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Protein

Probable deoxyuridine 5'-triphosphate nucleotidohydrolase YncF

Gene

yncF

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: -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

Keywordsi

Molecular functionHydrolase
Biological processNucleotide metabolism
LigandMagnesium, 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

PTM / Processingi

Molecule processing

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

Proteomic databases

PaxDbiO31801
PRIDEiO31801

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
OMAiDGKSDWI
PhylomeDBiO31801

Family and domain databases

CDDicd07557 trimeric_dUTPase, 1 hit
Gene3Di2.70.40.10, 1 hit
InterProiView protein in InterPro
IPR029054 dUTPase-like
IPR036157 dUTPase-like_sf
IPR033704 dUTPase_trimeric
PfamiView protein in Pfam
PF00692 dUTPase, 1 hit
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
PATRICifig|224308.179.peg.1917

Similar proteinsi

Entry informationi

Entry nameiYNCF_BACSU
AccessioniPrimary (citable) accession number: O31801
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 24, 2009
Last sequence update: January 1, 1998
Last modified: May 23, 2018
This is version 108 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

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