NUDG_ECOLI
ID NUDG_ECOLI Reviewed; 135 AA.
AC P77788;
DT 11-JAN-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1997, sequence version 1.
DT 03-AUG-2022, entry version 150.
DE RecName: Full=CTP pyrophosphohydrolase;
DE EC=3.6.1.65 {ECO:0000269|PubMed:11053429, ECO:0000269|PubMed:12509230, ECO:0000269|PubMed:15381107, ECO:0000269|PubMed:15823026};
GN Name=nudG; Synonyms=ynjG; OrderedLocusNames=b1759, JW1748;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9097039; DOI=10.1093/dnares/3.6.363;
RA Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K.,
RA Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S.,
RA Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G.,
RA Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y.,
RA Wada C., Yamamoto Y., Horiuchi T.;
RT "A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 28.0-40.1 min region on the linkage map.";
RL DNA Res. 3:363-377(1996).
RN [2]
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 [3]
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 [4]
RP CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, AND FUNCTION.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=11053429; DOI=10.1074/jbc.m004100200;
RA O'Handley S.F., Dunn C.A., Bessman M.J.;
RT "Orf135 from Escherichia coli is a Nudix hydrolase specific for CTP, dCTP,
RT and 5-methyl-dCTP.";
RL J. Biol. Chem. 276:5421-5426(2001).
RN [5]
RP CATALYTIC ACTIVITY, AND FUNCTION.
RX PubMed=12509230; DOI=10.1016/s1568-7864(02)00057-5;
RA Fujikawa K., Kasai H.;
RT "The oxidized pyrimidine ribonucleotide, 5-hydroxy-CTP, is hydrolyzed
RT efficiently by the Escherichia coli recombinant Orf135 protein.";
RL DNA Repair 1:571-576(2002).
RN [6]
RP CATALYTIC ACTIVITY, COFACTOR, AND MUTAGENESIS OF GLY-36; GLY-37; LYS-38;
RP GLU-43; ARG-51; GLU-52; LEU-53; GLU-55 AND GLU-56.
RX PubMed=15381107; DOI=10.1016/j.bbrc.2004.08.201;
RA Kamiya H., Iida E., Harashima H.;
RT "Important amino acids in the phosphohydrolase module of Escherichia coli
RT Orf135.";
RL Biochem. Biophys. Res. Commun. 323:1063-1068(2004).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP MUTAGENESIS OF GLU-33; ARG-72; ARG-77 AND ASP-118.
RX PubMed=15823026; DOI=10.1021/bi048071o;
RA Iida E., Satou K., Mishima M., Kojima C., Harashima H., Kamiya H.;
RT "Amino acid residues involved in substrate recognition of the Escherichia
RT coli Orf135 protein.";
RL Biochemistry 44:5683-5689(2005).
RN [8]
RP STRUCTURE BY NMR, SUBUNIT, AND SUBSTRATE-BINDING SITES.
RX PubMed=22414689; DOI=10.1016/j.bbrc.2012.02.146;
RA Kawasaki K., Kanaba T., Yoneyama M., Murata-Kamiya N., Kojima C., Ito Y.,
RA Kamiya H., Mishima M.;
RT "Insights into substrate recognition by the Escherichia coli Orf135 protein
RT through its solution structure.";
RL Biochem. Biophys. Res. Commun. 420:263-268(2012).
CC -!- FUNCTION: Hydrolase with a preference for pyrimidine substrates. Has
CC high activity with 5-methyl-dCTP, and much lower activity with CTP,
CC dCTP, 5-hydroxy-dCTP, 2-hydroxy-dATP and 8-hydroxy-dGTP.
CC {ECO:0000269|PubMed:11053429, ECO:0000269|PubMed:12509230,
CC ECO:0000269|PubMed:15823026}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=CTP + H2O = CMP + diphosphate + H(+); Xref=Rhea:RHEA:27762,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:37563, ChEBI:CHEBI:60377; EC=3.6.1.65;
CC Evidence={ECO:0000269|PubMed:11053429, ECO:0000269|PubMed:12509230,
CC ECO:0000269|PubMed:15381107, ECO:0000269|PubMed:15823026};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=dCTP + H2O = dCMP + diphosphate + H(+); Xref=Rhea:RHEA:22636,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:57566, ChEBI:CHEBI:61481; EC=3.6.1.65;
CC Evidence={ECO:0000269|PubMed:11053429, ECO:0000269|PubMed:12509230,
CC ECO:0000269|PubMed:15381107, ECO:0000269|PubMed:15823026};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:11053429, ECO:0000269|PubMed:15381107};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:11053429, ECO:0000269|PubMed:15381107};
CC Note=Divalent metal ions. Mg(2+) or Mn(2+).
