum; 6HDE; -.
DR   AlphaFoldDB; P06968; -.
DR   SMR; P06968; -.
DR   BioGRID; 4263424; 510.
DR   IntAct; P06968; 11.
DR   STRING; 511145.b3640; -.
DR   DrugBank; DB01965; 2'-Deoxyuridine 5'-alpha,beta-imido-triphosphate.
DR   DrugBank; DB03800; Deoxyuridine monophosphate.
DR   DrugBank; DB03413; Deoxyuridine-5'-Diphosphate.
DR   DrugBank; DB02333; Deoxyuridine-5'-Triphosphate.
DR   jPOST; P06968; -.
DR   PaxDb; 511145-b3640; -.
DR   EnsemblBacteria; AAC76664; AAC76664; b3640.
DR   GeneID; 948607; -.
DR   KEGG; ecj:JW3615; -.
DR   KEGG; eco:b3640; -.
DR   PATRIC; fig|511145.12.peg.3760; -.
DR   EchoBASE; EB0247; -.
DR   eggNOG; COG0756; Bacteria.
DR   HOGENOM; CLU_068508_1_1_6; -.
DR   InParanoid; P06968; -.
DR   OrthoDB; 9809956at2; -.
DR   PhylomeDB; P06968; -.
DR   BioCyc; EcoCyc:DUTP-PYROP-MONOMER; -.
DR   BioCyc; MetaCyc:DUTP-PYROP-MONOMER; -.
DR   BRENDA; 3.6.1.23; 2026.
DR   UniPathway; UPA00610; UER00666.
DR   EvolutionaryTrace; P06968; -.
DR   PRO; PR:P06968; -.
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:CAFA.
DR   GO; GO:0004170; F:dUTP diphosphatase activity; IDA:CAFA.
DR   GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
DR   GO; GO:0000287; F:magnesium ion binding; IDA:CAFA.
DR   GO; GO:0006226; P:dUMP biosynthetic process; IDA:CAFA.
DR   GO; GO:0046081; P:dUTP catabolic process; IDA:CAFA.
DR   GO; GO:0070207; P:protein homotrimerization; IDA:EcoCyc.
DR   CDD; cd07557; trimeric_dUTPase; 1.
DR   DisProt; DP00337; -.
DR   Gene3D; 2.70.40.10; -; 1.
DR   HAMAP; MF_00116; dUTPase_bact; 1.
DR   InterPro; IPR008181; dUTPase.
DR   InterPro; IPR029054; dUTPase-like.
DR   InterPro; IPR036157; dUTPase-like_sf.
DR   InterPro; IPR033704; dUTPase_trimeric.
DR   NCBIfam; TIGR00576; dut; 1.
DR   PANTHER; PTHR11241; DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE; 1.
DR   PANTHER; PTHR11241:SF0; DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE; 1.
DR   Pfam; PF00692; dUTPase; 1.
DR   SUPFAM; SSF51283; dUTPase-like; 1.
DR   SWISS-2DPAGE; P06968; -.
PE   1: Evidence at protein level;
KW   3D-structure; Cytoplasm; Direct protein sequencing; Hydrolase; Magnesium;
KW   Metal-binding; Nucleotide metabolism; Reference proteome.
FT   CHAIN           1..152
FT                   /note="Deoxyuridine 5'-triphosphate nucleotidohydrolase"
FT                   /id="PRO_0000182858"
FT   MOTIF           142..152
FT                   /note="Motif 5, important for activity"
FT                   /evidence="ECO:0000269|PubMed:9261872"
FT   BINDING         71..73
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         84
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000269|PubMed:15208312"
FT   BINDING         88..90
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000305"
FT   BINDING         98
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000269|PubMed:15208312"
FT   MUTAGEN         90
FT                   /note="D->N: Reduces catalytic activity 40000-fold."
FT                   /evidence="ECO:0000269|PubMed:15208312"
FT   STRAND          6..9
FT                   /evidence="ECO:0007829|PDB:1EUW"
FT   TURN            12..16
FT                   /evidence="ECO:0007829|PDB:1EUW"
FT   STRAND          31..34
FT                   /evidence="ECO:0007829|PDB:1EUW"
FT   STRAND          41..43
FT                   /evidence="ECO:0007829|PDB:1EUW"
FT   STRAND          48..58
FT                   /evidence="ECO:0007829|PDB:1EUW"
FT   STRAND          64..70
FT                   /evidence="ECO:0007829|PDB:1EUW"
FT   HELIX           72..78
FT                   /evidence="ECO:0007829|PDB:1EUW"
FT   STRAND          80..82
FT                   /evidence="ECO:0007829|PDB:1EUW"
FT   STRAND          85..89
FT                   /evidence="ECO:0007829|PDB:1EUW"
FT   STRAND          95..103
FT                   /evidence="ECO:0007829|PDB:1EUW"
FT   STRAND          105..107
FT                   /evidence="ECO:0007829|PDB:1EUW"
FT   STRAND          109..111
FT                   /evidence="ECO:0007829|PDB:1EUW"
FT   STRAND          116..124
FT                   /evidence="ECO:0007829|PDB:1EUW"
FT   STRAND          126..132
FT                   /evidence="ECO:0007829|PDB:6HDE"
FT   TURN            146..149
FT                   /evidence="ECO:0007829|PDB:6HDE"
SQ   SEQUENCE   152 AA;  16287 MW;  C527197DBC392B18 CRC64;
     MMKKIDVKIL DPRVGKEFPL PTYATSGSAG LDLRACLNDA VELAPGDTTL VPTGLAIHIA
     DPSLAAMMLP RSGLGHKHGI VLGNLVGLID SDYQGQLMIS VWNRGQDSFT IQPGERIAQM
     IFVPVVQAEF NLVEDFDATD RGEGGFGHSG RQ
//