IXTPA_ECOLI
ID IXTPA_ECOLI Reviewed; 197 AA.
AC P52061; Q2M9N9;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 1.
DT 03-AUG-2022, entry version 156.
DE RecName: Full=dITP/XTP pyrophosphatase {ECO:0000255|HAMAP-Rule:MF_01405, ECO:0000305|PubMed:12297000, ECO:0000305|PubMed:17976651};
DE EC=3.6.1.66 {ECO:0000255|HAMAP-Rule:MF_01405, ECO:0000269|PubMed:12297000, ECO:0000269|PubMed:17976651};
DE AltName: Full=Deoxyribonucleoside triphosphate pyrophosphohydrolase {ECO:0000303|PubMed:17090528};
DE AltName: Full=Inosine triphosphate pyrophosphatase {ECO:0000303|PubMed:17976651};
DE Short=ITPase {ECO:0000303|PubMed:17976651};
DE AltName: Full=Non-canonical purine NTP pyrophosphatase {ECO:0000255|HAMAP-Rule:MF_01405, ECO:0000305|PubMed:12297000};
DE AltName: Full=Non-standard purine NTP pyrophosphatase {ECO:0000255|HAMAP-Rule:MF_01405, ECO:0000305|PubMed:12297000};
DE AltName: Full=Nucleoside-triphosphate diphosphatase {ECO:0000255|HAMAP-Rule:MF_01405, ECO:0000305|PubMed:12297000};
DE AltName: Full=Nucleoside-triphosphate pyrophosphatase {ECO:0000255|HAMAP-Rule:MF_01405, ECO:0000305|PubMed:12297000};
DE Short=NTPase {ECO:0000255|HAMAP-Rule:MF_01405, ECO:0000303|PubMed:12297000};
GN Name=rdgB {ECO:0000312|EMBL:AAC75991.1}; Synonyms=yggV;
GN OrderedLocusNames=b2954, JW2921;
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 / 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 [2]
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 [3]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, SUBUNIT, COFACTOR, AND
RP BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=K12;
RX PubMed=12297000; DOI=10.5483/bmbrep.2002.35.4.403;
RA Chung J.H., Park H.-Y., Lee J.H., Jang Y.;
RT "Identification of the dITP- and XTP-hydrolyzing protein from Escherichia
RT coli.";
RL J. Biochem. Mol. Biol. 35:403-408(2002).
RN [4]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=12730170; DOI=10.1128/jb.185.10.3101-3110.2003;
RA Burgis N.E., Brucker J.J., Cunningham R.P.;
RT "Repair system for noncanonical purines in Escherichia coli.";
RL J. Bacteriol. 185:3101-3110(2003).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, AND BIOPHYSICOCHEMICAL
RP PROPERTIES.
RX PubMed=17090528; DOI=10.1074/jbc.m608708200;
RA Burgis N.E., Cunningham R.P.;
RT "Substrate specificity of RdgB protein, a deoxyribonucleoside triphosphate
RT pyrophosphohydrolase.";
RL J. Biol. Chem. 282:3531-3538(2007).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) OF WILD-TYPE APOENZYME AND MUTANT
RP ALA-69 IN COMPLEXES WITH IMP AND ITP, FUNCTION, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, MUTAGENESIS OF THR-8; ASN-10;
RP LYS-13; GLU-41; LYS-53; ASP-68; ASP-69; GLY-71; PHE-154; PHE-160 AND
RP ARG-183, REACTION MECHANISM, ACTIVE SITE, AND SUBUNIT.
RX PubMed=17976651; DOI=10.1016/j.jmb.2007.10.012;
RA Savchenko A., Proudfoot M., Skarina T., Singer A., Litvinova O.,
RA Sanishvili R., Brown G., Chirgadze N., Yakunin A.F.;
RT "Molecular basis of the antimutagenic activity of the house-cleaning
RT inosine triphosphate pyrophosphatase RdgB from Escherichia coli.";
RL J. Mol. Biol. 374:1091-1103(2007).
CC -!- FUNCTION: Pyrophosphatase that catalyzes the hydrolysis of nucleoside
CC triphosphates to their monophosphate derivatives, with a high
CC preference for the non-canonical purine nucleotides XTP (xanthosine
CC triphosphate), dITP (deoxyinosine triphosphate) and ITP
CC (PubMed:12297000, PubMed:17976651). Can also efficiently hydrolyze 2'-
CC deoxy-N-6-hydroxylaminopurine triphosphate (dHAPTP) (PubMed:17090528).
