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Pyrimidine 5'-nucleotidase YjjG (EC 3.1.3.5) (House-cleaning nucleotidase) (Non-canonical pyrimidine nucleotide phosphatase) (Nucleoside 5'-monophosphate phosphohydrolase) (dUMP phosphatase)

 YJJG_ECOLI              Reviewed;         225 AA.
P0A8Y1; P33999; P76818; Q2M5U4;
21-JUN-2005, integrated into UniProtKB/Swiss-Prot.
21-JUN-2005, sequence version 1.
05-DEC-2018, entry version 103.
RecName: Full=Pyrimidine 5'-nucleotidase YjjG;
EC=3.1.3.5;
AltName: Full=House-cleaning nucleotidase;
AltName: Full=Non-canonical pyrimidine nucleotide phosphatase;
AltName: Full=Nucleoside 5'-monophosphate phosphohydrolase;
AltName: Full=dUMP phosphatase;
Name=yjjG; OrderedLocusNames=b4374, JW4336;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=K12;
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.
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
Grentzmann G., Brechemier-Baey D., Heurgue V., Mora L.,
Buckingham R.H.;
Submitted (SEP-1993) to the EMBL/GenBank/DDBJ databases.
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=7610040; DOI=10.1093/nar/23.12.2105;
Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L.,
Blattner F.R.;
"Analysis of the Escherichia coli genome VI: DNA sequence of the
region from 92.8 through 100 minutes.";
Nucleic Acids Res. 23:2105-2119(1995).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
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.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[6]
IDENTIFICATION.
Rudd K.E.;
Unpublished observations (DEC-1993).
[7]
FUNCTION, CATALYTIC ACTIVITY, CHARACTERIZATION, COFACTOR, SUBUNIT, AND
BIOPHYSICOCHEMICAL PROPERTIES.
PubMed=15489502; DOI=10.1074/jbc.M411023200;
Proudfoot M., Kuznetsova E., Brown G., Rao N.N., Kitagawa M., Mori H.,
Savchenko A., Yakunin A.F.;
"General enzymatic screens identify three new nucleotidases in
Escherichia coli. Biochemical characterization of SurE, YfbR, and
YjjG.";
J. Biol. Chem. 279:54687-54694(2004).
[8]
FUNCTION, CATALYTIC ACTIVITY, KINETIC PARAMETERS, AND DISRUPTION
PHENOTYPE.
STRAIN=K12 / BW25113;
PubMed=17286574; DOI=10.1111/j.1574-6968.2007.00646.x;
Titz B., Hauser R., Engelbrecher A., Uetz P.;
"The Escherichia coli protein YjjG is a house-cleaning nucleotidase in
vivo.";
FEMS Microbiol. Lett. 270:49-57(2007).
[9]
FUNCTION, AND DISRUPTION PHENOTYPE.
STRAIN=K12;
PubMed=17189366; DOI=10.1128/JB.01645-06;
Weiss B.;
"YjjG, a dUMP phosphatase, is critical for thymine utilization by
Escherichia coli K-12.";
J. Bacteriol. 189:2186-2189(2007).
-!- 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. {ECO:0000269|PubMed:15489502,
ECO:0000269|PubMed:17189366, ECO:0000269|PubMed:17286574}.
-!- CATALYTIC ACTIVITY:
Reaction=a ribonucleoside 5'-phosphate + H2O = a ribonucleoside +
phosphate; Xref=Rhea:RHEA:12484, ChEBI:CHEBI:15377,
ChEBI:CHEBI:18254, ChEBI:CHEBI:43474, ChEBI:CHEBI:58043;
EC=3.1.3.5; Evidence={ECO:0000269|PubMed:15489502,
ECO:0000269|PubMed:17286574};
-!- COFACTOR:
Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
Evidence={ECO:0000269|PubMed:15489502};
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000269|PubMed:15489502};
Name=Co(2+); Xref=ChEBI:CHEBI:48828;
Evidence={ECO:0000269|PubMed:15489502};
Note=Divalent metal cation. Highest activity with Mn(2+) followed
by Mg(2+) and Co(2+). {ECO:0000269|PubMed:15489502};
-!- ACTIVITY REGULATION: In contrast to nucleotidases from other
families, is not inhibited by ribo- and deoxyribonucleoside
di- and triphosphates.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=0.51 mM for 5'-dTMP (in the presence of Mn(2+))
{ECO:0000269|PubMed:15489502, ECO:0000269|PubMed:17286574};
KM=2.14 mM for 5'-dTMP (in the presence of 5 mM Mg(2+) and 0.5
mM Mn(2+)) {ECO:0000269|PubMed:15489502,
ECO:0000269|PubMed:17286574};
KM=0.66 mM for 5'-UMP (in the presence of Mn(2+))
{ECO:0000269|PubMed:15489502, ECO:0000269|PubMed:17286574};
KM=0.77 mM for 5'-dUMP (in the presence of Mn(2+))
{ECO:0000269|PubMed:15489502, ECO:0000269|PubMed:17286574};
KM=0.237 mM for 5-FdUMP (in the presence of 5 mM Mg(2+) and 0.5
mM Mn(2+)) {ECO:0000269|PubMed:15489502,
ECO:0000269|PubMed:17286574};
KM=17.8 mM for pNPP (in the presence of Mg(2+))
{ECO:0000269|PubMed:15489502, ECO:0000269|PubMed:17286574};
Vmax=65.6 umol/min/mg enzyme with 5'-dTMP as substrate
{ECO:0000269|PubMed:15489502, ECO:0000269|PubMed:17286574};
Vmax=73.9 umol/min/mg enzyme with 5'-UMP as substrate
{ECO:0000269|PubMed:15489502, ECO:0000269|PubMed:17286574};
Vmax=46.3 umol/min/mg enzyme with 5'-dUMP as substrate
{ECO:0000269|PubMed:15489502, ECO:0000269|PubMed:17286574};
Vmax=8.86 umol/min/mg enzyme with pNPP as substrate
{ECO:0000269|PubMed:15489502, ECO:0000269|PubMed:17286574};
Note=The catalytic efficiency is 15-fold higher with 5-fluoro-
2'-deoxyuridine monophosphate (5-FdUMP) than with 5'-dUMP as
substrate.;
pH dependence:
Optimum pH is 7.5. {ECO:0000269|PubMed:15489502};
-!- SUBUNIT: Monomer, homodimer and possibly homotetramer in solution.
