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Protein

Dihydroneopterin triphosphate diphosphatase

Gene

nudB

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

Functioni

Catalyzes the hydrolysis of dihydroneopterin triphosphate to dihydroneopterin monophosphate and pyrophosphate. Required for efficient folate biosynthesis. Can also hydrolyze nucleoside triphosphates with a preference for dATP.2 Publications

Catalytic activityi

7,8-dihydroneopterin 3'-triphosphate + H2O = 7,8-dihydroneopterin 3'-phosphate + diphosphate.1 Publication

Cofactori

Mg2+1 PublicationNote: Binds 1 Mg2+ ion per subunit.1 Publication

Enzyme regulationi

Subject to product inhibition by pyrophosphate.1 Publication

Kineticsi

  1. KM=0.27 mM for dihydroneopterin triphosphate2 Publications
  2. KM=0.79 mM for dATP2 Publications

    pH dependencei

    Optimum pH is 8.5-9.2 Publications

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei7Substrate1
    Binding sitei29Substrate1
    Binding sitei40Substrate1
    Metal bindingi56Magnesium1
    Metal bindingi60Magnesium1
    Metal bindingi117Magnesium1
    Binding sitei135SubstrateSequence analysis1

    GO - Molecular functioni

    • dATP pyrophosphohydrolase activity Source: EcoCyc
    • dihydroneopterin triphosphate pyrophosphohydrolase activity Source: EcoCyc
    • magnesium ion binding Source: EcoCyc

    GO - Biological processi

    • folic acid biosynthetic process Source: EcoCyc
    • tetrahydrofolate biosynthetic process Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Folate biosynthesis

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:H2NEOPTERINP3PYROPHOSPHOHYDRO-MONOMER.
    ECOL316407:JW1854-MONOMER.
    MetaCyc:H2NEOPTERINP3PYROPHOSPHOHYDRO-MONOMER.
    BRENDAi3.6.1.B15. 2026.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Dihydroneopterin triphosphate diphosphatase (EC:3.6.1.671 Publication)
    Alternative name(s):
    Dihydroneopterin triphosphate pyrophosphatase
    dATP pyrophosphohydrolase
    Gene namesi
    Name:nudB
    Synonyms:ntpA
    Ordered Locus Names:b1865, JW1854
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11138. nudB.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000569521 – 150Dihydroneopterin triphosphate diphosphataseAdd BLAST150

    Proteomic databases

    PaxDbiP0AFC0.
    PRIDEiP0AFC0.

    Interactioni

    Protein-protein interaction databases

    BioGridi4260348. 315 interactors.
    DIPiDIP-10372N.
    IntActiP0AFC0. 7 interactors.
    STRINGi511145.b1865.

    Structurei

    Secondary structure

    1150
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi9 – 18Combined sources10
    Turni19 – 21Combined sources3
    Beta strandi23 – 28Combined sources6
    Beta strandi30 – 32Combined sources3
    Beta strandi36 – 42Combined sources7
    Helixi49 – 61Combined sources13
    Helixi65 – 68Combined sources4
    Beta strandi72 – 82Combined sources11
    Helixi85 – 90Combined sources6
    Beta strandi97 – 109Combined sources13
    Beta strandi116 – 119Combined sources4
    Beta strandi121 – 125Combined sources5
    Helixi126 – 132Combined sources7
    Helixi136 – 145Combined sources10

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2O1CX-ray1.80A/B/C/D1-150[»]
    2O5WX-ray2.60A/B/C/D1-150[»]
    ProteinModelPortaliP0AFC0.
    SMRiP0AFC0.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0AFC0.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini5 – 146Nudix hydrolasePROSITE-ProRule annotationAdd BLAST142

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni81 – 84Substrate bindingSequence analysis4

    Motif

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Motifi41 – 62Nudix boxAdd BLAST22

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiENOG4108TIT. Bacteria.
    COG0494. LUCA.
    HOGENOMiHOG000264405.
    InParanoidiP0AFC0.
    KOiK08310.
    OMAiVTRNTEH.

