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Q8Y8D7

- NADK1_LISMO

UniProt

Q8Y8D7 - NADK1_LISMO

Protein

NAD kinase 1

Gene

nadK1

Organism
Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 77 (01 Oct 2014)
      Sequence version 1 (01 Mar 2002)
      Previous versions | rss
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    Functioni

    Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP.2 PublicationsUniRule annotation

    Catalytic activityi

    ATP + NAD+ = ADP + NADP+.1 PublicationUniRule annotation

    Cofactori

    Divalent metal ions.UniRule annotation

    Enzyme regulationi

    Competitively inhibited by 5'-thioacetyladenosine (TAA) and di-(5'-thioadenosine) (DTA).2 Publications

    Kineticsi

    Kcat is 13.78 sec(-1) for kinase activity with ATP (at pH 7.5 and 30 degrees Celsius). Kcat is 13.12 sec(-1) for kinase activity with NAD (at pH 7.5 and 30 degrees Celsius).

    1. KM=2.8 mM for ATP (at pH 7.5 and 30 degrees Celsius)1 Publication

    Vmax=6.67 µmol/min/mg enzyme (at pH 7.5 and 30 degrees Celsius)1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei45 – 451Proton acceptor1 PublicationUniRule annotation
    Binding sitei46 – 461NAD; via amide nitrogen1 PublicationUniRule annotation
    Binding sitei148 – 1481NADUniRule annotation
    Binding sitei150 – 1501NAD1 Publication
    Binding sitei158 – 1581NAD; via carbonyl oxygen1 PublicationUniRule annotation
    Binding sitei223 – 2231NAD1 PublicationUniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi45 – 462NAD1 PublicationUniRule annotation
    Nucleotide bindingi122 – 1232NAD1 PublicationUniRule annotation
    Nucleotide bindingi161 – 1666NAD1 PublicationUniRule annotation

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB
    2. metal ion binding Source: UniProtKB-HAMAP
    3. NAD+ kinase activity Source: UniProtKB
    4. NAD binding Source: UniProtKB

    GO - Biological processi

    1. NAD metabolic process Source: InterPro
    2. NADP biosynthetic process Source: UniProtKB

    Keywords - Molecular functioni

    Kinase, Transferase

    Keywords - Ligandi

    ATP-binding, NAD, NADP, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciLMON169963:LMO0968-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    NAD kinase 1UniRule annotation (EC:2.7.1.23UniRule annotation)
    Alternative name(s):
    ATP-dependent NAD kinaseUniRule annotation
    Gene namesi
    Name:nadK1UniRule annotation
    Ordered Locus Names:lmo0968
    OrganismiListeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
    Taxonomic identifieri169963 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesListeriaceaeListeria
    ProteomesiUP000000817: Chromosome

    Organism-specific databases

    GenoListiLMO0968.

    Subcellular locationi

    Cytoplasm UniRule annotation

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi45 – 451D → N: Only minor changes in the structure and a 10-fold decrease in the kinase activity. 1 Publication
    Mutagenesisi223 – 2231H → E: Twice less active than the wild-type. Its activity toward DTA is increased 2-fold. 2 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 264264NAD kinase 1PRO_0000120632Add
    BLAST

    Interactioni

    Subunit structurei

    Homotetramer.2 Publications

    Protein-protein interaction databases

    STRINGi169963.lmo0968.

    Structurei

    Secondary structure

    1
    264
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi2 – 76
    Helixi11 – 2414
    Turni26 – 283
    Beta strandi33 – 353
    Beta strandi37 – 448
    Helixi45 – 5410
    Helixi56 – 583
    Turni59 – 613
    Beta strandi63 – 719
    Beta strandi74 – 763
    Helixi80 – 823
    Helixi83 – 919
    Beta strandi96 – 11217
    Beta strandi115 – 13117
    Beta strandi133 – 1397
    Beta strandi142 – 15514
    Helixi158 – 1614
    Helixi163 – 1664
    Beta strandi178 – 1858
    Beta strandi189 – 1913
    Beta strandi199 – 2024
    Beta strandi207 – 2137
    Beta strandi217 – 2215
    Beta strandi224 – 2285
    Beta strandi230 – 24718
    Helixi253 – 2619

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2I1WX-ray2.34A/B/C/D1-264[»]
    2I29X-ray2.10A1-264[»]
    2I2AX-ray2.10A1-264[»]
    2I2BX-ray2.10A1-264[»]
    2I2CX-ray1.85A1-264[»]
    2I2DX-ray2.22A1-264[»]
    2I2FX-ray1.90A1-264[»]
    2Q5FX-ray1.90A1-264[»]
    3V7UX-ray1.97A1-264[»]
    3V7WX-ray2.01A1-264[»]
    3V7YX-ray1.97A1-264[»]
    3V80X-ray2.03A1-264[»]
    3V8MX-ray2.48A1-264[»]
    3V8NX-ray2.38A1-264[»]
    3V8PX-ray2.29A1-264[»]
    3V8QX-ray2.37A1-264[»]
    3V8RX-ray2.39A1-264[»]
    4DY6X-ray2.20A1-264[»]
    ProteinModelPortaliQ8Y8D7.
    SMRiQ8Y8D7. Positions 1-264.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ8Y8D7.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the NAD kinase family.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0061.
    HOGENOMiHOG000275803.
    KOiK00858.
    OMAiQWITIVP.
    OrthoDBiEOG6PZXDR.
    PhylomeDBiQ8Y8D7.

