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Protein

dITP/XTP pyrophosphatase

Gene

rdgB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Pyrophosphatase that catalyzes the hydrolysis of nucleoside triphosphates to their monophosphate derivatives, with a high preference for the non-canonical purine nucleotides XTP (xanthosine triphosphate), dITP (deoxyinosine triphosphate) and ITP (PubMed:12297000, PubMed:17976651). Can also efficiently hydrolyze 2'-deoxy-N-6-hydroxylaminopurine triphosphate (dHAPTP) (PubMed:17090528). Seems to function as a house-cleaning enzyme that removes non-canonical purine nucleotides from the nucleotide pool, thus preventing their incorporation into DNA/RNA and avoiding chromosomal lesions (PubMed:12297000, PubMed:12730170, PubMed:17090528). To a much lesser extent, is also able to hydrolyze GTP, dGTP and dUTP, but shows very low activity toward the canonical nucleotides dATP, dCTP and dTTP and toward 8-oxo-dGTP, purine deoxyribose triphosphate, 2-aminopurine deoxyribose triphosphate and 2,6-diaminopurine deoxyribose triphosphate (PubMed:12297000, PubMed:17090528).UniRule annotation4 Publications

Miscellaneous

Modified or damaged nucleotides such as 6-chloropurine deoxyribose triphosphate, 8-Br-dGTP, 5-Br-dCTP, 5-Br-dUTP, 7-deaza-dGTP, 7-methyl-GTP, N6-etheno-ATP, NAD, NADH, FAD, ADP-ribose, UPD-glucose, AppA and ApppA are not hydrolyzed by the enzyme.1 Publication
The aberrant nucleotides XTP and dITP can be produced by oxidative deamination from purine nucleotides in cells; they are potentially mutagenic.Curated

Catalytic activityi

XTP + H2O = XMP + diphosphate.UniRule annotation2 Publications
dITP + H2O = dIMP + diphosphate.UniRule annotation3 Publications
ITP + H2O = IMP + diphosphate.UniRule annotation2 Publications

Cofactori

Mg2+2 Publications, Mn2+1 Publication, Ni2+1 PublicationNote: Binds 1 divalent metal cation per subunit. Maximum activity is obtained with Mg2+. Activity with Mn2+ or Ni2+ makes up 60-75% of the maximum rate.1 Publication

Kineticsi

Vmax values are similar for XTP, dITP and ITP. Activity toward dATP, dCTP and dTTP is less than 1% of the rate of XTP hydrolysis. dGTP and dUTP are hydrolyzed at 10-12% of the rate of XTP hydrolysis (PubMed:12297000). kcat is 5.7 sec(-1) with ITP or dHAPTP as substrate. kcat is 1.5 sec(-1) with dGTP as substrate (at pH 9.5 and 37 degrees Celsius) (PubMed:17090528). kcat is 19.9 sec(-1) with XTP as substrate. kcat is 13.2 sec(-1) with dITP as substrate. kcat is 18.9 sec(-1) with ITP as substrate. kcat is 0.85 sec(-1) with GTP as substrate. kcat is 0.37 sec(-1) with dGTP as substrate. kcat is 0.26 sec(-1) with TTP as substrate (at pH 9.0 and 37 degrees Celsius) (PubMed:17976651).3 Publications
  1. KM=0.33 mM for XTP (at pH 10.0 and 37 degrees Celsius)1 Publication
  2. KM=0.36 mM for dITP (at pH 10.0 and 37 degrees Celsius)1 Publication
  3. KM=0.41 mM for ITP (at pH 10.0 and 37 degrees Celsius)1 Publication
  4. KM=22.0 µM for dITP (at pH 9.5 and 37 degrees Celsius)1 Publication
  5. KM=792 µM for dGTP (at pH 9.5 and 37 degrees Celsius)1 Publication
  6. KM=16.5 µM for dHAPTP (at pH 9.5 and 37 degrees Celsius)1 Publication
  7. KM=23.3 µM for XTP (at pH 9.0 and 37 degrees Celsius)1 Publication
  8. KM=11.3 µM for dITP (at pH 9.0 and 37 degrees Celsius)1 Publication
  9. KM=5.6 µM for ITP (at pH 9.0 and 37 degrees Celsius)1 Publication
  10. KM=312.6 µM for GTP (at pH 9.0 and 37 degrees Celsius)1 Publication
  11. KM=181.5 µM for dGTP (at pH 9.0 and 37 degrees Celsius)1 Publication
  12. KM=289.1 µM for TTP (at pH 9.0 and 37 degrees Celsius)1 Publication

    pH dependencei

    Optimum pH is 10-10.5 (PubMed:12297000). Optimum pH is 9.0 (PubMed:17976651). Reaction rates under neutral conditions are <40% of the maximum (PubMed:12297000).2 Publications

