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Protein

Deoxyuridine 5'-triphosphate nucleotidohydrolase

Gene

DUT

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

This enzyme is involved in nucleotide metabolism: it produces dUMP, the immediate precursor of thymidine nucleotides and it decreases the intracellular concentration of dUTP, preventing uracil incorporation into DNA.1 Publication

Catalytic activityi

dUTP + H2O = dUMP + diphosphate.

Cofactori

Mg2+Note: Binds 1 Mg2+ per trimer.

Pathway: dUMP biosynthesis

This protein is involved in step 2 of the subpathway that synthesizes dUMP from dCTP (dUTP route).
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. no protein annotated in this organism
  2. Deoxyuridine 5'-triphosphate nucleotidohydrolase (DUT)
This subpathway is part of the pathway dUMP biosynthesis, which is itself part of Pyrimidine metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes dUMP from dCTP (dUTP route), the pathway dUMP biosynthesis and in Pyrimidine metabolism.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi138 – 1381Magnesium; shared with trimeric partners1 Publication

GO - Molecular functioni

  • dUTP diphosphatase activity Source: GO_Central
  • identical protein binding Source: UniProtKB
  • magnesium ion binding Source: UniProtKB

GO - Biological processi

  • DNA repair Source: TAIR
  • dUMP biosynthetic process Source: GO_Central
  • dUTP catabolic process Source: GO_Central
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Nucleotide metabolism

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciARA:AT3G46940-MONOMER.
MetaCyc:AT3G46940-MONOMER.
BRENDAi3.6.1.23. 399.
ReactomeiREACT_286672. Pyrimidine biosynthesis.
UniPathwayiUPA00610; UER00666.

Names & Taxonomyi

Protein namesi
Recommended name:
Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC:3.6.1.23)
Short name:
dUTPase
Alternative name(s):
dUTP pyrophosphatase
dUTP-pyrophosphatase-like 1
Short name:
AtDUT1
Gene namesi
Name:DUT
Synonyms:DUT1
Ordered Locus Names:At3g46940
ORF Names:T6H20.30
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548 Componenti: Chromosome 3

Organism-specific databases

TAIRiAT3G46940.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: GO_Central
  • cytosol Source: TAIR
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 166166Deoxyuridine 5'-triphosphate nucleotidohydrolasePRO_0000401366Add
BLAST

Proteomic databases

PaxDbiQ9STG6.
PRIDEiQ9STG6.

Interactioni

Subunit structurei

Homotrimer.1 Publication

Protein-protein interaction databases

STRINGi3702.AT3G46940.1.

Structurei

Secondary structure

1
166
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi30 – 356Combined sources
Beta strandi51 – 544Combined sources
Beta strandi59 – 613Combined sources
Beta strandi66 – 7611Combined sources
Beta strandi81 – 866Combined sources
Helixi89 – 957Combined sources
Beta strandi97 – 1004Combined sources
Beta strandi103 – 1053Combined sources
Beta strandi112 – 1187Combined sources
Beta strandi120 – 1223Combined sources
Beta strandi124 – 1263Combined sources
Beta strandi131 – 14111Combined sources
Beta strandi145 – 1473Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2P9OX-ray2.00A/B/C1-166[»]
2PC5X-ray2.20A/B/C1-166[»]
4OOPX-ray1.50A/B/C1-166[»]
ProteinModelPortaliQ9STG6.
SMRiQ9STG6. Positions 26-153.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9STG6.

Family & Domainsi

Sequence similaritiesi

Belongs to the dUTPase family.Curated

Phylogenomic databases

eggNOGiCOG0756.
HOGENOMiHOG000028966.
KOiK01520.
OMAiQEPPHKI.
PhylomeDBiQ9STG6.

Family and domain databases

Gene3Di2.70.40.10. 1 hit.
InterProiIPR029054. dUTPase-like.
IPR008180. dUTPase/dCTP_deaminase.
IPR008181. dUTPase_1.
[Graphical view]
PfamiPF00692. dUTPase. 1 hit.
[Graphical view]
SUPFAMiSSF51283. SSF51283. 1 hit.
TIGRFAMsiTIGR00576. dut. 1 hit.

Sequencei

Sequence statusi: Complete.