CC Seems to function as a house-cleaning enzyme that removes non-canonical
CC purine nucleotides from the nucleotide pool, thus preventing their
CC incorporation into DNA/RNA and avoiding chromosomal lesions
CC (PubMed:12297000, PubMed:12730170, PubMed:17090528). To a much lesser
CC extent, is also able to hydrolyze GTP, dGTP and dUTP, but shows very
CC low activity toward the canonical nucleotides dATP, dCTP and dTTP and
CC toward 8-oxo-dGTP, purine deoxyribose triphosphate, 2-aminopurine
CC deoxyribose triphosphate and 2,6-diaminopurine deoxyribose triphosphate
CC (PubMed:12297000, PubMed:17090528). {ECO:0000255|HAMAP-Rule:MF_01405,
CC ECO:0000269|PubMed:12297000, ECO:0000269|PubMed:12730170,
CC ECO:0000269|PubMed:17090528, ECO:0000269|PubMed:17976651}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + XTP = diphosphate + H(+) + XMP; Xref=Rhea:RHEA:28610,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:57464, ChEBI:CHEBI:61314; EC=3.6.1.66;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01405,
CC ECO:0000269|PubMed:12297000, ECO:0000269|PubMed:17976651};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=dITP + H2O = dIMP + diphosphate + H(+); Xref=Rhea:RHEA:28342,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:61194, ChEBI:CHEBI:61382; EC=3.6.1.66;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01405,
CC ECO:0000269|PubMed:12297000, ECO:0000269|PubMed:17090528,
CC ECO:0000269|PubMed:17976651};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + ITP = diphosphate + H(+) + IMP; Xref=Rhea:RHEA:29399,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:58053, ChEBI:CHEBI:61402; EC=3.6.1.66;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01405,
CC ECO:0000269|PubMed:12297000, ECO:0000269|PubMed:17976651};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:12297000, ECO:0000269|PubMed:17976651};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:12297000};
CC Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
CC Evidence={ECO:0000269|PubMed:12297000};
CC Note=Binds 1 divalent metal cation per subunit. Maximum activity is
CC obtained with Mg(2+). Activity with Mn(2+) or Ni(2+) makes up 60-75% of
CC the maximum rate. {ECO:0000269|PubMed:12297000};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.33 mM for XTP (at pH 10.0 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:12297000};
CC KM=0.36 mM for dITP (at pH 10.0 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:12297000};
CC KM=0.41 mM for ITP (at pH 10.0 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:12297000};
CC KM=22.0 uM for dITP (at pH 9.5 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:17090528};
CC KM=792 uM for dGTP (at pH 9.5 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:17090528};
CC KM=16.5 uM for dHAPTP (at pH 9.5 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:17090528};
CC KM=23.3 uM for XTP (at pH 9.0 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:17976651};
CC KM=11.3 uM for dITP (at pH 9.0 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:17976651};
CC KM=5.6 uM for ITP (at pH 9.0 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:17976651};
CC KM=312.6 uM for GTP (at pH 9.0 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:17976651};
CC KM=181.5 uM for dGTP (at pH 9.0 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:17976651};
CC KM=289.1 uM for TTP (at pH 9.0 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:17976651};
CC Note=Vmax values are similar for XTP, dITP and ITP. Activity toward
CC dATP, dCTP and dTTP is less than 1% of the rate of XTP hydrolysis.
CC dGTP and dUTP are hydrolyzed at 10-12% of the rate of XTP hydrolysis
CC (PubMed:12297000). kcat is 5.7 sec(-1) with ITP or dHAPTP as
CC substrate. kcat is 1.5 sec(-1) with dGTP as substrate (at pH 9.5 and
CC 37 degrees Celsius) (PubMed:17090528). kcat is 19.9 sec(-1) with XTP
CC as substrate. kcat is 13.2 sec(-1) with dITP as substrate. kcat is
CC 18.9 sec(-1) with ITP as substrate. kcat is 0.85 sec(-1) with GTP as
CC substrate. kcat is 0.37 sec(-1) with dGTP as substrate. kcat is 0.26
CC sec(-1) with TTP as substrate (at pH 9.0 and 37 degrees Celsius)
CC (PubMed:17976651). {ECO:0000269|PubMed:12297000,
CC ECO:0000269|PubMed:17090528, ECO:0000269|PubMed:17976651};
CC pH dependence:
CC Optimum pH is 10-10.5 (PubMed:12297000). Optimum pH is 9.0
CC (PubMed:17976651). Reaction rates under neutral conditions are <40%
CC of the maximum (PubMed:12297000). {ECO:0000269|PubMed:12297000,
CC ECO:0000269|PubMed:17976651};
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_01405,
CC ECO:0000269|PubMed:12297000, ECO:0000269|PubMed:17976651}.
CC -!- DISRUPTION PHENOTYPE: Inactivation of this gene in a moa background
CC (cells deficient in molybdopterin biosynthesis) results in increased N-
CC 6-hydroxylaminopurine (HAP) sensitivity, an increase in the level of
CC mutagenesis, and increased recombination and SOS induction upon HAP
CC exposure. {ECO:0000269|PubMed:12730170}.
