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Protein

Diadenosine hexaphosphate hydrolase

Gene

ndx1

Organism
Thermus thermophilus
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Specifically hydrolyzes (di)adenosine polyphosphates but not ATP or diadenosine triphosphate, generating ATP as the product. Diadenosine hexaphosphate (Ap6A) is the preferred substrate and its hydrolyzation yields 2 ATP. It is the only enzyme that symmetrically hydrolyzes Ap6A. It also hydrolyzes diadenosine pentaphosphate (Ap5A), diadenosine tetraphosphate (Ap4A), adenosine tetraphosphate (p4A) to produce ATP and ADP, ATP and AMP, ATP and inorganic orthophosphate, respectively.1 Publication

Catalytic activityi

P1,P(6)-bis(5'-adenosyl)hexaphosphate + H2O = 2 ATP.1 Publication
P1,P(5)-bis(5'-adenosyl)pentaphosphate + H2O = ATP + ADP.1 Publication
P1,P(4)-bis(5'-adenosyl)tetraphosphate + H2O = ATP + AMP.1 Publication

Cofactori

Mg2+1 Publication, Mn2+1 Publication, Zn2+1 Publication

Enzyme regulationi

Strongly inhibited by fluoride ions.1 Publication

Kineticsi

Kcat is 4.1 sec1- with Ap6A (at 25 degrees Celsius).

  1. KM=1 µM for p4A (at 25 degrees Celsius)1 Publication
  2. KM=1.1 µM for Ap4A (at 25 degrees Celsius)1 Publication
  3. KM=1.1 µM for Ap5A (at 25 degrees Celsius)1 Publication
  4. KM=1.4 µM for Ap6A (at 25 degrees Celsius)1 Publication
  5. KM=1.4 µM for diguanosine pentaphosphate (Gp5G) (at 25 degrees Celsius)1 Publication
  6. KM=9.3 µM for diguanosine tetraphosphate (Gp4G) (at 25 degrees Celsius)1 Publication

    pH dependencei

    Optimum pH is 8.1 Publication

    Temperature dependencei

    Optimum temperature is 70 degrees Celsius. Ndx1 is stable up to 95 degrees Celsius at pH 7.5.1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Metal bindingi46Magnesium, manganese or zinc1
    Metal bindingi50Magnesium, manganese or zincBy similarity1
    Binding sitei74Substrate1 Publication1
    Binding sitei112Substrate1 Publication1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi66 – 68ATP3
    Nucleotide bindingi110 – 112ATP3

    GO - Molecular functioni

    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Ligandi

    ATP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding, Zinc

    Enzyme and pathway databases

    BRENDAi3.6.1.61. 2305.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Diadenosine hexaphosphate hydrolase (EC:3.6.1.61)
    Short name:
    Ap6A hydrolase
    Alternative name(s):
    ATP-generating (di)nucleotide polyphosphate hydrolase
    ATP-generating Ap6A hydrolase
    Nudix protein
    Gene namesi
    Name:ndx1
    OrganismiThermus thermophilus
    Taxonomic identifieri274 [NCBI]
    Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi26W → A: Absence of protein-substrate interaction. 1 Publication1
    Mutagenesisi46E → Q: Strong decrease in catalytic efficiency. 1 Publication1
    Mutagenesisi49E → Q: Very little effect on hydrolase activity. 1 Publication1
    Mutagenesisi50E → Q: Strong decrease in catalytic efficiency. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00004227401 – 126Diadenosine hexaphosphate hydrolaseAdd BLAST126

    Interactioni

    Subunit structurei

    Homodimer.2 Publications

    Protein-protein interaction databases

    STRINGi262724.TTC1519.

