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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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei7 – 71Substrate
    Binding sitei29 – 291Substrate
    Binding sitei40 – 401Substrate
    Metal bindingi56 – 561Magnesium
    Metal bindingi60 – 601Magnesium
    Metal bindingi117 – 1171Magnesium
    Binding sitei135 – 1351SubstrateSequence analysis

    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11138. nudB.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 150150Dihydroneopterin triphosphate diphosphatasePRO_0000056952Add
    BLAST

    Proteomic databases

    PaxDbiP0AFC0.

    Interactioni

    Protein-protein interaction databases

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

    Structurei

    Secondary structure

    1
    150
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi9 – 1810Combined sources
    Turni19 – 213Combined sources
    Beta strandi23 – 286Combined sources
    Beta strandi30 – 323Combined sources
    Beta strandi36 – 427Combined sources
    Helixi49 – 6113Combined sources
    Helixi65 – 684Combined sources
    Beta strandi72 – 8211Combined sources
    Helixi85 – 906Combined sources
    Beta strandi97 – 10913Combined sources
    Beta strandi116 – 1194Combined sources
    Beta strandi121 – 1255Combined sources
    Helixi126 – 1327Combined sources
    Helixi136 – 14510Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2O1CX-ray1.80A/B/C/D1-150[»]
    2O5WX-ray2.60A/B/C/D1-150[»]
    ProteinModelPortaliP0AFC0.
    SMRiP0AFC0. Positions 2-148.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0AFC0.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini5 – 146142Nudix hydrolasePROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni81 – 844Substrate bindingSequence analysis

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi41 – 6222Nudix boxAdd
    BLAST

    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.
    OrthoDBiEOG69WFKW.

    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
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2O1CX-ray1.80A/B/C/D1-150[»]
    2O5WX-ray2.60A/B/C/D1-150[»]
    ProteinModelPortaliP0AFC0.
    SMRiP0AFC0. Positions 2-148.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

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

    Proteomic databases

    PaxDbiP0AFC0.

    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.
    OrthoDBiEOG69WFKW.

    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...

    Publicationsi

    « Hide 'large scale' publications
    1. "Resolution of Holliday junctions in Escherichia coli: identification of the ruvC gene product as a 19-kilodalton protein."
      Sharples G.J., Lloyd R.G.
      J. Bacteriol. 173:7711-7715(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Molecular analysis of the Escherichia coli ruvC gene, which encodes a Holliday junction-specific endonuclease."
      Takahagi M., Iwasaki H., Nakata A., Shinagawa H.
      J. Bacteriol. 173:5747-5753(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    5. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    6. "Purification of the MutX protein of Streptococcus pneumoniae, a homologue of Escherichia coli MutT. Identification of a novel catalytic domain for nucleoside triphosphate pyrophosphohydrolase activity."
      Bullions L.C., Mejean V., Claverys J.-P., Bessman M.J.
      J. Biol. Chem. 269:12339-12344(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.
    7. "Escherichia coli orf17 codes for a nucleoside triphosphate pyrophosphohydrolase member of the MutT family of proteins. Cloning, purification, and characterization of the enzyme."
      O'Handley S.F., Frick D.N., Bullions L.C., Mildvan A.S., Bessman M.J.
      J. Biol. Chem. 271:24649-24654(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR.
    8. "Structure and function of the E. coli dihydroneopterin triphosphate pyrophosphatase: a Nudix enzyme involved in folate biosynthesis."
      Gabelli S.B., Bianchet M.A., Xu W., Dunn C.A., Niu Z.-D., Amzel L.M., Bessman M.J.
      Structure 15:1014-1022(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH PYROPHOSPHATE AND SAMARIUM IONS, FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES.

    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: April 13, 2016
    This is version 84 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.