{ECO:0000269|PubMed:15489502}.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
-!- 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.
{ECO:0000269|PubMed:17189366, ECO:0000269|PubMed:17286574}.
-!- SIMILARITY: Belongs to the HAD-like hydrolase superfamily. YjjG
family. {ECO:0000305}.
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EMBL; D17724; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; Z26313; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; U14003; AAA97270.1; -; Genomic_DNA.
EMBL; U00096; AAC77327.1; -; Genomic_DNA.
EMBL; AP009048; BAE78362.1; -; Genomic_DNA.
PIR; S56598; S56598.
RefSeq; NP_418791.1; NC_000913.3.
RefSeq; WP_000870710.1; NZ_LN832404.1.
ProteinModelPortal; P0A8Y1; -.
SMR; P0A8Y1; -.
BioGrid; 4262174; 7.
STRING; 316385.ECDH10B_4531; -.
PaxDb; P0A8Y1; -.
PRIDE; P0A8Y1; -.
EnsemblBacteria; AAC77327; AAC77327; b4374.
EnsemblBacteria; BAE78362; BAE78362; BAE78362.
GeneID; 948899; -.
KEGG; ecj:JW4336; -.
KEGG; eco:b4374; -.
PATRIC; fig|1411691.4.peg.2314; -.
EchoBASE; EB2038; -.
EcoGene; EG12115; yjjG.
eggNOG; ENOG4105PAD; Bacteria.
eggNOG; COG1011; LUCA.
HOGENOM; HOG000248345; -.
InParanoid; P0A8Y1; -.
KO; K08723; -.
PhylomeDB; P0A8Y1; -.
BioCyc; EcoCyc:EG12115-MONOMER; -.
BioCyc; MetaCyc:EG12115-MONOMER; -.
SABIO-RK; P0A8Y1; -.
PRO; PR:P0A8Y1; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0008253; F:5'-nucleotidase activity; IDA:EcoCyc.
GO; GO:0030145; F:manganese ion binding; IDA:EcoCyc.
GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
GO; GO:0016791; F:phosphatase activity; IDA:EcoliWiki.
GO; GO:0043100; P:pyrimidine nucleobase salvage; IGI:EcoCyc.
GO; GO:0009410; P:response to xenobiotic stimulus; IMP:EcoCyc.
GO; GO:0019859; P:thymine metabolic process; IGI:EcoCyc.
Gene3D; 1.10.150.240; -; 1.
Gene3D; 3.40.50.1000; -; 1.
InterPro; IPR036412; HAD-like_sf.
InterPro; IPR006439; HAD-SF_hydro_IA.
InterPro; IPR011951; HAD-SF_hydro_IA_YjjG/YfnB.
InterPro; IPR023214; HAD_sf.
InterPro; IPR023198; PGP-like_dom2.
SUPFAM; SSF56784; SSF56784; 1.
TIGRFAMs; TIGR01549; HAD-SF-IA-v1; 1.
TIGRFAMs; TIGR01509; HAD-SF-IA-v3; 1.
TIGRFAMs; TIGR02254; YjjG/YfnB; 1.
1: Evidence at protein level;
Cobalt; Complete proteome; Cytoplasm; Hydrolase; Magnesium; Manganese;
Metal-binding; Nucleotide-binding; Reference proteome.
CHAIN 1 225 Pyrimidine 5'-nucleotidase YjjG.
/FTId=PRO_0000066274.
ACT_SITE 9 9 Nucleophile. {ECO:0000250}.
CONFLICT 75 75 L -> V (in Ref. 2). {ECO:0000305}.
CONFLICT 100 100 A -> R (in Ref. 2). {ECO:0000305}.
CONFLICT 130 130 R -> G (in Ref. 2). {ECO:0000305}.
SEQUENCE 225 AA; 25301 MW; D8A52E086567BA71 CRC64;
MKWDWIFFDA DETLFTFDSF TGLQRMFLDY SVTFTAEDFQ DYQAVNKPLW VDYQNGAITS
LQLQHGRFES WAERLNVEPG KLNEAFINAM AEICTPLPGA VSLLNAIRGN AKIGIITNGF
SALQQVRLER TGLRDYFDLL VISEEVGVAK PNKKIFDYAL EQAGNPDRSR VLMVGDTAES
DILGGINAGL ATCWLNAHHR EQPEGIAPTW TVSSLHELEQ LLCKH


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