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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 hydrolyzes the non-canonical purine nucleotides deoxyinosine triphosphate (dITP) and xanthosine triphosphate (XTP) as well as 2'-deoxy-N-6-hydroxylaminopurine triposphate (dHAPTP) to their respective monophosphate derivatives. Probably excludes non-canonical purines from DNA precursor pool, thus preventing their incorporation into DNA and avoiding chromosomal lesions.UniRule annotation1 Publication

Catalytic activityi

A nucleoside triphosphate + H2O = a nucleotide + diphosphate.UniRule annotation1 Publication

Cofactori

Mg2+1 Publication, 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.

  1. KM=0.33 mM for XTP2 Publications
  2. KM=0.36 mM for dITP2 Publications
  3. KM=0.41 mM for ITP2 Publications
  4. KM=16.5 µM for dHAPTP2 Publications

    pH dependencei

    Optimum pH is 10-10.5.2 Publications

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi40 – 401Magnesium or manganeseUniRule annotation
    Metal bindingi69 – 691Magnesium or manganeseUniRule annotation
    Binding sitei157 – 1571SubstrateUniRule annotation
    Binding sitei177 – 1771SubstrateUniRule annotation
    Binding sitei183 – 1831SubstrateUniRule annotation

    GO - Molecular functioni

    • magnesium ion binding Source: EcoCyc
    • nucleoside-triphosphatase activity Source: InterPro
    • nucleoside-triphosphate diphosphatase activity Source: EcoCyc
    • nucleotide binding Source: UniProtKB-KW

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Nucleotide metabolism

    Keywords - Ligandi

    Magnesium, Manganese, Metal-binding, Nickel, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:G7530-MONOMER.
    ECOL316407:JW2921-MONOMER.
    MetaCyc:G7530-MONOMER.
    BRENDAi3.6.1.19. 2026.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    dITP/XTP pyrophosphataseUniRule annotation (EC:3.6.1.19UniRule annotation)
    Alternative name(s):
    Non-canonical purine NTP pyrophosphataseUniRule annotation
    Non-standard purine NTP pyrophosphataseUniRule annotation
    Nucleoside-triphosphate diphosphataseUniRule annotation
    Nucleoside-triphosphate pyrophosphataseUniRule annotation
    Short name:
    NTPaseUniRule annotation
    Gene namesi
    Name:rdgBUniRule annotation
    Synonyms:yggV
    Ordered Locus Names:b2954, JW2921
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG12982. rdgB.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: EcoCyc
    Complete GO annotation...

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 197197dITP/XTP pyrophosphatasePRO_0000178164Add
    BLAST

    Proteomic databases

    PaxDbiP52061.
    PRIDEiP52061.

    Interactioni

    Subunit structurei

    Homodimer.UniRule annotation1 Publication

    Protein-protein interaction databases

    BioGridi4260898. 67 interactions.
    851750. 2 interactions.
    IntActiP52061. 3 interactions.
    MINTiMINT-1322479.
    STRINGi511145.b2954.

    Structurei

    Secondary structure

    1
    197
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi2 – 76Combined sources
    Helixi11 – 2111Combined sources
    Helixi22 – 243Combined sources
    Beta strandi26 – 305Combined sources
    Turni31 – 355Combined sources
    Helixi46 – 6116Combined sources
    Beta strandi65 – 7410Combined sources
    Helixi75 – 773Combined sources
    Helixi82 – 843Combined sources
    Turni86 – 894Combined sources
    Helixi95 – 10511Combined sources
    Turni106 – 1083Combined sources
    Helixi111 – 1133Combined sources
    Beta strandi115 – 12713Combined sources
    Beta strandi134 – 14411Combined sources
    Beta strandi152 – 1543Combined sources
    Helixi157 – 1593Combined sources
    Helixi163 – 1653Combined sources
    Beta strandi166 – 1683Combined sources
    Helixi169 – 1713Combined sources
    Helixi174 – 1807Combined sources
    Helixi182 – 19514Combined sources

    3D structure databases

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

    Miscellaneous databases

    EvolutionaryTraceiP52061.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni8 – 136Substrate bindingUniRule annotation
    Regioni69 – 702Substrate bindingUniRule annotation

    Sequence similaritiesi

    Belongs to the HAM1 NTPase family.UniRule annotation

    Phylogenomic databases

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

    Family and domain databases

    CDDicd00515. HAM1. 1 hit.
    Gene3Di3.90.950.10. 1 hit.
    HAMAPiMF_01405. Non_canon_purine_NTPase. 1 hit.
    InterProiIPR002637. Ham1p-like.
    IPR029001. ITPase-like_fam.
    IPR020922. NTPase.
    [Graphical view]
    PANTHERiPTHR11067. PTHR11067. 1 hit.
    PfamiPF01725. Ham1p_like. 1 hit.
    [Graphical view]
    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.
    PATRICi32121320. VBIEscCol129921_3048.

    Cross-referencesi

    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.

    3D structure databases

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

    Protein-protein interaction databases

    BioGridi4260898. 67 interactions.
    851750. 2 interactions.
    IntActiP52061. 3 interactions.
    MINTiMINT-1322479.
    STRINGi511145.b2954.

    Proteomic databases

    PaxDbiP52061.
    PRIDEiP52061.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC75991; AAC75991; b2954.
    BAE77017; BAE77017; BAE77017.
    GeneIDi947429.
    KEGGiecj:JW2921.
    eco:b2954.
    PATRICi32121320. VBIEscCol129921_3048.

    Organism-specific databases

    EchoBASEiEB2807.
    EcoGeneiEG12982. rdgB.

    Phylogenomic databases

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

    Enzyme and pathway databases

    BioCyciEcoCyc:G7530-MONOMER.
    ECOL316407:JW2921-MONOMER.
    MetaCyc:G7530-MONOMER.
    BRENDAi3.6.1.19. 2026.

    Miscellaneous databases

    EvolutionaryTraceiP52061.
    PROiP52061.

    Family and domain databases

    CDDicd00515. HAM1. 1 hit.
    Gene3Di3.90.950.10. 1 hit.
    HAMAPiMF_01405. Non_canon_purine_NTPase. 1 hit.
    InterProiIPR002637. Ham1p-like.
    IPR029001. ITPase-like_fam.
    IPR020922. NTPase.
    [Graphical view]
    PANTHERiPTHR11067. PTHR11067. 1 hit.
    PfamiPF01725. Ham1p_like. 1 hit.
    [Graphical view]
    SUPFAMiSSF52972. SSF52972. 1 hit.
    TIGRFAMsiTIGR00042. TIGR00042. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiRDGB_ECOLI
    AccessioniPrimary (citable) accession number: P52061
    Secondary accession number(s): Q2M9N9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1996
    Last sequence update: October 1, 1996
    Last modified: September 7, 2016
    This is version 126 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Activity toward dATP, dCTP and dTTP is less than 1% of the rate of XTP hydrolysis. Activity toward dGTP and dUTP is 10-12% lower than activity toward XTP. 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.

    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

    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.