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Protein

Probable deoxyuridine 5'-triphosphate nucleotidohydrolase YncF

Gene

yncF

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 3 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 so that uracil cannot be incorporated into DNA.By similarity

Catalytic activityi

dUTP + H2O = dUMP + diphosphate.

Cofactori

Mg2+By similarity

Pathwayi: 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. SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS (yosS), Probable deoxyuridine 5'-triphosphate nucleotidohydrolase YncF (yncF)
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)DescriptionActionsGraphical viewLength
Binding sitei76SubstrateBy similarity1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Nucleotide metabolism

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciBSUB:BSU17660-MONOMER.
UniPathwayiUPA00610; UER00666.

Names & Taxonomyi

Protein namesi
Recommended name:
Probable deoxyuridine 5'-triphosphate nucleotidohydrolase YncF (EC:3.6.1.23)
Short name:
dUTPase
Alternative name(s):
dUTP pyrophosphatase
Gene namesi
Name:yncF
Ordered Locus Names:BSU17660
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003890011 – 144Probable deoxyuridine 5'-triphosphate nucleotidohydrolase YncFAdd BLAST144

Proteomic databases

PaxDbiO31801.

Interactioni

Subunit structurei

Homotrimer.By similarity

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100009716.

Structurei

Secondary structure

1144
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 11Combined sources9
Beta strandi24 – 29Combined sources6
Beta strandi34 – 36Combined sources3
Beta strandi41 – 45Combined sources5
Beta strandi48 – 51Combined sources4
Beta strandi56 – 62Combined sources7
Helixi66 – 70Combined sources5
Beta strandi72 – 74Combined sources3
Beta strandi77 – 81Combined sources5
Beta strandi93 – 100Combined sources8
Beta strandi102 – 104Combined sources3
Beta strandi109 – 117Combined sources9
Beta strandi122 – 126Combined sources5
Turni138 – 141Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2XCDX-ray1.84A/B/C/D/E/F1-144[»]
2XCEX-ray1.85A/B/C/D/E/F1-144[»]
4AOOX-ray2.30A/B/C/D1-144[»]
4AOZX-ray2.05A/B/C1-144[»]
4APZX-ray2.011/2/3/4/5/6/7/8/9/A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U/V/W/X/Y/Z/a/b/c/d/e/f/g/h/i/j/k/l/m1-144[»]
4B0HX-ray1.18A/B/C1-144[»]
ProteinModelPortaliO31801.
SMRiO31801.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO31801.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni63 – 65Substrate bindingBy similarity3
Regioni80 – 82Substrate bindingBy similarity3

Sequence similaritiesi

Belongs to the dUTPase family.Curated

Phylogenomic databases

eggNOGiENOG4107YUK. Bacteria.
COG0756. LUCA.
HOGENOMiHOG000028966.
InParanoidiO31801.
KOiK01520.
OMAiGKSDWID.
PhylomeDBiO31801.

Family and domain databases

CDDicd07557. trimeric_dUTPase. 1 hit.
Gene3Di2.70.40.10. 1 hit.
InterProiIPR029054. dUTPase-like.
IPR008180. dUTPase/dCTP_deaminase.
IPR033704. dUTPase_trimeric.
[Graphical view]
PfamiPF00692. dUTPase. 1 hit.
[Graphical view]
SUPFAMiSSF51283. SSF51283. 1 hit.

Sequencei

Sequence statusi: Complete.

O31801-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTMQIKIKYL DETQTRISKI EQGDWIDLRA AEDVTIKKDE FKLVPLGVAM
60 70 80 90 100
ELPEGYEAHV VPRSSTYKNF GVIQTNSMGV IDESYKGDND FWFFPAYALR
110 120 130 140
DTEIKKGDRI CQFRIMKKMP AVELVEVEHL GNEDRGGLGS TGTK
Length:144
Mass (Da):16,410
Last modified:January 1, 1998 - v1
Checksum:i2E15AE84170ED23B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL009126 Genomic DNA. Translation: CAB13650.1.
PIRiH69888.
RefSeqiNP_389649.1. NC_000964.3.
WP_003245820.1. NZ_JNCM01000035.1.

Genome annotation databases

EnsemblBacteriaiCAB13650; CAB13650; BSU17660.
GeneIDi939541.
KEGGibsu:BSU17660.
PATRICi18975351. VBIBacSub10457_1867.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL009126 Genomic DNA. Translation: CAB13650.1.
PIRiH69888.
RefSeqiNP_389649.1. NC_000964.3.
WP_003245820.1. NZ_JNCM01000035.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2XCDX-ray1.84A/B/C/D/E/F1-144[»]
2XCEX-ray1.85A/B/C/D/E/F1-144[»]
4AOOX-ray2.30A/B/C/D1-144[»]
4AOZX-ray2.05A/B/C1-144[»]
4APZX-ray2.011/2/3/4/5/6/7/8/9/A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U/V/W/X/Y/Z/a/b/c/d/e/f/g/h/i/j/k/l/m1-144[»]
4B0HX-ray1.18A/B/C1-144[»]
ProteinModelPortaliO31801.
SMRiO31801.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100009716.

Proteomic databases

PaxDbiO31801.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB13650; CAB13650; BSU17660.
GeneIDi939541.
KEGGibsu:BSU17660.
PATRICi18975351. VBIBacSub10457_1867.

Phylogenomic databases

eggNOGiENOG4107YUK. Bacteria.
COG0756. LUCA.
HOGENOMiHOG000028966.
InParanoidiO31801.
KOiK01520.
OMAiGKSDWID.
PhylomeDBiO31801.

Enzyme and pathway databases

UniPathwayiUPA00610; UER00666.
BioCyciBSUB:BSU17660-MONOMER.

Miscellaneous databases

EvolutionaryTraceiO31801.

Family and domain databases

CDDicd07557. trimeric_dUTPase. 1 hit.
Gene3Di2.70.40.10. 1 hit.
InterProiIPR029054. dUTPase-like.
IPR008180. dUTPase/dCTP_deaminase.
IPR033704. dUTPase_trimeric.
[Graphical view]
PfamiPF00692. dUTPase. 1 hit.
[Graphical view]
SUPFAMiSSF51283. SSF51283. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiYNCF_BACSU
AccessioniPrimary (citable) accession number: O31801
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 24, 2009
Last sequence update: January 1, 1998
Last modified: November 2, 2016
This is version 99 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  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

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 one 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.