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Protein

Pyrimidine 5'-nucleotidase YjjG

Gene

yjjG

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

Functioni

Nucleotidase that shows high phosphatase activity toward non-canonical pyrimidine nucleotides and three canonical nucleoside 5'-monophosphates (UMP, dUMP, and dTMP), and very low activity against TDP, IMP, UDP, GMP, dGMP, AMP, dAMP, and 6-phosphogluconate. Appears to function as a house-cleaning nucleotidase in vivo, since the general nucleotidase activity of YjjG allows it to protect cells against non-canonical pyrimidine derivatives such as 5-fluoro-2'-deoxyuridine, 5-fluorouridine, 5-fluoroorotate, 5-fluorouracil, and 5-aza-2'-deoxycytidine, and prevents the incorporation of potentially mutagenic nucleotides into DNA. Its dUMP phosphatase activity that catalyzes the hydrolysis of dUMP to deoxyuridine is necessary for thymine utilization via the thymine salvage pathway. Is strictly specific to substrates with 5'-phosphates and shows no activity against nucleoside 2'- or 3'-monophosphates.3 Publications

Catalytic activityi

A 5'-ribonucleotide + H2O = a ribonucleoside + phosphate.2 Publications

Cofactori

Mn2+1 Publication, Mg2+1 Publication, Co2+1 PublicationNote: Divalent metal cation. Highest activity with Mn2+ followed by Mg2+ and Co2+.1 Publication

Enzyme regulationi

In contrast to nucleotidases from other families, is not inhibited by ribo- and deoxyribonucleoside di- and triphosphates.

Kineticsi

The catalytic efficiency is 15-fold higher with 5-fluoro-2'-deoxyuridine monophosphate (5-FdUMP) than with 5'-dUMP as substrate.

  1. KM=0.51 mM for 5'-dTMP (in the presence of Mn2+)2 Publications
  2. KM=2.14 mM for 5'-dTMP (in the presence of 5 mM Mg2+ and 0.5 mM Mn2+)2 Publications
  3. KM=0.66 mM for 5'-UMP (in the presence of Mn2+)2 Publications
  4. KM=0.77 mM for 5'-dUMP (in the presence of Mn2+)2 Publications
  5. KM=0.237 mM for 5-FdUMP (in the presence of 5 mM Mg2+ and 0.5 mM Mn2+)2 Publications
  6. KM=17.8 mM for pNPP (in the presence of Mg2+)2 Publications
  1. Vmax=65.6 µmol/min/mg enzyme with 5'-dTMP as substrate2 Publications
  2. Vmax=73.9 µmol/min/mg enzyme with 5'-UMP as substrate2 Publications
  3. Vmax=46.3 µmol/min/mg enzyme with 5'-dUMP as substrate2 Publications
  4. Vmax=8.86 µmol/min/mg enzyme with pNPP as substrate2 Publications

pH dependencei

Optimum pH is 7.5.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei9 – 91NucleophileBy similarity

GO - Molecular functioni

  • 5'-nucleotidase activity Source: EcoCyc
  • manganese ion binding Source: EcoCyc
  • nucleotide binding Source: UniProtKB-KW
  • phosphatase activity Source: EcoliWiki

GO - Biological processi

  • dephosphorylation Source: GOC
  • pyrimidine nucleobase salvage Source: EcoCyc
  • response to xenobiotic stimulus Source: EcoCyc
  • thymine metabolic process Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Cobalt, Magnesium, Manganese, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG12115-MONOMER.
ECOL316407:JW4336-MONOMER.
MetaCyc:EG12115-MONOMER.
SABIO-RKP0A8Y1.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyrimidine 5'-nucleotidase YjjG (EC:3.1.3.5)
Alternative name(s):
House-cleaning nucleotidase
Non-canonical pyrimidine nucleotide phosphatase
Nucleoside 5'-monophosphate phosphohydrolase
dUMP phosphatase
Gene namesi
Name:yjjG
Ordered Locus Names:b4374, JW4336
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12115. yjjG.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Cells lacking this gene become highly sensitive to toxic non-canonical pyrimidine derivatives such as 5-fluoro-2'-deoxyuridine (5-FdUMP); the growth is completely blocked. Disruption of yjjG in a thyA mutant blocks the utilization of thymine but not that of thymidine for growth.2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 225225Pyrimidine 5'-nucleotidase YjjGPRO_0000066274Add
BLAST

Proteomic databases

PaxDbiP0A8Y1.
PRIDEiP0A8Y1.

Interactioni

Subunit structurei

Monomer, homodimer and possibly homotetramer in solution.1 Publication

Protein-protein interaction databases

BioGridi4262174. 7 interactions.
STRINGi511145.b4374.

Structurei

3D structure databases

ProteinModelPortaliP0A8Y1.
SMRiP0A8Y1. Positions 6-222.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105PAD. Bacteria.
COG1011. LUCA.
HOGENOMiHOG000248345.
InParanoidiP0A8Y1.
KOiK08723.
OMAiPDARIFD.
OrthoDBiEOG6W19QD.
PhylomeDBiP0A8Y1.

Family and domain databases

Gene3Di1.10.150.240. 1 hit.
3.40.50.1000. 1 hit.
InterProiIPR023214. HAD-like_dom.
IPR006439. HAD-SF_hydro_IA.
IPR011951. HAD-SF_hydro_IA_YjjG/YfnB.
IPR023198. PGP_dom2.
[Graphical view]
PfamiPF13419. HAD_2. 1 hit.
[Graphical view]
SUPFAMiSSF56784. SSF56784. 1 hit.
TIGRFAMsiTIGR01549. HAD-SF-IA-v1. 1 hit.
TIGR01509. HAD-SF-IA-v3. 1 hit.
TIGR02254. YjjG/YfnB. 1 hit.

