DUT_ECOLI
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 03-AUG-2022, entry version 194.
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; Proteobacteria; 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>3.0.co;2-e;
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) is important for function;
CC its removal by trypsin decreases kcat about 40-fold with a less than 2-
CC 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=AAC76664.1; 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; AAC76664.1; ALT_INIT; 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 RefSeq; WP_001393518.1; NZ_CP047127.1.
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 SWISS-2DPAGE; P06968; -.
DR jPOST; P06968; -.
DR PaxDb; P06968; -.
DR PRIDE; P06968; -.
DR EnsemblBacteria; AAC76664; AAC76664; b3640.
DR EnsemblBacteria; BAE77652; BAE77652; BAE77652.
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 PhylomeDB; P06968; -.
DR BioCyc; EcoCyc:DUTP-PYROP-MON; -.
DR BioCyc; MetaCyc:DUTP-PYROP-MON; -.
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: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 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 PANTHER; PTHR11241; PTHR11241; 1.
DR Pfam; PF00692; dUTPase; 1.
DR SUPFAM; SSF51283; SSF51283; 1.
DR TIGRFAMs; TIGR00576; dut; 1.
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
