YJJG_ECOLI
ID YJJG_ECOLI Reviewed; 225 AA.
AC P0A8Y1; P33999; P76818; Q2M5U4;
DT 21-JUN-2005, integrated into UniProtKB/Swiss-Prot.
DT 21-JUN-2005, sequence version 1.
DT 03-AUG-2022, entry version 121.
DE RecName: Full=Pyrimidine 5'-nucleotidase YjjG;
DE EC=3.1.3.5 {ECO:0000269|PubMed:15489502};
DE AltName: Full=House-cleaning nucleotidase;
DE AltName: Full=Non-canonical pyrimidine nucleotide phosphatase;
DE AltName: Full=Nucleoside 5'-monophosphate phosphohydrolase;
DE AltName: Full=dUMP phosphatase;
GN Name=yjjG; OrderedLocusNames=b4374, JW4336;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RA Mikuni O., Ito K., Matsumura K., Mofatt J., Nobukuni T., McCaughan K.,
RA Tate W., Nakamura Y.;
RL Submitted (SEP-1993) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RA Grentzmann G., Brechemier-Baey D., Heurgue V., Mora L., Buckingham R.H.;
RL Submitted (SEP-1993) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=7610040; DOI=10.1093/nar/23.12.2105;
RA Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.;
RT "Analysis of the Escherichia coli genome VI: DNA sequence of the region
RT from 92.8 through 100 minutes.";
RL Nucleic Acids Res. 23:2105-2119(1995).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [6]
RP IDENTIFICATION.
RA Rudd K.E.;
RL Unpublished observations (DEC-1993).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, CHARACTERIZATION, COFACTOR, ACTIVITY
RP REGULATION, SUBUNIT, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=15489502; DOI=10.1074/jbc.m411023200;
RA Proudfoot M., Kuznetsova E., Brown G., Rao N.N., Kitagawa M., Mori H.,
RA Savchenko A., Yakunin A.F.;
RT "General enzymatic screens identify three new nucleotidases in Escherichia
RT coli. Biochemical characterization of SurE, YfbR, and YjjG.";
RL J. Biol. Chem. 279:54687-54694(2004).
RN [8]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND DISRUPTION
RP PHENOTYPE.
RC STRAIN=K12 / BW25113;
RX PubMed=17286574; DOI=10.1111/j.1574-6968.2007.00646.x;
RA Titz B., Hauser R., Engelbrecher A., Uetz P.;
RT "The Escherichia coli protein YjjG is a house-cleaning nucleotidase in
RT vivo.";
RL FEMS Microbiol. Lett. 270:49-57(2007).
RN [9]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12;
RX PubMed=17189366; DOI=10.1128/jb.01645-06;
RA Weiss B.;
RT "YjjG, a dUMP phosphatase, is critical for thymine utilization by
RT Escherichia coli K-12.";
RL J. Bacteriol. 189:2186-2189(2007).
