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Protein

Ribonucleotide monophosphatase NagD

Gene

nagD

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

Functioni

Catalyzes the dephosphorylation of an unusually broad range of substrate including deoxyribo- and ribonucleoside tri-, di-, and monophosphates, as well as polyphosphate and glucose-1-P (Glu1P).2 Publications

Catalytic activityi

A 5'-ribonucleotide + H2O = a ribonucleoside + phosphate.

Cofactori

Mg2+2 Publications, Mn2+2 Publications, Co2+2 Publications, Zn2+2 PublicationsNote: Magnesium. Can also use other divalent metal cations as manganese, cobalt or zinc.2 Publications

Kineticsi

  1. KM=160 µM for UMP (at pH 7 and at 25 degrees Celsius)1 Publication
  2. KM=400 µM for GMP (at pH 7 and at 25 degrees Celsius)1 Publication
  3. KM=840 µM for AMP (at pH 7 and at 25 degrees Celsius)1 Publication
  4. KM=840 µM for ribose-5-phosphate (at pH 7 and at 25 degrees Celsius)1 Publication
  5. KM=1470 µM for CMP (at pH 7 and at 25 degrees Celsius)1 Publication
  6. KM=1500 µM for dTMP (at pH 7 and at 25 degrees Celsius)1 Publication
  7. KM=1500 µM for pyridoxal 5-phosphate (at pH 7 and at 25 degrees Celsius)1 Publication
  8. KM=1700 µM for glycerol 3-phosphate (at pH 7 and at 25 degrees Celsius)1 Publication
  9. KM=5900 µM for glucose 6-phosphate (at pH 7 and at 25 degrees Celsius)1 Publication
  10. KM=6000 µM for glucosamine 6-phosphate (at pH 7 and at 25 degrees Celsius)1 Publication
  11. KM=6000 µM for dCMP (at pH 7 and at 25 degrees Celsius)1 Publication
  12. KM=6500 µM for dAMP (at pH 7 and at 25 degrees Celsius)1 Publication
  13. KM=7600 µM for dGMP (at pH 7 and at 25 degrees Celsius)1 Publication
  14. KM=7700 µM for dGMP (at pH 7 and at 25 degrees Celsius)1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Metal bindingi9Magnesium1
    Active sitei111
    Metal bindingi11Magnesium; via carbonyl oxygen1
    Binding sitei11Substrate1
    Sitei55Orients the Asp-11 for proton transfer during catalytic turnover1
    Sitei146Confers substrate specificity1
    Binding sitei176Substrate1
    Metal bindingi201Magnesium1

    GO - Molecular functioni

    • 5'-nucleotidase activity Source: UniProtKB
    • magnesium ion binding Source: UniProtKB

    GO - Biological processi

    • carbohydrate metabolic process Source: UniProtKB-KW
    • UMP catabolic process Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Carbohydrate metabolism

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:EG10634-MONOMER.
    ECOL316407:JW0661-MONOMER.
    MetaCyc:EG10634-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ribonucleotide monophosphatase NagD (EC:3.1.3.5)
    Gene namesi
    Name:nagD
    Ordered Locus Names:b0675, JW0661
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10634. nagD.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: EcoCyc
    Complete GO annotation...

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000966941 – 250Ribonucleotide monophosphatase NagDAdd BLAST250

    Proteomic databases

    EPDiP0AF24.
    PaxDbiP0AF24.
    PRIDEiP0AF24.

    Expressioni

    Inductioni

    By N-acetylglucosamine.Curated

    Interactioni

    Subunit structurei

    Monomer.1 Publication

    Protein-protein interaction databases

    BioGridi4259613. 9 interactors.
    DIPiDIP-6861N.
    IntActiP0AF24. 4 interactors.
    STRINGi511145.b0675.

    Structurei

    Secondary structure

    1250
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi5 – 9Combined sources5
    Turni12 – 14Combined sources3
    Helixi24 – 33Combined sources10
    Beta strandi38 – 43Combined sources6
    Helixi49 – 58Combined sources10
    Helixi65 – 67Combined sources3
    Beta strandi68 – 70Combined sources3
    Helixi71 – 80Combined sources10
    Beta strandi86 – 90Combined sources5
    Helixi94 – 101Combined sources8
    Beta strandi108 – 110Combined sources3
    Beta strandi112 – 116Combined sources5
    Helixi124 – 135Combined sources12
    Beta strandi139 – 143Combined sources5
    Beta strandi147 – 150Combined sources4
    Helixi156 – 167Combined sources12
    Helixi180 – 189Combined sources10
    Helixi193 – 195Combined sources3
    Beta strandi196 – 201Combined sources6
    Turni203 – 205Combined sources3
    Helixi206 – 212Combined sources7
    Beta strandi216 – 224Combined sources9
    Helixi227 – 230Combined sources4
    Beta strandi238 – 243Combined sources6
    Helixi244 – 246Combined sources3

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2C4NX-ray1.80A1-250[»]
    ProteinModelPortaliP0AF24.
    SMRiP0AF24.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0AF24.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni42 – 43Substrate binding2
    Regioni202 – 205Substrate binding4

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105D4U. Bacteria.
    COG0647. LUCA.
    HOGENOMiHOG000068105.
    InParanoidiP0AF24.
    KOiK02566.
    OMAiHSETSAM.
    PhylomeDBiP0AF24.

