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Protein

2-dehydro-3-deoxygluconokinase

Gene

kdgK

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

Functioni

Catalyzes the phosphorylation of 2-keto-3-deoxygluconate (KDG) to produce 2-keto-3-deoxy-6-phosphogluconate (KDPG).1 Publication

Catalytic activityi

ATP + 2-dehydro-3-deoxy-D-gluconate = ADP + 2-dehydro-3-deoxy-6-phospho-D-gluconate.1 Publication

Kineticsi

  1. KM=1 µM for ATP1 Publication
  2. KM=1 µM for KDG1 Publication

    pH dependencei

    Optimum pH is around 6.1 Publication

    Pathwayi: 2-dehydro-3-deoxy-D-gluconate degradation

    This protein is involved in step 1 of the subpathway that synthesizes D-glyceraldehyde 3-phosphate and pyruvate from 2-dehydro-3-deoxy-D-gluconate.
    Proteins known to be involved in the 2 steps of the subpathway in this organism are:
    1. 2-dehydro-3-deoxygluconokinase (kdgK)
    2. KHG/KDPG aldolase (eda)
    This subpathway is part of the pathway 2-dehydro-3-deoxy-D-gluconate degradation, which is itself part of Carbohydrate acid metabolism.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes D-glyceraldehyde 3-phosphate and pyruvate from 2-dehydro-3-deoxy-D-gluconate, the pathway 2-dehydro-3-deoxy-D-gluconate degradation and in Carbohydrate acid metabolism.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei88 – 881SubstrateBy similarity
    Binding sitei170 – 1701SubstrateBy similarity
    Binding sitei197 – 1971ATPBy similarity
    Active sitei264 – 2641Proton acceptorBy similarity
    Binding sitei264 – 2641SubstrateBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi168 – 1703ATPBy similarity
    Nucleotide bindingi228 – 2347ATPBy similarity
    Nucleotide bindingi261 – 2644ATPBy similarity

    GO - Molecular functioni

    • 2-dehydro-3-deoxygluconokinase activity Source: EcoCyc
    • ATP binding Source: UniProtKB-KW

    GO - Biological processi

    • carbohydrate phosphorylation Source: GOC
    • cellular response to DNA damage stimulus Source: EcoliWiki
    • D-galacturonate catabolic process Source: EcoCyc
    • D-glucuronate catabolic process Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Kinase, Transferase

    Keywords - Biological processi

    Carbohydrate metabolism

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:DEOXYGLUCONOKIN-MONOMER.
    ECOL316407:JW5668-MONOMER.
    MetaCyc:DEOXYGLUCONOKIN-MONOMER.
    UniPathwayiUPA00856; UER00828.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    2-dehydro-3-deoxygluconokinase (EC:2.7.1.45)
    Alternative name(s):
    2-keto-3-deoxygluconokinase
    3-deoxy-2-oxo-D-gluconate kinase
    KDG kinase
    Gene namesi
    Name:kdgK
    Synonyms:yhjI
    Ordered Locus Names:b3526, JW5668
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG12253. kdgK.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: EcoCyc
    Complete GO annotation...

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 3093092-dehydro-3-deoxygluconokinasePRO_0000080085Add
    BLAST

    Proteomic databases

    PaxDbiP37647.
    PRIDEiP37647.

    Interactioni

    Protein-protein interaction databases

    BioGridi4262528. 7 interactions.
    DIPiDIP-10056N.
    IntActiP37647. 3 interactions.
    MINTiMINT-1219186.
    STRINGi511145.b3526.

    Structurei

    3D structure databases

    ProteinModelPortaliP37647.
    SMRiP37647. Positions 2-308.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni102 – 1043Substrate bindingBy similarity

    Sequence similaritiesi

    Belongs to the carbohydrate kinase PfkB family.Curated

    Phylogenomic databases

    eggNOGiENOG4107SS6. Bacteria.
    COG0524. LUCA.
    HOGENOMiHOG000235952.
    InParanoidiP37647.
    KOiK00874.
    OMAiRGAESCL.
    OrthoDBiEOG6NGVTW.
    PhylomeDBiP37647.