CC -!- MISCELLANEOUS: Modified or damaged nucleotides such as 6-chloropurine
CC deoxyribose triphosphate, 8-Br-dGTP, 5-Br-dCTP, 5-Br-dUTP, 7-deaza-
CC dGTP, 7-methyl-GTP, N6-etheno-ATP, NAD, NADH, FAD, ADP-ribose, UPD-
CC glucose, AppA and ApppA are not hydrolyzed by the enzyme.
CC {ECO:0000269|PubMed:12297000}.
CC -!- MISCELLANEOUS: The aberrant nucleotides XTP and dITP can be produced by
CC oxidative deamination from purine nucleotides in cells; they are
CC potentially mutagenic. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the HAM1 NTPase family. {ECO:0000255|HAMAP-
CC Rule:MF_01405}.
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DR EMBL; U28377; AAA69121.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75991.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77017.1; -; Genomic_DNA.
DR PIR; A65081; A65081.
DR RefSeq; NP_417429.1; NC_000913.3.
DR RefSeq; WP_001174777.1; NZ_SSUV01000019.1.
DR PDB; 1K7K; X-ray; 1.50 A; A=1-197.
DR PDB; 2PYU; X-ray; 2.02 A; A=1-197.
DR PDB; 2Q16; X-ray; 1.95 A; A/B=1-197.
DR PDBsum; 1K7K; -.
DR PDBsum; 2PYU; -.
DR PDBsum; 2Q16; -.
DR AlphaFoldDB; P52061; -.
DR SMR; P52061; -.
DR BioGRID; 4260898; 103.
DR BioGRID; 851750; 2.
DR IntAct; P52061; 3.
DR STRING; 511145.b2954; -.
DR jPOST; P52061; -.
DR PaxDb; P52061; -.
DR PRIDE; P52061; -.
DR EnsemblBacteria; AAC75991; AAC75991; b2954.
DR EnsemblBacteria; BAE77017; BAE77017; BAE77017.
DR GeneID; 947429; -.
DR KEGG; ecj:JW2921; -.
DR KEGG; eco:b2954; -.
DR PATRIC; fig|1411691.4.peg.3778; -.
DR EchoBASE; EB2807; -.
DR eggNOG; COG0127; Bacteria.
DR HOGENOM; CLU_082080_0_3_6; -.
DR InParanoid; P52061; -.
DR OMA; DCFADDT; -.
DR PhylomeDB; P52061; -.
DR BioCyc; EcoCyc:G7530-MON; -.
DR BioCyc; MetaCyc:G7530-MON; -.
DR EvolutionaryTrace; P52061; -.
DR PRO; PR:P52061; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0035870; F:dITP diphosphatase activity; IDA:UniProtKB.
DR GO; GO:0036220; F:ITP diphosphatase activity; IDA:UniProtKB.
DR GO; GO:0000287; F:magnesium ion binding; IDA:EcoCyc.
DR GO; GO:0017111; F:nucleoside-triphosphatase activity; IEA:InterPro.
DR GO; GO:0047429; F:nucleoside-triphosphate diphosphatase activity; IDA:EcoCyc.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
DR GO; GO:0036222; F:XTP diphosphatase activity; IDA:UniProtKB.
DR GO; GO:0009143; P:nucleoside triphosphate catabolic process; IDA:EcoCyc.
DR GO; GO:0009117; P:nucleotide metabolic process; IEA:UniProtKB-KW.
DR GO; GO:0009146; P:purine nucleoside triphosphate catabolic process; IDA:UniProtKB.
DR CDD; cd00515; HAM1; 1.
DR Gene3D; 3.90.950.10; -; 1.
DR HAMAP; MF_01405; Non_canon_purine_NTPase; 1.
DR InterPro; IPR020922; dITP/XTP_pyrophosphatase.
DR InterPro; IPR002637; Ham1p-like.
DR InterPro; IPR029001; ITPase-like_fam.
DR PANTHER; PTHR11067; PTHR11067; 1.
DR Pfam; PF01725; Ham1p_like; 1.
DR SUPFAM; SSF52972; SSF52972; 1.
DR TIGRFAMs; TIGR00042; TIGR00042; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Magnesium; Manganese; Metal-binding; Nickel;
KW Nucleotide metabolism; Nucleotide-binding; Reference proteome.