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Metal bindingi40MagnesiumUniRule annotation1
    Active sitei69Proton acceptor1 Publication1
    Metal bindingi69MagnesiumUniRule annotation1
    Binding sitei70Substrate; via amide nitrogenCombined sources1 Publication1
    Binding sitei177SubstrateCombined sources1 Publication1

    GO - Molecular functioni

    • dITP diphosphatase activity Source: UniProtKB
    • ITP diphosphatase activity Source: UniProtKB
    • magnesium ion binding Source: EcoCyc
    • nucleoside-triphosphatase activity Source: InterPro
    • nucleoside-triphosphate diphosphatase activity Source: EcoCyc
    • nucleotide binding Source: UniProtKB-KW
    • protein homodimerization activity Source: UniProtKB
    • XTP diphosphatase activity Source: UniProtKB

    GO - Biological processi

    • nucleoside triphosphate catabolic process Source: EcoCyc
    • nucleotide metabolic process Source: UniProtKB-KW
    • purine nucleoside triphosphate catabolic process Source: UniProtKB

    Keywordsi

    Molecular functionHydrolase
    Biological processNucleotide metabolism
    LigandMagnesium, Manganese, Metal-binding, Nickel, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:G7530-MONOMER.
    MetaCyc:G7530-MONOMER.
    BRENDAi3.6.1.19. 2026.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    dITP/XTP pyrophosphataseUniRule annotation2 Publications (EC:3.6.1.66UniRule annotation2 Publications)
    Alternative name(s):
    Deoxyribonucleoside triphosphate pyrophosphohydrolase1 Publication
    Inosine triphosphate pyrophosphatase1 Publication
    Short name:
    ITPase1 Publication
    Non-canonical purine NTP pyrophosphataseUniRule annotation1 Publication
    Non-standard purine NTP pyrophosphataseUniRule annotation1 Publication
    Nucleoside-triphosphate diphosphataseUniRule annotation1 Publication
    Nucleoside-triphosphate pyrophosphataseUniRule annotation1 Publication
    Short name:
    NTPase1 PublicationUniRule annotation
    Gene namesi
    Name:rdgBImported
    Synonyms:yggV
    Ordered Locus Names:b2954, JW2921
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG12982. rdgB.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: EcoCyc

    Pathology & Biotechi

    Disruption phenotypei

    Inactivation of this gene in a moa background (cells deficient in molybdopterin biosynthesis) results in increased N-6-hydroxylaminopurine (HAP) sensitivity, an increase in the level of mutagenesis, and increased recombination and SOS induction upon HAP exposure.1 Publication

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi8T → A: Greatly reduced ITP pyrophosphatase activity. 1 Publication1
    Mutagenesisi10N → A: Greatly reduced ITP pyrophosphatase activity. 1 Publication1
    Mutagenesisi13K → A: Complete loss of enzymatic activity. 1 Publication1
    Mutagenesisi41E → A: Complete loss of enzymatic activity. 1 Publication1
    Mutagenesisi53K → A: Complete loss of enzymatic activity. 1 Publication1
    Mutagenesisi68D → A: Greatly reduced ITP pyrophosphatase activity. 1 Publication1
    Mutagenesisi69D → A: Complete loss of enzymatic activity. 1 Publication1
    Mutagenesisi71G → A: Greatly reduced ITP pyrophosphatase activity. 1 Publication1
    Mutagenesisi154F → A: Greatly reduced ITP pyrophosphatase activity. 1 Publication1
    Mutagenesisi160F → A: Greatly reduced ITP pyrophosphatase activity. 1 Publication1
    Mutagenesisi183R → A: Greatly reduced ITP pyrophosphatase activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001781641 – 197dITP/XTP pyrophosphataseAdd BLAST197

    Proteomic databases

    PaxDbiP52061.
    PRIDEiP52061.

