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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)LengthDescriptionGraphical viewFeature identifierActions
Sitei18 – 181Appears to be important in orienting the phosphate for catalysis
Metal bindingi33 – 331Cobalt; via tele nitrogen
Binding sitei33 – 331Substrate
Metal bindingi68 – 681Cobalt; via tele nitrogen
Metal bindingi69 – 691Cobalt
Binding sitei69 – 691Substrate
Metal bindingi137 – 1371Cobalt
Binding sitei137 – 1371Substrate

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
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)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi18 – 181R → A: Shows negligible enzymatic activity. 1 Publication
Mutagenesisi30 – 301V → A: Shows reduced activity and affinity compared to the wild-type. 1 Publication
Mutagenesisi33 – 331H → A: Shows negligible enzymatic activity. 1 Publication
Mutagenesisi68 – 681H → A: Shows negligible enzymatic activity. 1 Publication
Mutagenesisi69 – 691D → A: Shows negligible enzymatic activity. 1 Publication
Mutagenesisi72 – 721E → A: Shows negligible enzymatic activity. 1 Publication
Mutagenesisi72 – 721E → V: Shows wild-type activity and substrate affinity. 1 Publication
Mutagenesisi77 – 771D → A: Shows negligible enzymatic activity. 1 Publication
Mutagenesisi122 – 1221E → A: Shows reduced activity and affinity compared to the wild-type. 1 Publication
Mutagenesisi137 – 1371D → A: Shows negligible enzymatic activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 1991995'-deoxynucleotidase YfbRPRO_0000095049Add
BLAST

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 interactions.
DIPiDIP-28107N.
IntActiP76491. 2 interactions.
STRINGi511145.b2291.

Structurei

Secondary structure

1
199
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi6 – 105Combined sources
Helixi11 – 155Combined sources
Helixi30 – 5122Combined sources
Helixi58 – 6710Combined sources
Turni68 – 714Combined sources
Helixi72 – 754Combined sources
Helixi93 – 10513Combined sources
Helixi110 – 1123Combined sources
Helixi113 – 1208Combined sources
Turni121 – 1233Combined sources
Helixi127 – 15024Combined sources
Helixi154 – 1563Combined sources
Helixi157 – 16913Combined sources
Helixi173 – 18210Combined sources
Helixi184 – 1863Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2PAQX-ray2.10A/B1-199[»]
2PARX-ray2.10A/B1-199[»]
2PAUX-ray2.10A/B1-199[»]
ProteinModelPortaliP76491.
SMRiP76491. Positions 2-187.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP76491.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini31 – 139109HDUniRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni18 – 192Substrate binding
Regioni77 – 804Substrate binding

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
EntryMethodResolution (Å)ChainPositionsPDBsum
2PAQX-ray2.10A/B1-199[»]
2PARX-ray2.10A/B1-199[»]
2PAUX-ray2.10A/B1-199[»]
ProteinModelPortaliP76491.
SMRiP76491. Positions 2-187.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262969. 19 interactions.
DIPiDIP-28107N.
IntActiP76491. 2 interactions.
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: September 7, 2016
This is version 128 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.