    Family and domain databases

    Gene3Di3.90.79.10. 1 hit.
    InterProiIPR003564. DHNTPase.
    IPR020084. NUDIX_hydrolase_CS.
    IPR000086. NUDIX_hydrolase_dom.
    IPR015797. NUDIX_hydrolase_dom-like.
    [Graphical view]
    PfamiPF00293. NUDIX. 1 hit.
    [Graphical view]
    PRINTSiPR01404. NPPPHYDRLASE.
    SUPFAMiSSF55811. SSF55811. 1 hit.
    PROSITEiPS51462. NUDIX. 1 hit.
    PS00893. NUDIX_BOX. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P0AFC0-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKDKVYKRPV SILVVIYAQD TKRVLMLQRR DDPDFWQSVT GSVEEGETAP
    60 70 80 90 100
    QAAMREVKEE VTIDVVAEQL TLIDCQRTVE FEIFSHLRHR YAPGVTRNTE
    110 120 130 140 150
    SWFCLALPHE RQIVFTEHLA YKWLDAPAAA ALTKSWSNRQ AIEQFVINAA
    Length:150
    Mass (Da):17,306
    Last modified:December 20, 2005 - v1
    Checksum:iB4F05FA056F3BA07
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X59551 Genomic DNA. Translation: CAA42124.1.
    D10165 Genomic DNA. Translation: BAA01029.1.
    U00096 Genomic DNA. Translation: AAC74935.1.
    AP009048 Genomic DNA. Translation: BAA15676.1.
    PIRiB38113.
    RefSeqiNP_416379.1. NC_000913.3.

    Genome annotation databases

    EnsemblBacteriaiAAC74935; AAC74935; b1865.
    BAA15676; BAA15676; BAA15676.
    GeneIDi946383.
    KEGGiecj:JW1854.
    eco:b1865.
    PATRICi32119053. VBIEscCol129921_1944.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X59551 Genomic DNA. Translation: CAA42124.1.
    D10165 Genomic DNA. Translation: BAA01029.1.
    U00096 Genomic DNA. Translation: AAC74935.1.
    AP009048 Genomic DNA. Translation: BAA15676.1.
    PIRiB38113.
    RefSeqiNP_416379.1. NC_000913.3.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2O1CX-ray1.80A/B/C/D1-150[»]
    2O5WX-ray2.60A/B/C/D1-150[»]
    ProteinModelPortaliP0AFC0.
    SMRiP0AFC0.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4260348. 315 interactors.
    DIPiDIP-10372N.
    IntActiP0AFC0. 7 interactors.
    STRINGi511145.b1865.

    Proteomic databases

    PaxDbiP0AFC0.
    PRIDEiP0AFC0.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC74935; AAC74935; b1865.
    BAA15676; BAA15676; BAA15676.
    GeneIDi946383.
    KEGGiecj:JW1854.
    eco:b1865.
    PATRICi32119053. VBIEscCol129921_1944.

    Organism-specific databases

    EchoBASEiEB1128.
    EcoGeneiEG11138. nudB.

    Phylogenomic databases

    eggNOGiENOG4108TIT. Bacteria.
    COG0494. LUCA.
    HOGENOMiHOG000264405.
    InParanoidiP0AFC0.
    KOiK08310.
    OMAiVTRNTEH.

    Enzyme and pathway databases

    BioCyciEcoCyc:H2NEOPTERINP3PYROPHOSPHOHYDRO-MONOMER.
    ECOL316407:JW1854-MONOMER.
    MetaCyc:H2NEOPTERINP3PYROPHOSPHOHYDRO-MONOMER.
    BRENDAi3.6.1.B15. 2026.

    Miscellaneous databases

    EvolutionaryTraceiP0AFC0.
    PROiP0AFC0.

    Family and domain databases

    Gene3Di3.90.79.10. 1 hit.
    InterProiIPR003564. DHNTPase.
    IPR020084. NUDIX_hydrolase_CS.
    IPR000086. NUDIX_hydrolase_dom.
    IPR015797. NUDIX_hydrolase_dom-like.
    [Graphical view]
    PfamiPF00293. NUDIX. 1 hit.
    [Graphical view]
    PRINTSiPR01404. NPPPHYDRLASE.
    SUPFAMiSSF55811. SSF55811. 1 hit.
    PROSITEiPS51462. NUDIX. 1 hit.
    PS00893. NUDIX_BOX. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiNUDB_ECOLI
    AccessioniPrimary (citable) accession number: P0AFC0
    Secondary accession number(s): P24236
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 20, 2005
    Last sequence update: December 20, 2005
    Last modified: November 2, 2016
    This is version 87 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, 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.