DUT_DICDI
ID DUT_DICDI Reviewed; 179 AA.
AC Q54BW5;
DT 08-APR-2008, integrated into UniProtKB/Swiss-Prot.
DT 24-MAY-2005, sequence version 1.
DT 03-AUG-2022, entry version 109.
DE RecName: Full=Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial {ECO:0000303|PubMed:31910901};
DE Short=dUTPase {ECO:0000303|PubMed:31910901};
DE EC=3.6.1.23 {ECO:0000269|PubMed:31910901};
DE AltName: Full=dUTP pyrophosphatase {ECO:0000305};
DE Flags: Precursor;
GN Name=dut; ORFNames=DDB_G0293374;
OS Dictyostelium discoideum (Slime mold).
OC Eukaryota; Amoebozoa; Evosea; Eumycetozoa; Dictyostelia; Dictyosteliales;
OC Dictyosteliaceae; Dictyostelium.
OX NCBI_TaxID=44689;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AX4;
RX PubMed=15875012; DOI=10.1038/nature03481;
RA Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R.,
RA Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B.,
RA Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T.,
RA Lehmann R., Hamlin N., Davies R., Gaudet P., Fey P., Pilcher K., Chen G.,
RA Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N.,
RA Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E.,
RA Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N.,
RA Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D.,
RA Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T.,
RA Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D.,
RA Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A.,
RA Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M.,
RA Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A.,
RA Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y.,
RA Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C.,
RA Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R.,
RA Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.;
RT "The genome of the social amoeba Dictyostelium discoideum.";
RL Nature 435:43-57(2005).
RN [2] {ECO:0007744|PDB:5F9K}
RP X-RAY CRYSTALLOGRAPHY (2.18 ANGSTROMS) OF 38-179 IN COMPLEX WITH SUBSTRATE
RP ANALOG DUP, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL
RP PROPERTIES, PATHWAY, SUBUNIT, SUBCELLULAR LOCATION, AND CLEAVAGE OF TRANSIT
RP PEPTIDE AFTER GLY-41.
RX PubMed=31910901; DOI=10.1186/s13104-019-4879-7;
RA Chia C.P., Inoguchi N., Varon K.C., Bartholomai B.M., Moriyama H.;
RT "Mitochondrial localization of Dictyostelium discoideum dUTPase mediated by
RT its N-terminus.";
RL BMC Res. Notes 13:16-16(2020).
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:31910901}.
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:31910901};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:31910901};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.5 uM for dUTP {ECO:0000269|PubMed:31910901};
CC Note=kcat is 9.3 sec(-1) with dUTP as substrate.
CC {ECO:0000269|PubMed:31910901};
CC pH dependence:
CC Optimum pH is 8. {ECO:0000269|PubMed:31910901};
CC Temperature dependence:
CC Optimum temperature is 60 degrees Celsius.
CC {ECO:0000269|PubMed:31910901};
CC -!- PATHWAY: Pyrimidine metabolism; dUMP biosynthesis; dUMP from dCTP (dUTP
CC route): step 2/2. {ECO:0000269|PubMed:31910901}.
CC -!- SUBUNIT: Homotrimer. {ECO:0000269|PubMed:31910901}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:31910901}.
CC -!- SIMILARITY: Belongs to the dUTPase family. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AAFI02000204; EAL60754.1; -; Genomic_DNA.
DR RefSeq; XP_629169.1; XM_629167.1.
DR PDB; 5F9K; X-ray; 2.18 A; A/B/C=38-179.
DR PDBsum; 5F9K; -.
DR AlphaFoldDB; Q54BW5; -.
DR SMR; Q54BW5; -.
DR STRING; 44689.DDB0230111; -.
DR PaxDb; Q54BW5; -.
DR EnsemblProtists; EAL60754; EAL60754; DDB_G0293374.
DR GeneID; 8629190; -.
DR KEGG; ddi:DDB_G0293374; -.
DR dictyBase; DDB_G0293374; dut.
DR eggNOG; KOG3370; Eukaryota.
DR HOGENOM; CLU_068508_2_1_1; -.
DR InParanoid; Q54BW5; -.
DR OMA; YAAFVHP; -.
DR PhylomeDB; Q54BW5; -.