Sequencei

Sequence statusi: Complete.

P0A8Y1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKWDWIFFDA DETLFTFDSF TGLQRMFLDY SVTFTAEDFQ DYQAVNKPLW
60 70 80 90 100
VDYQNGAITS LQLQHGRFES WAERLNVEPG KLNEAFINAM AEICTPLPGA
110 120 130 140 150
VSLLNAIRGN AKIGIITNGF SALQQVRLER TGLRDYFDLL VISEEVGVAK
160 170 180 190 200
PNKKIFDYAL EQAGNPDRSR VLMVGDTAES DILGGINAGL ATCWLNAHHR
210 220
EQPEGIAPTW TVSSLHELEQ LLCKH
Length:225
Mass (Da):25,301
Last modified:June 21, 2005 - v1
Checksum:iD8A52E086567BA71
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti75 – 751L → V (Ref. 2) Curated
Sequence conflicti100 – 1001A → R (Ref. 2) Curated
Sequence conflicti130 – 1301R → G (Ref. 2) Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D17724 Genomic DNA. No translation available.
Z26313 Genomic DNA. No translation available.
U14003 Genomic DNA. Translation: AAA97270.1.
U00096 Genomic DNA. Translation: AAC77327.1.
AP009048 Genomic DNA. Translation: BAE78362.1.
PIRiS56598.
RefSeqiNP_418791.1. NC_000913.3.
WP_000870710.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC77327; AAC77327; b4374.
BAE78362; BAE78362; BAE78362.
GeneIDi948899.
KEGGiecj:JW4336.
eco:b4374.
PATRICi32124358. VBIEscCol129921_4519.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D17724 Genomic DNA. No translation available.
Z26313 Genomic DNA. No translation available.
U14003 Genomic DNA. Translation: AAA97270.1.
U00096 Genomic DNA. Translation: AAC77327.1.
AP009048 Genomic DNA. Translation: BAE78362.1.
PIRiS56598.
RefSeqiNP_418791.1. NC_000913.3.
WP_000870710.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP0A8Y1.
SMRiP0A8Y1. Positions 6-222.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262174. 7 interactions.
STRINGi511145.b4374.

Proteomic databases

PaxDbiP0A8Y1.
PRIDEiP0A8Y1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC77327; AAC77327; b4374.
BAE78362; BAE78362; BAE78362.
GeneIDi948899.
KEGGiecj:JW4336.
eco:b4374.
PATRICi32124358. VBIEscCol129921_4519.

Organism-specific databases

EchoBASEiEB2038.
EcoGeneiEG12115. yjjG.

Phylogenomic databases

eggNOGiENOG4105PAD. Bacteria.
COG1011. LUCA.
HOGENOMiHOG000248345.
InParanoidiP0A8Y1.
KOiK08723.
OMAiPDARIFD.
OrthoDBiEOG6W19QD.
PhylomeDBiP0A8Y1.

Enzyme and pathway databases

BioCyciEcoCyc:EG12115-MONOMER.
ECOL316407:JW4336-MONOMER.
MetaCyc:EG12115-MONOMER.
SABIO-RKP0A8Y1.

Miscellaneous databases

PROiP0A8Y1.

Family and domain databases

Gene3Di1.10.150.240. 1 hit.
3.40.50.1000. 1 hit.
InterProiIPR023214. HAD-like_dom.
IPR006439. HAD-SF_hydro_IA.
IPR011951. HAD-SF_hydro_IA_YjjG/YfnB.
IPR023198. PGP_dom2.
[Graphical view]
PfamiPF13419. HAD_2. 1 hit.
[Graphical view]
SUPFAMiSSF56784. SSF56784. 1 hit.
TIGRFAMsiTIGR01549. HAD-SF-IA-v1. 1 hit.
TIGR01509. HAD-SF-IA-v3. 1 hit.
TIGR02254. YjjG/YfnB. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Mikuni O., Ito K., Matsumura K., Mofatt J., Nobukuni T., McCaughan K., Tate W., Nakamura Y.
    Submitted (SEP-1993) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  2. Grentzmann G., Brechemier-Baey D., Heurgue V., Mora L., Buckingham R.H.
    Submitted (SEP-1993) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. "Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes."
    Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.
    Nucleic Acids Res. 23:2105-2119(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  5. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  6. Rudd K.E.
    Unpublished observations (DEC-1993)
    Cited for: IDENTIFICATION.
  7. "General enzymatic screens identify three new nucleotidases in Escherichia coli. Biochemical characterization of SurE, YfbR, and YjjG."
    Proudfoot M., Kuznetsova E., Brown G., Rao N.N., Kitagawa M., Mori H., Savchenko A., Yakunin A.F.
    J. Biol. Chem. 279:54687-54694(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, CHARACTERIZATION, COFACTOR, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES.
  8. "The Escherichia coli protein YjjG is a house-cleaning nucleotidase in vivo."
    Titz B., Hauser R., Engelbrecher A., Uetz P.
    FEMS Microbiol. Lett. 270:49-57(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, KINETIC PARAMETERS, DISRUPTION PHENOTYPE.
    Strain: K12 / BW25113.
  9. "YjjG, a dUMP phosphatase, is critical for thymine utilization by Escherichia coli K-12."
    Weiss B.
    J. Bacteriol. 189:2186-2189(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE.
    Strain: K12.

Entry informationi

Entry nameiYJJG_ECOLI
AccessioniPrimary (citable) accession number: P0A8Y1
Secondary accession number(s): P33999, P76818, Q2M5U4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 21, 2005
Last sequence update: June 21, 2005
Last modified: January 20, 2016
This is version 89 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

Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. 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.