    Family and domain databases

    Gene3Di3.40.50.1000. 2 hits.
    3.40.50.10410. 1 hit.
    InterProiIPR023214. HAD-like_dom.
    IPR006357. HAD-SF_hydro_IIA.
    IPR023215. NPhePase-like_dom.
    [Graphical view]
    PfamiPF13344. Hydrolase_6. 1 hit.
    [Graphical view]
    SUPFAMiSSF56784. SSF56784. 1 hit.
    TIGRFAMsiTIGR01460. HAD-SF-IIA. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P0AF24-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MTIKNVICDI DGVLMHDNVA VPGAAEFLHG IMDKGLPLVL LTNYPSQTGQ
    60 70 80 90 100
    DLANRFATAG VDVPDSVFYT SAMATADFLR RQEGKKAYVV GEGALIHELY
    110 120 130 140 150
    KAGFTITDVN PDFVIVGETR SYNWDMMHKA AYFVANGARF IATNPDTHGR
    160 170 180 190 200
    GFYPACGALC AGIEKISGRK PFYVGKPSPW IIRAALNKMQ AHSEETVIVG
    210 220 230 240 250
    DNLRTDILAG FQAGLETILV LSGVSSLDDI DSMPFRPSWI YPSVAEIDVI
    Length:250
    Mass (Da):27,163
    Last modified:December 20, 2005 - v1
    Checksum:iCC256AE6FF58DEBA
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti97H → Y in AAC09327 (PubMed:2190615).Curated1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X14135 Genomic DNA. Translation: CAA32355.1.
    AF052007 Genomic DNA. Translation: AAC09327.1.
    U00096 Genomic DNA. Translation: AAC73769.1.
    AP009048 Genomic DNA. Translation: BAA35318.1.
    PIRiB64802.
    RefSeqiNP_415201.1. NC_000913.3.
    WP_000153129.1. NZ_LN832404.1.
    WP_000153136.1. NZ_CP014272.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73769; AAC73769; b0675.
    BAA35318; BAA35318; BAA35318.
    GeneIDi945283.
    KEGGiecj:JW0661.
    eco:b0675.
    PATRICi32116535. VBIEscCol129921_0700.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X14135 Genomic DNA. Translation: CAA32355.1.
    AF052007 Genomic DNA. Translation: AAC09327.1.
    U00096 Genomic DNA. Translation: AAC73769.1.
    AP009048 Genomic DNA. Translation: BAA35318.1.
    PIRiB64802.
    RefSeqiNP_415201.1. NC_000913.3.
    WP_000153129.1. NZ_LN832404.1.
    WP_000153136.1. NZ_CP014272.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2C4NX-ray1.80A1-250[»]
    ProteinModelPortaliP0AF24.
    SMRiP0AF24.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4259613. 9 interactors.
    DIPiDIP-6861N.
    IntActiP0AF24. 4 interactors.
    STRINGi511145.b0675.

    Proteomic databases

    EPDiP0AF24.
    PaxDbiP0AF24.
    PRIDEiP0AF24.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC73769; AAC73769; b0675.
    BAA35318; BAA35318; BAA35318.
    GeneIDi945283.
    KEGGiecj:JW0661.
    eco:b0675.
    PATRICi32116535. VBIEscCol129921_0700.

    Organism-specific databases

    EchoBASEiEB0628.
    EcoGeneiEG10634. nagD.

    Phylogenomic databases

    eggNOGiENOG4105D4U. Bacteria.
    COG0647. LUCA.
    HOGENOMiHOG000068105.
    InParanoidiP0AF24.
    KOiK02566.
    OMAiHSETSAM.
    PhylomeDBiP0AF24.

    Enzyme and pathway databases

    BioCyciEcoCyc:EG10634-MONOMER.
    ECOL316407:JW0661-MONOMER.
    MetaCyc:EG10634-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiP0AF24.
    PROiP0AF24.

    Family and domain databases

    Gene3Di3.40.50.1000. 2 hits.
    3.40.50.10410. 1 hit.
    InterProiIPR023214. HAD-like_dom.
    IPR006357. HAD-SF_hydro_IIA.
    IPR023215. NPhePase-like_dom.
    [Graphical view]
    PfamiPF13344. Hydrolase_6. 1 hit.
    [Graphical view]
    SUPFAMiSSF56784. SSF56784. 1 hit.
    TIGRFAMsiTIGR01460. HAD-SF-IIA. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiNAGD_ECOLI
    AccessioniPrimary (citable) accession number: P0AF24
    Secondary accession number(s): P15302
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 20, 2005
    Last sequence update: December 20, 2005
    Last modified: November 2, 2016
    This is version 90 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.