DR Reactome; R-DDI-499943; Interconversion of nucleotide di- and triphosphates.
DR UniPathway; UPA00610; UER00666.
DR PRO; PR:Q54BW5; -.
DR Proteomes; UP000002195; Chromosome 6.
DR GO; GO:0005739; C:mitochondrion; IDA:dictyBase.
DR GO; GO:0004170; F:dUTP diphosphatase activity; IDA:dictyBase.
DR GO; GO:0000287; F:magnesium ion binding; IDA:dictyBase.
DR GO; GO:0006226; P:dUMP biosynthetic process; IBA:GO_Central.
DR GO; GO:0046081; P:dUTP catabolic process; IBA:GO_Central.
DR GO; GO:0009213; P:pyrimidine deoxyribonucleoside triphosphate catabolic process; ISS:dictyBase.
DR CDD; cd07557; trimeric_dUTPase; 1.
DR DisProt; DP02689; -.
DR Gene3D; 2.70.40.10; -; 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; Hydrolase; Magnesium; Metal-binding; Mitochondrion;
KW Nucleotide metabolism; Reference proteome; Transit peptide.
FT TRANSIT 1..41
FT /note="Mitochondrion"
FT /evidence="ECO:0000269|PubMed:31910901"
FT CHAIN 42..179
FT /note="Deoxyuridine 5'-triphosphate nucleotidohydrolase,
FT mitochondrial"
FT /id="PRO_0000327582"
FT BINDING 97..99
FT /ligand="dUTP"
FT /ligand_id="ChEBI:CHEBI:61555"
FT /evidence="ECO:0000305|PubMed:31910901,
FT ECO:0007744|PDB:5F9K"
FT BINDING 111..114
FT /ligand="dUTP"
FT /ligand_id="ChEBI:CHEBI:61555"
FT /evidence="ECO:0000305|PubMed:31910901,
FT ECO:0007744|PDB:5F9K"
FT BINDING 122
FT /ligand="dUTP"
FT /ligand_id="ChEBI:CHEBI:61555"
FT /evidence="ECO:0000305|PubMed:31910901,
FT ECO:0007744|PDB:5F9K"
FT BINDING 165
FT /ligand="dUTP"
FT /ligand_id="ChEBI:CHEBI:61555"
FT /evidence="ECO:0000250|UniProtKB:P33316"
FT BINDING 170..171
FT /ligand="dUTP"
FT /ligand_id="ChEBI:CHEBI:61555"
FT /evidence="ECO:0000250|UniProtKB:P33316"
FT STRAND 38..44
FT /evidence="ECO:0007829|PDB:5F9K"
FT STRAND 51..54
FT /evidence="ECO:0007829|PDB:5F9K"
FT STRAND 58..63
FT /evidence="ECO:0007829|PDB:5F9K"
FT STRAND 68..70
FT /evidence="ECO:0007829|PDB:5F9K"
FT STRAND 74..79
FT /evidence="ECO:0007829|PDB:5F9K"
FT STRAND 82..84
FT /evidence="ECO:0007829|PDB:5F9K"
FT STRAND 90..95
FT /evidence="ECO:0007829|PDB:5F9K"
FT HELIX 98..104
FT /evidence="ECO:0007829|PDB:5F9K"
FT STRAND 106..110
FT /evidence="ECO:0007829|PDB:5F9K"
FT STRAND 122..127
FT /evidence="ECO:0007829|PDB:5F9K"
FT STRAND 129..131
FT /evidence="ECO:0007829|PDB:5F9K"
FT STRAND 133..135
FT /evidence="ECO:0007829|PDB:5F9K"
FT STRAND 140..150
FT /evidence="ECO:0007829|PDB:5F9K"
SQ SEQUENCE 179 AA; 19532 MW; 46187E1F460A533F CRC64;
MPIEQKYFSL FSNLFKRLTT NNNNNNYLKM APPNFETFKV KKLSDKAIIP QRGSKGAAGY
DLSSAHELVV PAHGKALAMT DLQIAIPDGT YGRIAPRSGL AWKNFIDCGA GVIDSDYRGN
VGVVLFNHSD VDFKVAVGDR VAQLIFERIV TPEPLEVDEI DETQRGAGGF GSTGVKVQN