CC {ECO:0000269|PubMed:11053429, ECO:0000269|PubMed:15381107};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.028 mM for 5-methyl-dCTP {ECO:0000269|PubMed:11053429,
CC ECO:0000269|PubMed:15823026};
CC KM=0.027 mM for 2-hydroxy-dATP {ECO:0000269|PubMed:11053429,
CC ECO:0000269|PubMed:15823026};
CC KM=0.41 mM for 8-hydroxy-dGTP {ECO:0000269|PubMed:11053429,
CC ECO:0000269|PubMed:15823026};
CC KM=0.99 mM for dCTP {ECO:0000269|PubMed:11053429,
CC ECO:0000269|PubMed:15823026};
CC pH dependence:
CC Optimum pH is 8.5-9. {ECO:0000269|PubMed:11053429,
CC ECO:0000269|PubMed:15823026};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:22414689}.
CC -!- INTERACTION:
CC P77788; P03813: ygeA; NbExp=2; IntAct=EBI-545184, EBI-545190;
CC -!- SIMILARITY: Belongs to the Nudix hydrolase family. {ECO:0000305}.
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DR EMBL; U00096; AAC74829.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA15549.1; -; Genomic_DNA.
DR PIR; G64935; G64935.
DR RefSeq; NP_416273.1; NC_000913.3.
DR RefSeq; WP_000781888.1; NZ_LN832404.1.
DR PDB; 2RRK; NMR; -; A=1-135.
DR PDBsum; 2RRK; -.
DR AlphaFoldDB; P77788; -.
DR BMRB; P77788; -.
DR SMR; P77788; -.
DR BioGRID; 4260320; 120.
DR DIP; DIP-10376N; -.
DR IntAct; P77788; 3.
DR STRING; 511145.b1759; -.
DR PaxDb; P77788; -.
DR PRIDE; P77788; -.
DR EnsemblBacteria; AAC74829; AAC74829; b1759.
DR EnsemblBacteria; BAA15549; BAA15549; BAA15549.
DR GeneID; 946277; -.
DR KEGG; ecj:JW1748; -.
DR KEGG; eco:b1759; -.
DR PATRIC; fig|1411691.4.peg.496; -.
DR EchoBASE; EB3765; -.
DR eggNOG; COG0494; Bacteria.
DR HOGENOM; CLU_037162_19_1_6; -.
DR InParanoid; P77788; -.
DR OMA; HADQPGM; -.
DR PhylomeDB; P77788; -.
DR BioCyc; EcoCyc:G6954-MON; -.
DR BioCyc; MetaCyc:G6954-MON; -.
DR BRENDA; 3.6.1.65; 2026.
DR SABIO-RK; P77788; -.
DR PRO; PR:P77788; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0035539; F:8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity; IBA:GO_Central.
DR GO; GO:0008413; F:8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity; IBA:GO_Central.
DR GO; GO:0044715; F:8-oxo-dGDP phosphatase activity; IBA:GO_Central.
DR GO; GO:0044716; F:8-oxo-GDP phosphatase activity; IBA:GO_Central.
DR GO; GO:0047840; F:dCTP diphosphatase activity; IEA:RHEA.
DR GO; GO:0016787; F:hydrolase activity; IDA:EcoCyc.
DR GO; GO:0006281; P:DNA repair; IBA:GO_Central.
DR InterPro; IPR020476; Nudix_hydrolase.
DR InterPro; IPR015797; NUDIX_hydrolase-like_dom_sf.
DR InterPro; IPR020084; NUDIX_hydrolase_CS.
DR InterPro; IPR000086; NUDIX_hydrolase_dom.
DR Pfam; PF00293; NUDIX; 1.
DR PRINTS; PR00502; NUDIXFAMILY.
DR SUPFAM; SSF55811; SSF55811; 1.
DR PROSITE; PS51462; NUDIX; 1.
DR PROSITE; PS00893; NUDIX_BOX; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Magnesium; Manganese; Reference proteome.
FT CHAIN 1..135
FT /note="CTP pyrophosphohydrolase"
FT /id="PRO_0000056990"
FT DOMAIN 2..127
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00794"
FT MOTIF 37..58
FT /note="Nudix box"
FT BINDING 34..39
FT /ligand="substrate"
FT /evidence="ECO:0000305"
FT BINDING 72
FT /ligand="substrate"
FT /evidence="ECO:0000305"
FT BINDING 118
FT /ligand="substrate"
FT /evidence="ECO:0000305"
FT MUTAGEN 33
FT /note="E->A,Q: Increases enzyme activity with 2-hydroxy-
FT ATP. Decreases enzyme activity with dCTP, 5-methyl-dCTP and
FT 8-hydroxy-ATP."