    Structurei

    Secondary structure

    1126
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi2 – 10Combined sources9
    Beta strandi16 – 20Combined sources5
    Helixi39 – 51Combined sources13
    Beta strandi54 – 67Combined sources14
    Beta strandi73 – 85Combined sources13
    Beta strandi95 – 99Combined sources5
    Helixi101 – 107Combined sources7
    Helixi111 – 123Combined sources13

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1VC8X-ray2.00A/B1-126[»]
    1VC9X-ray2.30A/B1-126[»]
    1VCDX-ray1.70A/B1-126[»]
    ProteinModelPortaliQ75UV1.
    SMRiQ75UV1.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ75UV1.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini1 – 121Nudix hydrolasePROSITE-ProRule annotationAdd BLAST121

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni21 – 23Substrate binding3
    Regioni30 – 32Substrate binding3
    Regioni66 – 68Substrate binding3

    Motif

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Motifi31 – 52Nudix boxAdd BLAST22

    Sequence similaritiesi

    Belongs to the Nudix hydrolase family.Curated
    Contains 1 nudix hydrolase domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiENOG41062IR. Bacteria.
    COG0494. LUCA.
    KOiK18445.

    Family and domain databases

    Gene3Di3.90.79.10. 1 hit.
    InterProiIPR020476. Nudix_hydrolase.
    IPR020084. NUDIX_hydrolase_CS.
    IPR000086. NUDIX_hydrolase_dom.
    IPR015797. NUDIX_hydrolase_dom-like.
    [Graphical view]
    PfamiPF00293. NUDIX. 1 hit.
    [Graphical view]
    PRINTSiPR00502. NUDIXFAMILY.
    SUPFAMiSSF55811. SSF55811. 1 hit.
    PROSITEiPS51462. NUDIX. 1 hit.
    PS00893. NUDIX_BOX. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q75UV1-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MELGAGGVVF NAKREVLLLR DRMGFWVFPK GHPEPGESLE EAAVREVWEE
    60 70 80 90 100
    TGVRAEVLLP LYPTRYVNPK GVEREVHWFL MRGEGAPRLE EGMTGAGWFS
    110 120
    PEEARALLAF PEDLGLLEVA LERLPL
    Length:126
    Mass (Da):14,170
    Last modified:July 5, 2004 - v1
    Checksum:iDD5E2B3ECC839F4B
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB125632 Genomic DNA. Translation: BAD18071.1.
    RefSeqiYP_145146.1. NC_006461.1.

    Genome annotation databases

    GeneIDi3169127.
    KEGGittj:TTHA1880.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB125632 Genomic DNA. Translation: BAD18071.1.
    RefSeqiYP_145146.1. NC_006461.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1VC8X-ray2.00A/B1-126[»]
    1VC9X-ray2.30A/B1-126[»]
    1VCDX-ray1.70A/B1-126[»]
    ProteinModelPortaliQ75UV1.
    SMRiQ75UV1.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi262724.TTC1519.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    GeneIDi3169127.
    KEGGittj:TTHA1880.

    Phylogenomic databases

    eggNOGiENOG41062IR. Bacteria.
    COG0494. LUCA.
    KOiK18445.

    Enzyme and pathway databases

    BRENDAi3.6.1.61. 2305.

    Miscellaneous databases

    EvolutionaryTraceiQ75UV1.

    Family and domain databases

    Gene3Di3.90.79.10. 1 hit.
    InterProiIPR020476. Nudix_hydrolase.
    IPR020084. NUDIX_hydrolase_CS.
    IPR000086. NUDIX_hydrolase_dom.
    IPR015797. NUDIX_hydrolase_dom-like.
    [Graphical view]
    PfamiPF00293. NUDIX. 1 hit.
    [Graphical view]
    PRINTSiPR00502. NUDIXFAMILY.
    SUPFAMiSSF55811. SSF55811. 1 hit.
    PROSITEiPS51462. NUDIX. 1 hit.
    PS00893. NUDIX_BOX. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiNDX1_THETH
    AccessioniPrimary (citable) accession number: Q75UV1
    Secondary accession number(s): F6DFL8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 26, 2013
    Last sequence update: July 5, 2004
    Last modified: November 2, 2016
    This is version 77 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Direct protein sequencing

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. 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.