FT CHAIN 1..197
FT /note="dITP/XTP pyrophosphatase"
FT /id="PRO_0000178164"
FT ACT_SITE 69
FT /note="Proton acceptor"
FT /evidence="ECO:0000305|PubMed:17976651"
FT BINDING 8..13
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01405,
FT ECO:0000269|PubMed:17976651, ECO:0007744|PDB:2Q16"
FT BINDING 40
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01405"
FT BINDING 69
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01405"
FT BINDING 70
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17976651,
FT ECO:0007744|PDB:2Q16"
FT BINDING 154..157
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01405,
FT ECO:0000269|PubMed:17976651, ECO:0007744|PDB:2Q16"
FT BINDING 177
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17976651,
FT ECO:0007744|PDB:2Q16"
FT BINDING 182..183
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01405,
FT ECO:0000269|PubMed:17976651, ECO:0007744|PDB:2Q16"
FT MUTAGEN 8
FT /note="T->A: Greatly reduced ITP pyrophosphatase activity."
FT /evidence="ECO:0000269|PubMed:17976651"
FT MUTAGEN 10
FT /note="N->A: Greatly reduced ITP pyrophosphatase activity."
FT /evidence="ECO:0000269|PubMed:17976651"
FT MUTAGEN 13
FT /note="K->A: Complete loss of enzymatic activity."
FT /evidence="ECO:0000269|PubMed:17976651"
FT MUTAGEN 41
FT /note="E->A: Complete loss of enzymatic activity."
FT /evidence="ECO:0000269|PubMed:17976651"
FT MUTAGEN 53
FT /note="K->A: Complete loss of enzymatic activity."
FT /evidence="ECO:0000269|PubMed:17976651"
FT MUTAGEN 68
FT /note="D->A: Greatly reduced ITP pyrophosphatase activity."
FT /evidence="ECO:0000269|PubMed:17976651"
FT MUTAGEN 69
FT /note="D->A: Complete loss of enzymatic activity."
FT /evidence="ECO:0000269|PubMed:17976651"
FT MUTAGEN 71
FT /note="G->A: Greatly reduced ITP pyrophosphatase activity."
FT /evidence="ECO:0000269|PubMed:17976651"
FT MUTAGEN 154
FT /note="F->A: Greatly reduced ITP pyrophosphatase activity."
FT /evidence="ECO:0000269|PubMed:17976651"
FT MUTAGEN 160
FT /note="F->A: Greatly reduced ITP pyrophosphatase activity."
FT /evidence="ECO:0000269|PubMed:17976651"
FT MUTAGEN 183
FT /note="R->A: Greatly reduced ITP pyrophosphatase activity."
FT /evidence="ECO:0000269|PubMed:17976651"
FT STRAND 2..7
FT /evidence="ECO:0007829|PDB:1K7K"
FT HELIX 11..21
FT /evidence="ECO:0007829|PDB:1K7K"
FT HELIX 22..24
FT /evidence="ECO:0007829|PDB:1K7K"
FT STRAND 26..30
FT /evidence="ECO:0007829|PDB:1K7K"
FT TURN 31..35
FT /evidence="ECO:0007829|PDB:1K7K"
FT HELIX 46..61
FT /evidence="ECO:0007829|PDB:1K7K"
FT STRAND 65..74
FT /evidence="ECO:0007829|PDB:1K7K"
FT HELIX 75..77
FT /evidence="ECO:0007829|PDB:1K7K"
FT HELIX 82..84
FT /evidence="ECO:0007829|PDB:1K7K"
FT TURN 86..89
FT /evidence="ECO:0007829|PDB:1K7K"
FT HELIX 95..105
FT /evidence="ECO:0007829|PDB:1K7K"
FT TURN 106..108
FT /evidence="ECO:0007829|PDB:1K7K"
FT HELIX 111..113
FT /evidence="ECO:0007829|PDB:1K7K"
FT STRAND 115..127
FT /evidence="ECO:0007829|PDB:1K7K"
FT STRAND 134..144
FT /evidence="ECO:0007829|PDB:1K7K"
FT STRAND 152..154
FT /evidence="ECO:0007829|PDB:1K7K"
FT HELIX 157..159
FT /evidence="ECO:0007829|PDB:1K7K"
FT HELIX 163..165
FT /evidence="ECO:0007829|PDB:1K7K"
FT STRAND 166..168
FT /evidence="ECO:0007829|PDB:1K7K"
FT HELIX 169..171
FT /evidence="ECO:0007829|PDB:1K7K"
FT HELIX 174..180
FT /evidence="ECO:0007829|PDB:1K7K"
FT HELIX 182..195
FT /evidence="ECO:0007829|PDB:1K7K"
SQ SEQUENCE 197 AA; 21039 MW; 74E82A59B1A9E294 CRC64;
MQKVVLATGN VGKVRELASL LSDFGLDIVA QTDLGVDSAE ETGLTFIENA ILKARHAAKV
TALPAIADDS GLAVDVLGGA PGIYSARYSG EDATDQKNLQ KLLETMKDVP DDQRQARFHC
VLVYLRHAED PTPLVCHGSW PGVITREPAG TGGFGYDPIF FVPSEGKTAA ELTREEKSAI
SHRGQALKLL LDALRNG