FT /evidence="ECO:0000269|PubMed:15823026"
FT MUTAGEN 33
FT /note="E->D: Decreases enzyme activity with 2-hydroxy-ATP,
FT dCTP, 5-dmethyl-CTP and 8-hydroxy-ATP."
FT /evidence="ECO:0000269|PubMed:15823026"
FT MUTAGEN 36
FT /note="G->A: Abolishes enzyme activity."
FT /evidence="ECO:0000269|PubMed:15381107"
FT MUTAGEN 37
FT /note="G->A: Abolishes enzyme activity."
FT /evidence="ECO:0000269|PubMed:15381107"
FT MUTAGEN 38
FT /note="K->A,R: Strongly reduces enzyme activity with dCTP,
FT and to a lesser degree with 5-methyl-dCTP."
FT /evidence="ECO:0000269|PubMed:15381107"
FT MUTAGEN 43
FT /note="E->A: Abolishes enzyme activity with dCTP and
FT reduces enzyme activity with 5-methyl-dCTP."
FT /evidence="ECO:0000269|PubMed:15381107"
FT MUTAGEN 51
FT /note="R->A: Abolishes enzyme activity with dCTP. Nearly
FT abolishes enzyme activity with 5-methyl-dCTP."
FT /evidence="ECO:0000269|PubMed:15381107"
FT MUTAGEN 52
FT /note="E->A,D,Q: Abolishes enzyme activity."
FT /evidence="ECO:0000269|PubMed:15381107"
FT MUTAGEN 53
FT /note="L->A: Reduces enzyme activity."
FT /evidence="ECO:0000269|PubMed:15381107"
FT MUTAGEN 55
FT /note="E->A: Abolishes enzyme activity with dCTP and
FT reduces enzyme activity with 5-methyl-dCTP."
FT /evidence="ECO:0000269|PubMed:15381107"
FT MUTAGEN 55
FT /note="E->D,Q: Abolishes enzyme activity with dCTP and
FT reduces enzyme activity with 5-methyl-dCTP."
FT /evidence="ECO:0000269|PubMed:15381107"
FT MUTAGEN 56
FT /note="E->A,D,Q: Abolishes enzyme activity."
FT /evidence="ECO:0000269|PubMed:15381107"
FT MUTAGEN 72
FT /note="R->A: Strongly decreases the activity with 2-
FT hydroxy-ATP."
FT /evidence="ECO:0000269|PubMed:15823026"
FT MUTAGEN 77
FT /note="R->A: No effect."
FT /evidence="ECO:0000269|PubMed:15823026"
FT MUTAGEN 118
FT /note="D->A,N: Abolishes enzyme activity with 2-hydroxy-
FT ATP. No effect on activity with dCTP, 5-methyl-dCTP and 8-
FT hydroxy-ATP."
FT /evidence="ECO:0000269|PubMed:15823026"
FT MUTAGEN 118
FT /note="D->A: Abolishes enzyme activity with dCTP and 2-
FT hydroxy-ATP and decreases activity with 5-methyl-dCTP.
FT Increases activity with 8-hydroxy-ATP."
FT /evidence="ECO:0000269|PubMed:15823026"
FT MUTAGEN 118
FT /note="D->E: Increases the activity with 2-hydroxy-ATP.
FT Strongly decreases activity with 8-hydroxy-ATP."
FT /evidence="ECO:0000269|PubMed:15823026"
FT STRAND 3..13
FT /evidence="ECO:0007829|PDB:2RRK"
FT STRAND 16..21
FT /evidence="ECO:0007829|PDB:2RRK"
FT STRAND 36..38
FT /evidence="ECO:0007829|PDB:2RRK"
FT HELIX 45..56
FT /evidence="ECO:0007829|PDB:2RRK"
FT STRAND 59..62
FT /evidence="ECO:0007829|PDB:2RRK"
FT STRAND 65..74
FT /evidence="ECO:0007829|PDB:2RRK"
FT STRAND 77..91
FT /evidence="ECO:0007829|PDB:2RRK"
FT STRAND 101..104
FT /evidence="ECO:0007829|PDB:2RRK"
FT HELIX 106..109
FT /evidence="ECO:0007829|PDB:2RRK"
FT HELIX 118..131
FT /evidence="ECO:0007829|PDB:2RRK"
SQ SEQUENCE 135 AA; 15046 MW; D85D8B3A6532CA82 CRC64;
MKMIEVVAAI IERDGKILLA QRPAQSDQAG LWEFAGGKVE PDESQRQALV RELREELGIE
ATVGEYVASH QREVSGRIIH LHAWHVPDFH GTLQAHEHQA LVWCSPEEAL QYPLAPADIP
LLEAFMALRA ARPAD