CC -!- FUNCTION: Nucleotidase that shows high phosphatase activity toward non-
CC canonical pyrimidine nucleotides and three canonical nucleoside 5'-
CC monophosphates (UMP, dUMP, and dTMP), and very low activity against
CC TDP, IMP, UDP, GMP, dGMP, AMP, dAMP, and 6-phosphogluconate. Appears to
CC function as a house-cleaning nucleotidase in vivo, since the general
CC nucleotidase activity of YjjG allows it to protect cells against non-
CC canonical pyrimidine derivatives such as 5-fluoro-2'-deoxyuridine, 5-
CC fluorouridine, 5-fluoroorotate, 5-fluorouracil, and 5-aza-2'-
CC deoxycytidine, and prevents the incorporation of potentially mutagenic
CC nucleotides into DNA. Its dUMP phosphatase activity that catalyzes the
CC hydrolysis of dUMP to deoxyuridine is necessary for thymine utilization
CC via the thymine salvage pathway. Is strictly specific to substrates
CC with 5'-phosphates and shows no activity against nucleoside 2'- or 3'-
CC monophosphates. {ECO:0000269|PubMed:15489502,
CC ECO:0000269|PubMed:17189366, ECO:0000269|PubMed:17286574}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a ribonucleoside 5'-phosphate + H2O = a ribonucleoside +
CC phosphate; Xref=Rhea:RHEA:12484, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:18254, ChEBI:CHEBI:43474, ChEBI:CHEBI:58043; EC=3.1.3.5;
CC Evidence={ECO:0000269|PubMed:15489502};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 2'-deoxyribonucleoside 5'-phosphate + H2O = a 2'-
CC deoxyribonucleoside + phosphate; Xref=Rhea:RHEA:36167,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:18274, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:65317; Evidence={ECO:0000269|PubMed:15489502,
CC ECO:0000269|PubMed:17286574};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + UMP = phosphate + uridine; Xref=Rhea:RHEA:29359,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:16704, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:57865; Evidence={ECO:0000269|PubMed:15489502};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=dUMP + H2O = 2'-deoxyuridine + phosphate;
CC Xref=Rhea:RHEA:29355, ChEBI:CHEBI:15377, ChEBI:CHEBI:16450,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:246422;
CC Evidence={ECO:0000269|PubMed:15489502};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=dTMP + H2O = phosphate + thymidine; Xref=Rhea:RHEA:11080,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:17748, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:63528; Evidence={ECO:0000269|PubMed:15489502,
CC ECO:0000269|PubMed:17286574};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:15489502};
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:15489502};
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000269|PubMed:15489502};
CC Note=Divalent metal cation. Highest activity with Mn(2+) followed by
CC Mg(2+) and Co(2+). {ECO:0000269|PubMed:15489502};
CC -!- ACTIVITY REGULATION: In contrast to nucleotidases from other families,
CC is not inhibited by ribo- and deoxyribonucleoside di- and
CC triphosphates. {ECO:0000269|PubMed:15489502}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.51 mM for 5'-dTMP (in the presence of Mn(2+))
CC {ECO:0000269|PubMed:15489502};
CC KM=2.14 mM for 5'-dTMP (in the presence of 5 mM Mg(2+) and 0.5 mM
CC Mn(2+)) {ECO:0000269|PubMed:17286574};
CC KM=0.66 mM for 5'-UMP (in the presence of Mn(2+))
CC {ECO:0000269|PubMed:15489502};
CC KM=0.77 mM for 5'-dUMP (in the presence of Mn(2+))
CC {ECO:0000269|PubMed:15489502};
CC KM=0.237 mM for 5-FdUMP (in the presence of 5 mM Mg(2+) and 0.5 mM
CC Mn(2+)) {ECO:0000269|PubMed:17286574};
CC KM=17.8 mM for pNPP (in the presence of Mg(2+))
CC {ECO:0000269|PubMed:15489502};
CC Vmax=65.6 umol/min/mg enzyme with 5'-dTMP as substrate
CC {ECO:0000269|PubMed:15489502};
CC Vmax=73.9 umol/min/mg enzyme with 5'-UMP as substrate
CC {ECO:0000269|PubMed:15489502};
CC Vmax=46.3 umol/min/mg enzyme with 5'-dUMP as substrate
CC {ECO:0000269|PubMed:15489502};
CC Vmax=8.86 umol/min/mg enzyme with pNPP as substrate
CC {ECO:0000269|PubMed:15489502};
CC Note=The catalytic efficiency is 15-fold higher with 5-fluoro-2'-
CC deoxyuridine monophosphate (5-FdUMP) than with 5'-dUMP as substrate.;
CC pH dependence:
CC Optimum pH is 7.5. {ECO:0000269|PubMed:15489502};
CC -!- SUBUNIT: Monomer, homodimer and possibly homotetramer in solution.
CC {ECO:0000269|PubMed:15489502}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene become highly sensitive
CC to toxic non-canonical pyrimidine derivatives such as 5-fluoro-2'-
CC deoxyuridine (5-FdUMP); the growth is completely blocked. Disruption of
CC yjjG in a thyA mutant blocks the utilization of thymine but not that of
CC thymidine for growth. {ECO:0000269|PubMed:17189366,
CC ECO:0000269|PubMed:17286574}.
