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Protein

5'-deoxynucleotidase YfbR

Gene

yfbR

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Essential component of the deoxycytidine triphosphate (dCTP) pathway for de novo synthesis of thymidylate. Catalyzes the strictly specific dephosphorylation of 2'-deoxyribonucleoside 5'-monophosphates (dAMP, dGMP, dTMP, dUMP, dIMP and dCMP) and does not dephosphorylate 5'-ribonucleotides or ribonucleoside 3'-monophosphates.3 Publications

Catalytic activityi

A 2'-deoxyribonucleoside 5'-monophosphate + H2O = a 2'-deoxyribonucleoside + phosphate.UniRule annotation2 Publications

Cofactori

Co2+1 Publication, Mn2+1 Publication, Cu2+1 PublicationNote: A divalent metal cation. Highest activity with Co2+, followed by Mn2+ and Cu2+.1 Publication

Enzyme regulationi

Inhibited by both ribo- and deoxyribonucleoside di- and triphosphates.1 Publication

Kineticsi

  1. KM=0.012 mM for 5'-dAMP2 Publications
  2. KM=0.047 mM for 5'-dGMP2 Publications
  3. KM=0.008 mM for 5'-dTMP2 Publications
  4. KM=0.020 mM for 5'-dUMP2 Publications
  5. KM=0.017 mM for 5'-dIMP2 Publications
  6. KM=0.036 mM for 5'-dCMP2 Publications
  7. KM=2.09 mM for pNPP2 Publications
  1. Vmax=0.71 µmol/min/mg enzyme with 5'-dAMP as substrate2 Publications
  2. Vmax=0.46 µmol/min/mg enzyme with 5'-dGMP as substrate2 Publications
  3. Vmax=0.37 µmol/min/mg enzyme with 5'-dTMP as substrate2 Publications
  4. Vmax=0.54 µmol/min/mg enzyme with 5'-dUMP as substrate2 Publications
  5. Vmax=0.56 µmol/min/mg enzyme with 5'-dIMP as substrate2 Publications
  6. Vmax=0.53 µmol/min/mg enzyme with 5'-dCMP as substrate2 Publications
  7. Vmax=1.32 µmol/min/mg enzyme with pNPP as substrate2 Publications

pH dependencei

Optimum pH is 8.0.2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei18Appears to be important in orienting the phosphate for catalysis1
Metal bindingi33Cobalt; via tele nitrogen1
Binding sitei33Substrate1
Metal bindingi68Cobalt; via tele nitrogen1
Metal bindingi69Cobalt1
Binding sitei69Substrate1
Metal bindingi137Cobalt1
Binding sitei137Substrate1

GO - Molecular functioni

  • cobalt ion binding Source: EcoCyc
  • identical protein binding Source: EcoCyc
  • nucleotidase activity Source: EcoCyc
  • nucleotide binding Source: UniProtKB-KW

GO - Biological processi

  • dUMP biosynthetic process Source: EcoCyc
  • pyrimidine deoxyribonucleotide salvage Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Cobalt, Copper, Manganese, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:G7185-MONOMER.
ECOL316407:JW2288-MONOMER.
MetaCyc:G7185-MONOMER.
BRENDAi3.1.3.5. 2026.
3.1.3.89. 2026.
SABIO-RKP76491.

Names & Taxonomyi

Protein namesi
Recommended name:
5'-deoxynucleotidase YfbRUniRule annotation (EC:3.1.3.89UniRule annotation)
Alternative name(s):
5'-deoxyribonucleotidaseUniRule annotation
Nucleoside 5'-monophosphate phosphohydrolaseUniRule annotation
Gene namesi
Name:yfbRUniRule annotation
Ordered Locus Names:b2291, JW2288
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG14102. yfbR.

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi18R → A: Shows negligible enzymatic activity. 1 Publication1
Mutagenesisi30V → A: Shows reduced activity and affinity compared to the wild-type. 1 Publication1
Mutagenesisi33H → A: Shows negligible enzymatic activity. 1 Publication1
Mutagenesisi68H → A: Shows negligible enzymatic activity. 1 Publication1
Mutagenesisi69D → A: Shows negligible enzymatic activity. 1 Publication1
Mutagenesisi72E → A: Shows negligible enzymatic activity. 1 Publication1
Mutagenesisi72E → V: Shows wild-type activity and substrate affinity. 1 Publication1
Mutagenesisi77D → A: Shows negligible enzymatic activity. 1 Publication1
Mutagenesisi122E → A: Shows reduced activity and affinity compared to the wild-type. 1 Publication1
Mutagenesisi137D → A: Shows negligible enzymatic activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000950491 – 1995'-deoxynucleotidase YfbRAdd BLAST199

Proteomic databases

PaxDbiP76491.
PRIDEiP76491.

Interactioni

Subunit structurei

Homodimer.UniRule annotation2 Publications

GO - Molecular functioni

  • identical protein binding Source: EcoCyc

Protein-protein interaction databases

BioGridi4262969. 19 interactors.
DIPiDIP-28107N.
IntActiP76491. 2 interactors.
STRINGi511145.b2291.

