DUT_ARATH
ID DUT_ARATH Reviewed; 166 AA.
AC Q9STG6;
DT 30-NOV-2010, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 135.
DE RecName: Full=Deoxyuridine 5'-triphosphate nucleotidohydrolase;
DE Short=dUTPase;
DE EC=3.6.1.23;
DE AltName: Full=dUTP pyrophosphatase;
DE AltName: Full=dUTP-pyrophosphatase-like 1;
DE Short=AtDUT1;
GN Name=DUT; Synonyms=DUT1; OrderedLocusNames=At3g46940; ORFNames=T6H20.30;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP FUNCTION.
RX PubMed=20227352; DOI=10.1016/j.dnarep.2010.02.009;
RA Siaud N., Dubois E., Massot S., Richaud A., Dray E., Collier J.,
RA Doutriaux M.P.;
RT "The SOS screen in Arabidopsis: a search for functions involved in DNA
RT metabolism.";
RL DNA Repair 9:567-578(2010).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) IN COMPLEX WITH MAGNESIUM, AND
RP SUBUNIT.
RX PubMed=17565183; DOI=10.1107/s1744309107016004;
RA Bajaj M., Moriyama H.;
RT "Purification, crystallization and preliminary crystallographic analysis of
RT deoxyuridine triphosphate nucleotidohydrolase from Arabidopsis thaliana.";
RL Acta Crystallogr. F 63:409-411(2007).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS).
RA Bajaj M., Moriyama H.;
RT "Structure of dutpase from Arabidopsis thaliana.";
RL Submitted (FEB-2009) to the PDB data bank.
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, preventing uracil
CC incorporation into DNA. {ECO:0000269|PubMed:20227352}.
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 -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Note=Binds 1 Mg(2+) per trimer.;
CC -!- PATHWAY: Pyrimidine metabolism; dUMP biosynthesis; dUMP from dCTP (dUTP
CC route): step 2/2.
CC -!- SUBUNIT: Homotrimer. {ECO:0000269|PubMed:17565183}.
CC -!- MISCELLANEOUS: Silencing of DUT leads to high seedling mortality and
CC affects plant growth and flower organ morphology in surviving plants.
CC -!- SIMILARITY: Belongs to the dUTPase family. {ECO:0000305}.
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DR EMBL; AL096859; CAB51171.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE78222.1; -; Genomic_DNA.
DR EMBL; AF370334; AAK44149.1; -; mRNA.
DR EMBL; AY062989; AAL34163.1; -; mRNA.
DR PIR; T12954; T12954.
DR RefSeq; NP_190278.1; NM_114561.4.
DR PDB; 2PC5; X-ray; 2.20 A; A/B/C=1-166.
DR PDB; 4OOP; X-ray; 1.50 A; A/B/C=1-166.
DR PDB; 4OOQ; X-ray; 2.00 A; A/B/C=1-166.
DR PDBsum; 2PC5; -.
DR PDBsum; 4OOP; -.
DR PDBsum; 4OOQ; -.
DR AlphaFoldDB; Q9STG6; -.
DR SMR; Q9STG6; -.
DR BioGRID; 9167; 1.
DR STRING; 3702.AT3G46940.1; -.
DR iPTMnet; Q9STG6; -.
DR PaxDb; Q9STG6; -.
DR PRIDE; Q9STG6; -.
DR EnsemblPlants; AT3G46940.1; AT3G46940.1; AT3G46940.
DR GeneID; 823847; -.
DR Gramene; AT3G46940.1; AT3G46940.1; AT3G46940.
DR KEGG; ath:AT3G46940; -.
DR Araport; AT3G46940; -.
DR TAIR; locus:2102817; AT3G46940.
DR eggNOG; KOG3370; Eukaryota.
DR HOGENOM; CLU_068508_2_1_1; -.
DR PhylomeDB; Q9STG6; -.
DR BioCyc; ARA:AT3G46940-MON; -.
DR BioCyc; MetaCyc:AT3G46940-MON; -.
DR BRENDA; 3.6.1.23; 399.
DR UniPathway; UPA00610; UER00666.
DR EvolutionaryTrace; Q9STG6; -.
DR PRO; PR:Q9STG6; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9STG6; baseline and differential.
DR Genevisible; Q9STG6; AT.
DR GO; GO:0004170; F:dUTP diphosphatase activity; IBA:GO_Central.
DR GO; GO:0042802; F:identical protein binding; IPI:UniProtKB.
DR GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
DR GO; GO:0006281; P:DNA repair; IMP:TAIR.
DR GO; GO:0006226; P:dUMP biosynthetic process; IBA:GO_Central.
DR GO; GO:0046081; P:dUTP catabolic process; IBA:GO_Central.
DR CDD; cd07557; trimeric_dUTPase; 1.
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; Nucleotide metabolism;
KW Reference proteome.
FT CHAIN 1..166
FT /note="Deoxyuridine 5'-triphosphate nucleotidohydrolase"
FT /id="PRO_0000401366"
FT REGION 1..24
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 138
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="ligand shared between trimeric partners"
FT /evidence="ECO:0000269|PubMed:17565183"
FT STRAND 30..35
FT /evidence="ECO:0007829|PDB:4OOP"
FT STRAND 42..45
FT /evidence="ECO:0007829|PDB:4OOP"
FT STRAND 51..54
FT /evidence="ECO:0007829|PDB:4OOP"
FT STRAND 59..61
FT /evidence="ECO:0007829|PDB:4OOP"
FT STRAND 66..70
FT /evidence="ECO:0007829|PDB:4OOP"
FT STRAND 73..76
FT /evidence="ECO:0007829|PDB:4OOP"
FT STRAND 81..86
FT /evidence="ECO:0007829|PDB:4OOP"
FT HELIX 89..95
FT /evidence="ECO:0007829|PDB:4OOP"
FT STRAND 97..100
FT /evidence="ECO:0007829|PDB:4OOP"
FT STRAND 103..105
FT /evidence="ECO:0007829|PDB:2PC5"
FT STRAND 113..118
FT /evidence="ECO:0007829|PDB:4OOP"
FT STRAND 120..122
FT /evidence="ECO:0007829|PDB:4OOP"
FT STRAND 124..126
FT /evidence="ECO:0007829|PDB:4OOP"
FT STRAND 131..141
FT /evidence="ECO:0007829|PDB:4OOP"
FT STRAND 145..147
FT /evidence="ECO:0007829|PDB:4OOP"
SQ SEQUENCE 166 AA; 17557 MW; 5487738DF4A55BFF CRC64;
MACVNEPSPK LQKLDRNGIH GDSSPSPFFK VKKLSEKAVI PTRGSPLSAG YDLSSAVDSK
VPARGKALIP TDLSIAVPEG TYARIAPRSG LAWKHSIDVG AGVIDADYRG PVGVILFNHS
DADFEVKFGD RIAQLIIEKI VTPDVVEVDD LDETVRGDGG FGSTGV