    Family and domain databases

    Gene3Di3.40.1190.20. 1 hit.
    InterProiIPR002173. Carboh/pur_kinase_PfkB_CS.
    IPR011611. PfkB_dom.
    IPR029056. Ribokinase-like.
    [Graphical view]
    PfamiPF00294. PfkB. 1 hit.
    [Graphical view]
    SUPFAMiSSF53613. SSF53613. 1 hit.
    PROSITEiPS00584. PFKB_KINASES_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P37647-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSKKIAVIGE CMIELSEKGA DVKRGFGGDT LNTSVYIARQ VDPAALTVHY
    60 70 80 90 100
    VTALGTDSFS QQMLDAWHGE NVDTSLTQRM ENRLPGLYYI ETDSTGERTF
    110 120 130 140 150
    YYWRNEAAAK FWLESEQSAA ICEELANFDY LYLSGISLAI LSPTSREKLL
    160 170 180 190 200
    SLLRECRANG GKVIFDNNYR PRLWASKEET QQVYQQMLEC TDIAFLTLDD
    210 220 230 240 250
    EDALWGQQPV EDVIARTHNA GVKEVVVKRG ADSCLVSIAG EGLVDVPAVK
    260 270 280 290 300
    LPKEKVIDTT AAGDSFSAGY LAVRLTGGSA EDAAKRGHLT ASTVIQYRGA

    IIPREAMPA
    Length:309
    Mass (Da):33,962
    Last modified:October 1, 1994 - v1
    Checksum:i53FCD14696BCFA33
    GO

    Sequence cautioni

    The sequence AAB18503.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00039 Genomic DNA. Translation: AAB18503.1. Different initiation.
    U00096 Genomic DNA. Translation: AAC76551.2.
    AP009048 Genomic DNA. Translation: BAE77768.1.
    PIRiS47747.
    RefSeqiNP_417983.2. NC_000913.3.
    WP_000037562.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC76551; AAC76551; b3526.
    BAE77768; BAE77768; BAE77768.
    GeneIDi948041.
    KEGGiecj:JW5668.
    eco:b3526.
    PATRICi32122516. VBIEscCol129921_3636.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00039 Genomic DNA. Translation: AAB18503.1. Different initiation.
    U00096 Genomic DNA. Translation: AAC76551.2.
    AP009048 Genomic DNA. Translation: BAE77768.1.
    PIRiS47747.
    RefSeqiNP_417983.2. NC_000913.3.
    WP_000037562.1. NZ_LN832404.1.

    3D structure databases

    ProteinModelPortaliP37647.
    SMRiP37647. Positions 2-308.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4262528. 7 interactions.
    DIPiDIP-10056N.
    IntActiP37647. 3 interactions.
    MINTiMINT-1219186.
    STRINGi511145.b3526.

    Proteomic databases

    PaxDbiP37647.
    PRIDEiP37647.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC76551; AAC76551; b3526.
    BAE77768; BAE77768; BAE77768.
    GeneIDi948041.
    KEGGiecj:JW5668.
    eco:b3526.
    PATRICi32122516. VBIEscCol129921_3636.

    Organism-specific databases

    EchoBASEiEB2163.
    EcoGeneiEG12253. kdgK.

    Phylogenomic databases

    eggNOGiENOG4107SS6. Bacteria.
    COG0524. LUCA.
    HOGENOMiHOG000235952.
    InParanoidiP37647.
    KOiK00874.
    OMAiRGAESCL.
    OrthoDBiEOG6NGVTW.
    PhylomeDBiP37647.

    Enzyme and pathway databases

    UniPathwayiUPA00856; UER00828.
    BioCyciEcoCyc:DEOXYGLUCONOKIN-MONOMER.
    ECOL316407:JW5668-MONOMER.
    MetaCyc:DEOXYGLUCONOKIN-MONOMER.

    Miscellaneous databases

    PROiP37647.

    Family and domain databases

    Gene3Di3.40.1190.20. 1 hit.
    InterProiIPR002173. Carboh/pur_kinase_PfkB_CS.
    IPR011611. PfkB_dom.
    IPR029056. Ribokinase-like.
    [Graphical view]
    PfamiPF00294. PfkB. 1 hit.
    [Graphical view]
    SUPFAMiSSF53613. SSF53613. 1 hit.
    PROSITEiPS00584. PFKB_KINASES_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Analysis of the Escherichia coli genome. V. DNA sequence of the region from 76.0 to 81.5 minutes."
      Sofia H.J., Burland V., Daniels D.L., Plunkett G. III, Blattner F.R.
      Nucleic Acids Res. 22:2576-2586(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    3. "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.
    4. "Study of the common degradative pathway of hexuronates in Escherichia coli K 12. Purification, properties and individuality of 2-keto-3-deoxy-D-gluconnokinase."
      Pouyssegur J., Stoeber F.
      Biochimie 53:771-781(1971) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES.

    Entry informationi

    Entry nameiKDGK_ECOLI
    AccessioniPrimary (citable) accession number: P37647
    Secondary accession number(s): P78117, Q2M7I8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1994
    Last sequence update: October 1, 1994
    Last modified: January 20, 2016
    This is version 124 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

    Complete proteome, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    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.