    Interactioni

    Subunit structurei

    Homodimer.UniRule annotation2 Publications

    GO - Molecular functioni

    • protein homodimerization activity Source: UniProtKB

    Protein-protein interaction databases

    BioGridi4260898. 67 interactors.
    851750. 2 interactors.
    IntActiP52061. 3 interactors.
    MINTiMINT-1322479.
    STRINGi316385.ECDH10B_3129.

    Structurei

    Secondary structure

    1197
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi2 – 7Combined sources6
    Helixi11 – 21Combined sources11
    Helixi22 – 24Combined sources3
    Beta strandi26 – 30Combined sources5
    Turni31 – 35Combined sources5
    Helixi46 – 61Combined sources16
    Beta strandi65 – 74Combined sources10
    Helixi75 – 77Combined sources3
    Helixi82 – 84Combined sources3
    Turni86 – 89Combined sources4
    Helixi95 – 105Combined sources11
    Turni106 – 108Combined sources3
    Helixi111 – 113Combined sources3
    Beta strandi115 – 127Combined sources13
    Beta strandi134 – 144Combined sources11
    Beta strandi152 – 154Combined sources3
    Helixi157 – 159Combined sources3
    Helixi163 – 165Combined sources3
    Beta strandi166 – 168Combined sources3
    Helixi169 – 171Combined sources3
    Helixi174 – 180Combined sources7
    Helixi182 – 195Combined sources14

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1K7KX-ray1.50A1-197[»]
    2PYUX-ray2.02A1-197[»]
    2Q16X-ray1.95A/B1-197[»]
    ProteinModelPortaliP52061.
    SMRiP52061.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP52061.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni8 – 13Substrate bindingUniRule annotationCombined sources1 Publication6
    Regioni154 – 157Substrate bindingUniRule annotationCombined sources1 Publication4
    Regioni182 – 183Substrate bindingUniRule annotationCombined sources1 Publication2

    Sequence similaritiesi

    Belongs to the HAM1 NTPase family.UniRule annotation

    Phylogenomic databases

    eggNOGiENOG4108V82. Bacteria.
    COG0127. LUCA.
    HOGENOMiHOG000293319.
    InParanoidiP52061.
    KOiK02428.
    PhylomeDBiP52061.

    Family and domain databases

    CDDicd00515. HAM1. 1 hit.
    Gene3Di3.90.950.10. 1 hit.
    HAMAPiMF_01405. Non_canon_purine_NTPase. 1 hit.
    InterProiView protein in InterPro
    IPR020922. dITP/XTP_pyrophosphatase.
    IPR002637. Ham1p-like.
    IPR029001. ITPase-like_fam.
    PANTHERiPTHR11067. PTHR11067. 1 hit.
    PfamiView protein in Pfam
    PF01725. Ham1p_like. 1 hit.
    SUPFAMiSSF52972. SSF52972. 1 hit.
    TIGRFAMsiTIGR00042. TIGR00042. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P52061-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MQKVVLATGN VGKVRELASL LSDFGLDIVA QTDLGVDSAE ETGLTFIENA
    60 70 80 90 100
    ILKARHAAKV TALPAIADDS GLAVDVLGGA PGIYSARYSG EDATDQKNLQ
    110 120 130 140 150
    KLLETMKDVP DDQRQARFHC VLVYLRHAED PTPLVCHGSW PGVITREPAG
    160 170 180 190
    TGGFGYDPIF FVPSEGKTAA ELTREEKSAI SHRGQALKLL LDALRNG
    Length:197
    Mass (Da):21,039
    Last modified:October 1, 1996 - v1
    Checksum:i74E82A59B1A9E294
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U28377 Genomic DNA. Translation: AAA69121.1.
    U00096 Genomic DNA. Translation: AAC75991.1.
    AP009048 Genomic DNA. Translation: BAE77017.1.
    PIRiA65081.
    RefSeqiNP_417429.1. NC_000913.3.
    WP_001174777.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75991; AAC75991; b2954.
    BAE77017; BAE77017; BAE77017.
    GeneIDi947429.
    KEGGiecj:JW2921.
    eco:b2954.
    PATRICifig|1411691.4.peg.3778.

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.

    Entry informationi

    Entry nameiIXTPA_ECOLI
    AccessioniPrimary (citable) accession number: P52061
    Secondary accession number(s): Q2M9N9
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1996
    Last sequence update: October 1, 1996
    Last modified: July 5, 2017
    This is version 134 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families