Structurei

Secondary structure

1199
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi6 – 10Combined sources5
Helixi11 – 15Combined sources5
Helixi30 – 51Combined sources22
Helixi58 – 67Combined sources10
Turni68 – 71Combined sources4
Helixi72 – 75Combined sources4
Helixi93 – 105Combined sources13
Helixi110 – 112Combined sources3
Helixi113 – 120Combined sources8
Turni121 – 123Combined sources3
Helixi127 – 150Combined sources24
Helixi154 – 156Combined sources3
Helixi157 – 169Combined sources13
Helixi173 – 182Combined sources10
Helixi184 – 186Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2PAQX-ray2.10A/B1-199[»]
2PARX-ray2.10A/B1-199[»]
2PAUX-ray2.10A/B1-199[»]
ProteinModelPortaliP76491.
SMRiP76491.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP76491.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini31 – 139HDUniRule annotationAdd BLAST109

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni18 – 19Substrate binding2
Regioni77 – 80Substrate binding4

Sequence similaritiesi

Belongs to the 5DNU family.UniRule annotation
Contains 1 HD domain.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105DK2. Bacteria.
COG1896. LUCA.
HOGENOMiHOG000276964.
InParanoidiP76491.
KOiK08722.
OMAiMPTPIKY.
PhylomeDBiP76491.

Family and domain databases

Gene3Di1.10.3210.10. 1 hit.
HAMAPiMF_01100. 5DNU. 1 hit.
InterProiIPR003607. HD/PDEase_dom.
IPR006674. HD_domain.
IPR022971. YfbR.
[Graphical view]
PfamiPF13023. HD_3. 1 hit.
[Graphical view]
SMARTiSM00471. HDc. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P76491-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKQSHFFAHL SRLKLINRWP LMRNVRTENV SEHSLQVAMV AHALAAIKNR
60 70 80 90 100
KFGGNVNAER IALLAMYHDA SEVLTGDLPT PVKYFNSQIA QEYKAIEKIA
110 120 130 140 150
QQKLVDMVPE ELRDIFAPLI DEHAYSDEEK SLVKQADALC AYLKCLEELA
160 170 180 190
AGNNEFLLAK TRLEATLEAR RSQEMDYFME IFVPSFHLSL DEISQDSPL
Length:199
Mass (Da):22,708
Last modified:February 1, 1997 - v1
Checksum:i895E9A06130DA057
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC75351.1.
AP009048 Genomic DNA. Translation: BAE76684.1.
PIRiA65001.
RefSeqiNP_416794.1. NC_000913.3.
WP_000813859.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75351; AAC75351; b2291.
BAE76684; BAE76684; BAE76684.
GeneIDi946771.
KEGGiecj:JW2288.
eco:b2291.
PATRICi32119951. VBIEscCol129921_2385.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC75351.1.
AP009048 Genomic DNA. Translation: BAE76684.1.
PIRiA65001.
RefSeqiNP_416794.1. NC_000913.3.
WP_000813859.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2PAQX-ray2.10A/B1-199[»]
2PARX-ray2.10A/B1-199[»]
2PAUX-ray2.10A/B1-199[»]
ProteinModelPortaliP76491.
SMRiP76491.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262969. 19 interactors.
DIPiDIP-28107N.
IntActiP76491. 2 interactors.
STRINGi511145.b2291.

Proteomic databases

PaxDbiP76491.
PRIDEiP76491.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75351; AAC75351; b2291.
BAE76684; BAE76684; BAE76684.
GeneIDi946771.
KEGGiecj:JW2288.
eco:b2291.
PATRICi32119951. VBIEscCol129921_2385.

Organism-specific databases

EchoBASEiEB3855.
EcoGeneiEG14102. yfbR.

Phylogenomic databases

eggNOGiENOG4105DK2. Bacteria.
COG1896. LUCA.
HOGENOMiHOG000276964.
InParanoidiP76491.
KOiK08722.
OMAiMPTPIKY.
PhylomeDBiP76491.

Enzyme and pathway databases

BioCyciEcoCyc:G7185-MONOMER.
ECOL316407:JW2288-MONOMER.
MetaCyc:G7185-MONOMER.
BRENDAi3.1.3.5. 2026.
3.1.3.89. 2026.
SABIO-RKP76491.

Miscellaneous databases

EvolutionaryTraceiP76491.
PROiP76491.

Family and domain databases

Gene3Di1.10.3210.10. 1 hit.
HAMAPiMF_01100. 5DNU. 1 hit.
InterProiIPR003607. HD/PDEase_dom.
IPR006674. HD_domain.
IPR022971. YfbR.
[Graphical view]
PfamiPF13023. HD_3. 1 hit.
[Graphical view]
SMARTiSM00471. HDc. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry namei5DNU_ECOLI
AccessioniPrimary (citable) accession number: P76491
Secondary accession number(s): Q2MAM2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 27, 2002
Last sequence update: February 1, 1997
Last modified: November 2, 2016
This is version 129 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. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
  4. Uncharacterized protein families (UPF)
    List of uncharacterized protein family (UPF) entries

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.