    Family and domain databases

    Gene3Di2.60.200.30. 1 hit.
    3.40.50.10330. 1 hit.
    HAMAPiMF_00361. NAD_kinase.
    InterProiIPR017438. ATP-NAD_kinase_dom_1.
    IPR016064. ATP-NAD_kinase_PpnK-typ.
    IPR017437. ATP-NAD_kinase_PpnK-typ_all-b.
    IPR002504. PolyP/ATP_NADK.
    [Graphical view]
    PANTHERiPTHR20275. PTHR20275. 1 hit.
    PfamiPF01513. NAD_kinase. 1 hit.
    [Graphical view]
    SUPFAMiSSF111331. SSF111331. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q8Y8D7-1 [UniParc]FASTAAdd to Basket

    « Hide

    MKYMITSKGD EKSDLLRLNM IAGFGEYDME YDDVEPEIVI SIGGDGTFLS    50
    AFHQYEERLD EIAFIGIHTG HLGFYADWRP AEADKLVKLL AKGEYQKVSY 100
    PLLKTTVKYG IGKKEATYLA LNESTVKSSG GPFVVDVVIN DIHFERFRGD 150
    GLCMSTPSGT TAYNKSLGGA LMHPSIEAMQ LTEMASINNR VYRTIGSPLV 200
    FPKHHVVSLQ PVNDKDFQIS VDHLSILHRD VQEIRYEVSA KKIHFARFRS 250
    FPFWRRVHDS FIED 264
    Length:264
    Mass (Da):29,933
    Last modified:March 1, 2002 - v1
    Checksum:i00E0BCC4CAD30653
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AL591977 Genomic DNA. Translation: CAC99046.1.
    PIRiAH1195.
    RefSeqiNP_464493.1. NC_003210.1.

    Genome annotation databases

    EnsemblBacteriaiCAC99046; CAC99046; CAC99046.
    GeneIDi986453.
    KEGGilmo:lmo0968.
    PATRICi20311034. VBILisMon69206_0995.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AL591977 Genomic DNA. Translation: CAC99046.1 .
    PIRi AH1195.
    RefSeqi NP_464493.1. NC_003210.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2I1W X-ray 2.34 A/B/C/D 1-264 [» ]
    2I29 X-ray 2.10 A 1-264 [» ]
    2I2A X-ray 2.10 A 1-264 [» ]
    2I2B X-ray 2.10 A 1-264 [» ]
    2I2C X-ray 1.85 A 1-264 [» ]
    2I2D X-ray 2.22 A 1-264 [» ]
    2I2F X-ray 1.90 A 1-264 [» ]
    2Q5F X-ray 1.90 A 1-264 [» ]
    3V7U X-ray 1.97 A 1-264 [» ]
    3V7W X-ray 2.01 A 1-264 [» ]
    3V7Y X-ray 1.97 A 1-264 [» ]
    3V80 X-ray 2.03 A 1-264 [» ]
    3V8M X-ray 2.48 A 1-264 [» ]
    3V8N X-ray 2.38 A 1-264 [» ]
    3V8P X-ray 2.29 A 1-264 [» ]
    3V8Q X-ray 2.37 A 1-264 [» ]
    3V8R X-ray 2.39 A 1-264 [» ]
    4DY6 X-ray 2.20 A 1-264 [» ]
    ProteinModelPortali Q8Y8D7.
    SMRi Q8Y8D7. Positions 1-264.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 169963.lmo0968.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai CAC99046 ; CAC99046 ; CAC99046 .
    GeneIDi 986453.
    KEGGi lmo:lmo0968.
    PATRICi 20311034. VBILisMon69206_0995.

    Organism-specific databases

    GenoListi LMO0968.

    Phylogenomic databases

    eggNOGi COG0061.
    HOGENOMi HOG000275803.
    KOi K00858.
    OMAi QWITIVP.
    OrthoDBi EOG6PZXDR.
    PhylomeDBi Q8Y8D7.

    Enzyme and pathway databases

    BioCyci LMON169963:LMO0968-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei Q8Y8D7.

    Family and domain databases

    Gene3Di 2.60.200.30. 1 hit.
    3.40.50.10330. 1 hit.
    HAMAPi MF_00361. NAD_kinase.
    InterProi IPR017438. ATP-NAD_kinase_dom_1.
    IPR016064. ATP-NAD_kinase_PpnK-typ.
    IPR017437. ATP-NAD_kinase_PpnK-typ_all-b.
    IPR002504. PolyP/ATP_NADK.
    [Graphical view ]
    PANTHERi PTHR20275. PTHR20275. 1 hit.
    Pfami PF01513. NAD_kinase. 1 hit.
    [Graphical view ]
    SUPFAMi SSF111331. SSF111331. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC BAA-679 / EGD-e.
    2. "NAD kinases use substrate-assisted catalysis for specific recognition of NAD."
      Poncet-Montange G., Assairi L., Arold S., Pochet S., Labesse G.
      J. Biol. Chem. 282:33925-33934(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF WILD-TYPE AND MUTANT ASN-45 IN COMPLEX WITH NAD AND NAD ANALOGS, FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF ASP-45 AND HIS-223, ACTIVE SITE, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
    3. "Screening and in situ synthesis using crystals of a NAD kinase lead to a potent antistaphylococcal compound."
      Gelin M., Poncet-Montange G., Assairi L., Morellato L., Huteau V., Dugue L., Dussurget O., Pochet S., Labesse G.
      Structure 20:1107-1117(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.97 ANGSTROMS) OF WILD-TYPE AND MUTANT GLU-223 IN COMPLEX WITH NAD ANALOGS, FUNCTION, MUTAGENESIS OF HIS-223, ENZYME REGULATION.

    Entry informationi

    Entry nameiNADK1_LISMO
    AccessioniPrimary (citable) accession number: Q8Y8D7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 25, 2002
    Last sequence update: March 1, 2002
    Last modified: October 1, 2014
    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, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3