CC -!- SIMILARITY: Belongs to the HAD-like hydrolase superfamily. YjjG family.
CC {ECO:0000305}.
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DR EMBL; D17724; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; Z26313; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; U14003; AAA97270.1; -; Genomic_DNA.
DR EMBL; U00096; AAC77327.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE78362.1; -; Genomic_DNA.
DR PIR; S56598; S56598.
DR RefSeq; NP_418791.1; NC_000913.3.
DR RefSeq; WP_000870710.1; NZ_SSZK01000015.1.
DR AlphaFoldDB; P0A8Y1; -.
DR SMR; P0A8Y1; -.
DR BioGRID; 4262174; 7.
DR STRING; 511145.b4374; -.
DR PaxDb; P0A8Y1; -.
DR PRIDE; P0A8Y1; -.
DR DNASU; 948899; -.
DR EnsemblBacteria; AAC77327; AAC77327; b4374.
DR EnsemblBacteria; BAE78362; BAE78362; BAE78362.
DR GeneID; 948899; -.
DR KEGG; ecj:JW4336; -.
DR KEGG; eco:b4374; -.
DR PATRIC; fig|1411691.4.peg.2314; -.
DR EchoBASE; EB2038; -.
DR eggNOG; COG1011; Bacteria.
DR HOGENOM; CLU_045011_8_1_6; -.
DR InParanoid; P0A8Y1; -.
DR OMA; DHTLWDF; -.
DR PhylomeDB; P0A8Y1; -.
DR BioCyc; EcoCyc:EG12115-MON; -.
DR BioCyc; MetaCyc:EG12115-MON; -.
DR SABIO-RK; P0A8Y1; -.
DR PRO; PR:P0A8Y1; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0008253; F:5'-nucleotidase activity; IDA:EcoCyc.
DR GO; GO:0030145; F:manganese ion binding; IDA:EcoCyc.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0016791; F:phosphatase activity; IDA:EcoliWiki.
DR GO; GO:0050340; F:thymidylate 5'-phosphatase activity; IEA:RHEA.
DR GO; GO:0106411; F:XMP 5'-nucleosidase activity; IEA:UniProtKB-EC.
DR GO; GO:0009410; P:response to xenobiotic stimulus; IMP:EcoCyc.
DR Gene3D; 1.10.150.240; -; 1.
DR Gene3D; 3.40.50.1000; -; 1.
DR InterPro; IPR036412; HAD-like_sf.
DR InterPro; IPR006439; HAD-SF_hydro_IA.
DR InterPro; IPR011951; HAD-SF_hydro_IA_YjjG/PynA.
DR InterPro; IPR041492; HAD_2.
DR InterPro; IPR023214; HAD_sf.
DR InterPro; IPR023198; PGP-like_dom2.
DR Pfam; PF13419; HAD_2; 1.
DR SUPFAM; SSF56784; SSF56784; 1.
DR TIGRFAMs; TIGR01549; HAD-SF-IA-v1; 1.
DR TIGRFAMs; TIGR01509; HAD-SF-IA-v3; 1.
DR TIGRFAMs; TIGR02254; YjjG/YfnB; 1.
PE 1: Evidence at protein level;
KW Cobalt; Cytoplasm; Hydrolase; Magnesium; Manganese; Metal-binding;
KW Nucleotide-binding; Reference proteome.
FT CHAIN 1..225
FT /note="Pyrimidine 5'-nucleotidase YjjG"
FT /id="PRO_0000066274"
FT ACT_SITE 9
FT /note="Nucleophile"
FT /evidence="ECO:0000250"
FT CONFLICT 75
FT /note="L -> V (in Ref. 2)"
FT /evidence="ECO:0000305"
FT CONFLICT 100
FT /note="A -> R (in Ref. 2)"
FT /evidence="ECO:0000305"
FT CONFLICT 130
FT /note="R -> G (in Ref. 2)"
FT /evidence="ECO:0000305"
SQ 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
