P0A8Y1 (YJJG_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 names

Name:	yjjG
Ordered Locus Names:	b4374, JW4336

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	225 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.7 Ref.8 Ref.9
Catalytic activity	A 5'-ribonucleotide + H2O = a ribonucleoside + phosphate. Ref.7 Ref.8
Cofactor	Divalent metal cation. Highest activity with manganese followed by magnesium and cobalt. Ref.7
Enzyme regulation	In contrast to nucleotidases from other families, is not inhibited by ribo- and deoxyribonucleoside di- and triphosphates.
Subunit structure	Monomer, homodimer and possibly homotetramer in solution. Ref.7
Subcellular location	Cytoplasm Potential.
Disruption phenotype	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. Ref.8 Ref.9
Sequence similarities	Belongs to the HAD-like hydrolase superfamily. YjjG family.
Biophysicochemical properties	Kinetic parameters: The catalytic efficiency is 15-fold higher with 5-fluoro-2'-deoxyuridine monophosphate (5-FdUMP) than with 5'-dUMP as substrate. KM=0.51 mM for 5'-dTMP (in the presence of Mn2+) Ref.7 Ref.8 KM=2.14 mM for 5'-dTMP (in the presence of 5 mM Mg2+ and 0.5 mM Mn2+) KM=0.66 mM for 5'-UMP (in the presence of Mn2+) KM=0.77 mM for 5'-dUMP (in the presence of Mn2+) KM=0.237 mM for 5-FdUMP (in the presence of 5 mM Mg2+ and 0.5 mM Mn2+) KM=17.8 mM for pNPP (in the presence of Mg2+) Vmax=65.6 µmol/min/mg enzyme with 5'-dTMP as substrate Vmax=73.9 µmol/min/mg enzyme with 5'-UMP as substrate Vmax=46.3 µmol/min/mg enzyme with 5'-dUMP as substrate Vmax=8.86 µmol/min/mg enzyme with pNPP as substrate pH dependence: Optimum pH is 7.5.

Ontologies

Keywords
Cellular component	Cytoplasm
Ligand	Cobalt Magnesium Manganese Metal-binding Nucleotide-binding
Molecular function	Hydrolase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	pyrimidine nucleobase salvage Inferred from genetic interaction Ref.9. Source: EcoCyc response to xenobiotic stimulus Inferred from mutant phenotype Ref.8. Source: EcoCyc thymine metabolic process Inferred from genetic interaction Ref.9. Source: EcoCyc
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	5'-nucleotidase activity Inferred from direct assay PubMed 16990279. Source: EcoCyc manganese ion binding Inferred from direct assay PubMed 16990279. Source: EcoCyc nucleotide binding Inferred from electronic annotation. Source: UniProtKB-KW phosphoglycolate phosphatase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 225	225	Pyrimidine 5'-nucleotidase YjjG		PRO_0000066274
Sites
	Active site	9	1	Nucleophile By similarity
Experimental info
	Sequence conflict	75	1	L → V Ref.2
	Sequence conflict	100	1	A → R Ref.2
	Sequence conflict	130	1	R → G Ref.2

Sequences

	Sequence		Length	Mass (Da)
	P0A8Y1 [UniParc]. Last modified June 21, 2005. Version 1. Checksum: D8A52E086567BA71	FASTA	225	25,301
	10 20 30 40 50 60 MKWDWIFFDA DETLFTFDSF TGLQRMFLDY SVTFTAEDFQ DYQAVNKPLW VDYQNGAITS 70 80 90 100 110 120 LQLQHGRFES WAERLNVEPG KLNEAFINAM AEICTPLPGA VSLLNAIRGN AKIGIITNGF 130 140 150 160 170 180 SALQQVRLER TGLRDYFDLL VISEEVGVAK PNKKIFDYAL EQAGNPDRSR VLMVGDTAES 190 200 210 220 DILGGINAGL ATCWLNAHHR EQPEGIAPTW TVSSLHELEQ LLCKH

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] 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.

Cross-references

Sequence databases
EMBL GenBank DDBJ	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.
PIR	S56598.
RefSeq	NP_418791.1. NC_000913.2. YP_492503.1. NC_007779.1.
3D structure databases
ProteinModelPortal	P0A8Y1.
SMR	P0A8Y1. Positions 1-222.
ModBase	Search...
Protein-protein interaction databases
STRING	511145.b4374.
Proteomic databases
PaxDb	P0A8Y1.
PRIDE	P0A8Y1.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAC77327; AAC77327; b4374. BAE78362; BAE78362; BAE78362.
GeneID	12933180. 948899.
KEGG	ecj:Y75_p4257. eco:b4374.
PATRIC	32124358. VBIEscCol129921_4519.
Organism-specific databases
EchoBASE	EB2038.
EcoGene	EG12115. yjjG.
Phylogenomic databases
eggNOG	COG1011.
HOGENOM	HOG000248345.
KO	K08723.
OMA	ICAPLPG.
ProtClustDB	PRK09449.
Enzyme and pathway databases
BioCyc	EcoCyc:EG12115-MONOMER. ECOL316407:JW4336-MONOMER. MetaCyc:EG12115-MONOMER.
SABIO-RK	P0A8Y1.
Gene expression databases
Genevestigator	P0A8Y1.
Family and domain databases
Gene3D	1.10.150.240. 1 hit. 3.40.50.1000. 1 hit.
InterPro	IPR023214. HAD-like_dom. IPR006439. HAD-SF_hydro_IA_v1. IPR006402. HAD-SF_hydro_IA_v3. IPR011951. HAD-SF_hydro_IA_YjjG/YfnB. IPR023198. PGP_dom2. [Graphical view]
Pfam	PF00702. Hydrolase. 1 hit. [Graphical view]
SUPFAM	SSF56784. HAD-like_dom. 1 hit.
TIGRFAMs	TIGR01549. HAD-SF-IA-v1. 1 hit. TIGR01509. HAD-SF-IA-v3. 1 hit. TIGR02254. YjjG/YfnB. 1 hit.
ProtoNet	Search...

Entry information

Entry name

YJJG_ECOLI

Accession

Primary (citable) accession number: P0A8Y1
Secondary accession number(s): P33999, P76818, Q2M5U4

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 21, 2005
Last sequence update:	June 21, 2005
Last modified:	May 1, 2013
This is version 71 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program