Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

dITP/XTP pyrophosphatase

Gene

MJ0226

Organism
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
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 xanthosine triphosphate (XTP), deoxyinosine triphosphate (dITP) and ITP (PubMed:10404228, PubMed:11452035). Probably functions 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:11452035). Shows very low activity on GTP or dGTP, both of which are hydrolyzed more than 100-fold less efficiently than XTP, and has nearly no activity toward the canonical nucleotides ATP, CTP, and TTP, and toward 6-N-hydroxylaminopurine deoxynucleoside triphosphate (dHAPTP) (PubMed:10404228, PubMed:11452035). Displays neither endonuclease nor 3'-exonuclease activities (PubMed:11452035).2 Publications

Catalytic activityi

XTP + H2O = XMP + diphosphate.2 Publications
dITP + H2O = dIMP + diphosphate.1 Publication
ITP + H2O = IMP + diphosphate.2 Publications

Cofactori

Mg2+2 PublicationsNote: Binds 1 Mg2+ ion per subunit (By similarity). Magnesium ions are required for optimal activity, with Mn2+, Zn2+ and Ni2+ supporting <50% of the maximum rate (PubMed:11452035).UniRule annotation2 Publications

Kineticsi

kcat is 1009 sec(-1) with XTP as substrate. kcat is 911.7 sec(-1) with ITP as substrate. kcat is 97.6 sec(-1) with GTP as substrate. kcat is 96.6 sec(-1) with dGTP as substrate (at pH 7.6 and 80 degrees Celsius) (PubMed:10404228). kcat is 176.4 sec(-1) with XTP as substrate. kcat is 152.4 sec(-1) with dITP as substrate. kcat is 155.8 sec(-1) with ITP as substrate. kcat is 9.3 sec(-1) with dGTP as substrate. kcat is 9.1 sec(-1) with GTP as substrate. kcat is 8.2 sec(-1) with 3'dGTP as substrate. kcat is 3.3 sec(-1) with ddGTP as substrate. kcat is 0.44 sec(-1) with dATP as substrate. kcat is 0.44 sec(-1) with dCTP as substrate. kcat is 1.8 sec(-1) with dTTP as substrate. kcat is 5.8 sec(-1) with dUTP as substrate. kcat is 2.4 sec(-1) with 8-oxo-dGTP as substrate. kcat is 1.8 sec(-1) with dHAPTP as substrate (at pH 10.5 and 80 degrees Celsius) (PubMed:11452035).2 Publications
  1. KM=0.10 mM for XTP (at pH 7.6 and 80 degrees Celsius)1 Publication
  2. KM=0.15 mM for ITP (at pH 7.6 and 80 degrees Celsius)1 Publication
  3. KM=1.11 mM for GTP (at pH 7.6 and 80 degrees Celsius)1 Publication
  4. KM=1.13 mM for dGTP (at pH 7.6 and 80 degrees Celsius)1 Publication
  5. KM=0.22 mM for XTP (at pH 10.5 and 80 degrees Celsius)1 Publication
  6. KM=0.25 mM for dITP (at pH 10.5 and 80 degrees Celsius)1 Publication
  7. KM=0.24 mM for ITP (at pH 10.5 and 80 degrees Celsius)1 Publication
  8. KM=2.12 mM for dGTP (at pH 10.5 and 80 degrees Celsius)1 Publication
  9. KM=1.94 mM for GTP (at pH 10.5 and 80 degrees Celsius)1 Publication
  10. KM=2.87 mM for 3'dGTP (at pH 10.5 and 80 degrees Celsius)1 Publication
  11. KM=2.78 mM for ddGTP (at pH 10.5 and 80 degrees Celsius)1 Publication
  12. KM=7.3 mM for dATP (at pH 10.5 and 80 degrees Celsius)1 Publication
  13. KM=5.47 mM for dCTP (at pH 10.5 and 80 degrees Celsius)1 Publication
  14. KM=4.4 mM for dTTP (at pH 10.5 and 80 degrees Celsius)1 Publication
  15. KM=4.22 mM for dUTP (at pH 10.5 and 80 degrees Celsius)1 Publication
  16. KM=5.3 mM for 8-oxo-dGTP (at pH 10.5 and 80 degrees Celsius)1 Publication
  17. KM=3.3 mM for dHAPTP (at pH 10.5 and 80 degrees Celsius)1 Publication

    pH dependencei

    Optimum pH is 10.5 with dITP as substrate. The reaction rates under neutral conditions are <30% of maximum.1 Publication

    Temperature dependencei

    Optimum temperature is 80 degrees Celsius. At low temperature (30 degrees Celsius), shows about 5-fold decrease in activity compared to the maximum activity at 80 degrees Celsius. Is highly thermostable. The half-life of the protein at 95 degrees Celsius is about 200 minutes.1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Metal bindingi37MagnesiumUniRule annotation1
    Active sitei65Proton acceptorUniRule annotation1
    Metal bindingi65MagnesiumUniRule annotation1
    Binding sitei66Substrate; via amide nitrogenUniRule annotation1
    Binding sitei164SubstrateUniRule annotation1