Q9STG6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MACVNEPSPK LQKLDRNGIH GDSSPSPFFK VKKLSEKAVI PTRGSPLSAG
60 70 80 90 100
YDLSSAVDSK VPARGKALIP TDLSIAVPEG TYARIAPRSG LAWKHSIDVG
110 120 130 140 150
AGVIDADYRG PVGVILFNHS DADFEVKFGD RIAQLIIEKI VTPDVVEVDD
160
LDETVRGDGG FGSTGV
Length:166
Mass (Da):17,557
Last modified:May 1, 2000 - v1
Checksum:i5487738DF4A55BFF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL096859 Genomic DNA. Translation: CAB51171.1.
CP002686 Genomic DNA. Translation: AEE78222.1.
AF370334 mRNA. Translation: AAK44149.1.
AY062989 mRNA. Translation: AAL34163.1.
PIRiT12954.
RefSeqiNP_190278.1. NM_114561.3.
UniGeneiAt.48742.
At.71138.

Genome annotation databases

EnsemblPlantsiAT3G46940.1; AT3G46940.1; AT3G46940.
GeneIDi823847.
KEGGiath:AT3G46940.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL096859 Genomic DNA. Translation: CAB51171.1.
CP002686 Genomic DNA. Translation: AEE78222.1.
AF370334 mRNA. Translation: AAK44149.1.
AY062989 mRNA. Translation: AAL34163.1.
PIRiT12954.
RefSeqiNP_190278.1. NM_114561.3.
UniGeneiAt.48742.
At.71138.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2P9OX-ray2.00A/B/C1-166[»]
2PC5X-ray2.20A/B/C1-166[»]
4OOPX-ray1.50A/B/C1-166[»]
ProteinModelPortaliQ9STG6.
SMRiQ9STG6. Positions 26-153.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi3702.AT3G46940.1.

Proteomic databases

PaxDbiQ9STG6.
PRIDEiQ9STG6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT3G46940.1; AT3G46940.1; AT3G46940.
GeneIDi823847.
KEGGiath:AT3G46940.

Organism-specific databases

TAIRiAT3G46940.

Phylogenomic databases

eggNOGiCOG0756.
HOGENOMiHOG000028966.
KOiK01520.
OMAiQEPPHKI.
PhylomeDBiQ9STG6.

Enzyme and pathway databases

UniPathwayiUPA00610; UER00666.
BioCyciARA:AT3G46940-MONOMER.
MetaCyc:AT3G46940-MONOMER.
BRENDAi3.6.1.23. 399.
ReactomeiREACT_286672. Pyrimidine biosynthesis.

Miscellaneous databases

EvolutionaryTraceiQ9STG6.
PROiQ9STG6.

Family and domain databases

Gene3Di2.70.40.10. 1 hit.
InterProiIPR029054. dUTPase-like.
IPR008180. dUTPase/dCTP_deaminase.
IPR008181. dUTPase_1.
[Graphical view]
PfamiPF00692. dUTPase. 1 hit.
[Graphical view]
SUPFAMiSSF51283. SSF51283. 1 hit.
TIGRFAMsiTIGR00576. dut. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana."
    Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B., Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M., Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V., Choisne N., Artiguenave F.
    , Robert C., Brottier P., Wincker P., Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H., Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H., Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A., Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H., Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J., Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B., Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D., de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E., Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G., Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X., Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M., Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B., Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J., Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C., Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y., Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K., Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S.
    Nature 408:820-822(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  2. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  3. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  4. "The SOS screen in Arabidopsis: a search for functions involved in DNA metabolism."
    Siaud N., Dubois E., Massot S., Richaud A., Dray E., Collier J., Doutriaux M.P.
    DNA Repair 9:567-578(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  5. "Purification, crystallization and preliminary crystallographic analysis of deoxyuridine triphosphate nucleotidohydrolase from Arabidopsis thaliana."
    Bajaj M., Moriyama H.
    Acta Crystallogr. F 63:409-411(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) IN COMPLEX WITH MAGNESIUM, SUBUNIT.
  6. "Structure of dutpase from Arabidopsis thaliana."
    Bajaj M., Moriyama H.
    Submitted (FEB-2009) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS).

Entry informationi

Entry nameiDUT_ARATH
AccessioniPrimary (citable) accession number: Q9STG6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 30, 2010
Last sequence update: May 1, 2000
Last modified: June 24, 2015
This is version 97 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

Silencing of DUT leads to high seedling mortality and affects plant growth and flower organ morphology in surviving plants.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.