    GO - Molecular functioni

    GO - Biological processi

    Keywordsi

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

    Enzyme and pathway databases

    BRENDAi3.6.1.66. 3260.
    3.6.1.B14. 3260.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    dITP/XTP pyrophosphatase1 Publication (EC:3.6.1.661 Publication)
    Alternative name(s):
    Hypoxanthine/xanthine dNTP pyrophosphatase1 Publication
    Non-canonical purine NTP pyrophosphatase1 Publication
    Non-standard purine NTP pyrophosphatase1 Publication
    Nucleoside-triphosphate diphosphatase1 Publication
    Nucleoside-triphosphate pyrophosphatase1 Publication
    Short name:
    NTPase1 Publication
    Nucleotide triphosphatase1 Publication
    Gene namesi
    Ordered Locus Names:MJ0226
    OrganismiMethanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
    Taxonomic identifieri243232 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaMethanococciMethanococcalesMethanocaldococcaceaeMethanocaldococcus
    Proteomesi
    • UP000000805 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001782741 – 185dITP/XTP pyrophosphataseAdd BLAST185

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    STRINGi243232.MJ_0226.

    Structurei

    Secondary structure

    1185
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi3 – 6Combined sources4
    Helixi10 – 19Combined sources10
    Turni20 – 22Combined sources3
    Beta strandi28 – 31Combined sources4
    Beta strandi38 – 40Combined sources3
    Helixi42 – 57Combined sources16
    Beta strandi61 – 70Combined sources10
    Helixi71 – 73Combined sources3
    Helixi81 – 87Combined sources7
    Helixi89 – 97Combined sources9
    Beta strandi104 – 115Combined sources12
    Beta strandi118 – 130Combined sources13
    Helixi142 – 145Combined sources4
    Beta strandi146 – 149Combined sources4
    Helixi156 – 158Combined sources3
    Helixi161 – 164Combined sources4
    Turni165 – 167Combined sources3
    Helixi169 – 182Combined sources14

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1B78X-ray2.20A/B1-185[»]
    2MJPX-ray2.20A/B1-185[»]
    SMRiQ57679.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ57679.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni7 – 12Substrate bindingUniRule annotation6
    Regioni141 – 144Substrate bindingUniRule annotation4
    Regioni169 – 170Substrate bindingUniRule annotationCombined sources1 Publication2

    Sequence similaritiesi

    Belongs to the HAM1 NTPase family.UniRule annotation

    Phylogenomic databases

    eggNOGiarCOG04184. Archaea.
    COG0127. LUCA.
    InParanoidiQ57679.
    KOiK02428.
    OrthoDBiPOG093Z0DTZ.

    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
    IPR002637. Ham1p-like.
    IPR029001. ITPase-like_fam.
    IPR020922. NTPase.
    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.

    Q57679-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKIYFATGNP NKIKEANIIL KDLKDVEIEQ IKISYPEIQG TLEEVAEFGA
    60 70 80 90 100
    KWVYNILKKP VIVEDSGFFV EALNGFPGTY SKFVQETIGN EGILKLLEGK
    110 120 130 140 150
    DNRNAYFKTV IGYCDENGVR LFKGIVKGRV SEEIRSKGYG FAYDSIFIPE
    160 170 180
    EEERTFAEMT TEEKSQISHR KKAFEEFKKF LLDRI
    Length:185
    Mass (Da):21,273
    Last modified:June 28, 2011 - v2
    Checksum:i97EC2DA5C0D21D67
    GO

    Sequence cautioni

    The sequence AAB98211 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L77117 Genomic DNA. Translation: AAB98211.1. Different initiation.
    PIRiC64328.
    RefSeqiWP_064496428.1. NC_000909.1.

    Genome annotation databases

    EnsemblBacteriaiAAB98211; AAB98211; MJ_0226.
    GeneIDi1451077.
    KEGGimja:MJ_0226.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L77117 Genomic DNA. Translation: AAB98211.1. Different initiation.
    PIRiC64328.
    RefSeqiWP_064496428.1. NC_000909.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1B78X-ray2.20A/B1-185[»]
    2MJPX-ray2.20A/B1-185[»]
    SMRiQ57679.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi243232.MJ_0226.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAB98211; AAB98211; MJ_0226.
    GeneIDi1451077.
    KEGGimja:MJ_0226.

    Phylogenomic databases

    eggNOGiarCOG04184. Archaea.
    COG0127. LUCA.
    InParanoidiQ57679.
    KOiK02428.
    OrthoDBiPOG093Z0DTZ.

    Enzyme and pathway databases

    BRENDAi3.6.1.66. 3260.
    3.6.1.B14. 3260.

    Miscellaneous databases

    EvolutionaryTraceiQ57679.

    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
    IPR002637. Ham1p-like.
    IPR029001. ITPase-like_fam.
    IPR020922. NTPase.
    PANTHERiPTHR11067. PTHR11067. 1 hit.
    PfamiView protein in Pfam
    PF01725. Ham1p_like. 1 hit.
    SUPFAMiSSF52972. SSF52972. 1 hit.
    TIGRFAMsiTIGR00042. TIGR00042. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiIXTPA_METJA
    AccessioniPrimary (citable) accession number: Q57679
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: June 28, 2011
    Last modified: April 12, 2017
    This is version 117 of the entry and version 2 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. Methanococcus jannaschii
      Methanococcus jannaschii: entries and gene names
    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.