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Protein

2-dehydro-3-deoxygluconokinase

Gene

kdgK

Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the degradation of glucose via the semi-phosphorylative Entner-Doudoroff pathway. 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

Kcat is 11 (sec-1) for KDG and 2.2 (sec-1) for 2-keto-D-gluconate (at 35 degrees Celsius and pH 7.4).

  1. KM=0.32 mM for KDG (at 35 degrees Celsius and pH 7.4)1 Publication
  2. KM=3.6 mM for 2-keto-D-gluconate (at 35 degrees Celsius and pH 7.4)1 Publication

    pH dependencei

    Optimum pH is between 6 and 9.1 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. no protein annotated in this organism
    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 sitei89 – 891SubstrateBy similarity
    Binding sitei167 – 1671Substrate
    Binding sitei193 – 1931ATP1 Publication
    Active sitei251 – 2511Proton acceptor1 Publication
    Binding sitei251 – 2511Substrate
    Binding sitei275 – 2751ATP1 Publication
    Binding sitei287 – 2871Substrate

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi165 – 1673ATPBy similarity
    Nucleotide bindingi219 – 2257ATP1 Publication
    Nucleotide bindingi248 – 2514ATP1 Publication

    GO - Molecular functioni

    • 2-dehydro-3-deoxygluconokinase activity Source: UniProtKB
    • ATP binding Source: UniProtKB
    • nucleotide binding Source: UniProtKB
    • ribokinase activity Source: InterPro

    GO - Biological processi

    • carbohydrate phosphorylation Source: GOC
    • D-ribose metabolic process Source: InterPro
    • phosphorylation Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Kinase, Transferase

    Keywords - Biological processi

    Carbohydrate metabolism

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciTTHE300852:GH8R-2102-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
    Ordered Locus Names:TTHB079
    Encoded oniPlasmid pTT270 Publication
    OrganismiThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
    Taxonomic identifieri300852 [NCBI]
    Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus
    Proteomesi
    • UP000000532 Componenti: Plasmid pTT27

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 3093092-dehydro-3-deoxygluconokinasePRO_0000422662Add
    BLAST

    Interactioni

    Subunit structurei

    Homohexamer; trimer of dimers.1 Publication

    Structurei

    Secondary structure

    1
    309
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 86Combined sources
    Beta strandi11 – 155Combined sources
    Beta strandi17 – 204Combined sources
    Helixi22 – 243Combined sources
    Beta strandi27 – 337Combined sources
    Helixi35 – 4511Combined sources
    Beta strandi50 – 567Combined sources
    Helixi60 – 7213Combined sources
    Beta strandi79 – 813Combined sources
    Beta strandi88 – 936Combined sources
    Beta strandi99 – 1046Combined sources
    Helixi110 – 1123Combined sources
    Helixi120 – 1234Combined sources
    Beta strandi127 – 1326Combined sources
    Helixi135 – 1373Combined sources
    Helixi140 – 15415Combined sources
    Turni155 – 1573Combined sources
    Beta strandi159 – 1635Combined sources
    Turni168 – 1703Combined sources
    Helixi173 – 18311Combined sources
    Helixi184 – 1863Combined sources
    Beta strandi188 – 1936Combined sources
    Helixi194 – 2018Combined sources
    Helixi204 – 2107Combined sources
    Beta strandi214 – 2196Combined sources
    Helixi221 – 2233Combined sources
    Beta strandi225 – 2295Combined sources
    Beta strandi232 – 2354Combined sources
    Helixi249 – 26214Combined sources
    Helixi267 – 28216Combined sources
    Turni286 – 2905Combined sources
    Helixi294 – 2974Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1V19X-ray2.30A/B1-309[»]
    1V1AX-ray2.10A/B1-309[»]
    1V1BX-ray2.60A/B/C/D1-309[»]
    1V1SX-ray3.20A/B/C/D/E/F1-309[»]
    ProteinModelPortaliQ53W83.
    SMRiQ53W83. Positions 1-301.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ53W83.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni34 – 385Substrate binding
    Regioni103 – 1053Substrate binding

    Sequence similaritiesi

    Belongs to the carbohydrate kinase pfkB family.Curated

    Phylogenomic databases

    HOGENOMiHOG000235951.
    KOiK00874.
    OMAiIRQTDIC.
    OrthoDBiEOG68SW0Q.
    PhylomeDBiQ53W83.

    Family and domain databases

    Gene3Di3.40.1190.20. 1 hit.
    InterProiIPR002173. Carboh/pur_kinase_PfkB_CS.
    IPR011611. PfkB_dom.
    IPR002139. Ribokinase.
    IPR029056. Ribokinase-like.
    [Graphical view]
    PfamiPF00294. PfkB. 1 hit.
    [Graphical view]
    PRINTSiPR00990. RIBOKINASE.
    SUPFAMiSSF53613. SSF53613. 1 hit.
    PROSITEiPS00584. PFKB_KINASES_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q53W83-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MLEVVTAGEP LVALVPQEPG HLRGKRLLEV YVGGAEVNVA VALARLGVKV
    60 70 80 90 100
    GFVGRVGEDE LGAMVEERLR AEGVDLTHFR RAPGFTGLYL REYLPLGQGR
    110 120 130 140 150
    VFYYRKGSAG SALAPGAFDP DYLEGVRFLH LSGITPALSP EARAFSLWAM
    160 170 180 190 200
    EEAKRRGVRV SLDVNYRQTL WSPEEARGFL ERALPGVDLL FLSEEEAELL
    210 220 230 240 250
    FGRVEEALRA LSAPEVVLKR GAKGAWAFVD GRRVEGSAFA VEAVDPVGAG
    260 270 280 290 300
    DAFAAGYLAG AVWGLPVEER LRLANLLGAS VAASRGDHEG APYREDLEVL

    LKATQTFMR
    Length:309
    Mass (Da):33,430
    Last modified:May 24, 2005 - v1
    Checksum:iAC817D04B2B0A19B
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AP008227 Genomic DNA. Translation: BAD71875.1.
    RefSeqiWP_011229211.1. NC_006462.1.
    YP_145318.1. NC_006462.1.

    Genome annotation databases

    EnsemblBacteriaiBAD71875; BAD71875; BAD71875.
    GeneIDi3167896.
    KEGGittj:TTHB079.
    PATRICi23959084. VBITheThe93045_2023.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AP008227 Genomic DNA. Translation: BAD71875.1.
    RefSeqiWP_011229211.1. NC_006462.1.
    YP_145318.1. NC_006462.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1V19X-ray2.30A/B1-309[»]
    1V1AX-ray2.10A/B1-309[»]
    1V1BX-ray2.60A/B/C/D1-309[»]
    1V1SX-ray3.20A/B/C/D/E/F1-309[»]
    ProteinModelPortaliQ53W83.
    SMRiQ53W83. Positions 1-301.
    ModBaseiSearch...
    MobiDBiSearch...

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiBAD71875; BAD71875; BAD71875.
    GeneIDi3167896.
    KEGGittj:TTHB079.
    PATRICi23959084. VBITheThe93045_2023.

    Phylogenomic databases

    HOGENOMiHOG000235951.
    KOiK00874.
    OMAiIRQTDIC.
    OrthoDBiEOG68SW0Q.
    PhylomeDBiQ53W83.

    Enzyme and pathway databases

    UniPathwayiUPA00856; UER00828.
    BioCyciTTHE300852:GH8R-2102-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiQ53W83.

    Family and domain databases

    Gene3Di3.40.1190.20. 1 hit.
    InterProiIPR002173. Carboh/pur_kinase_PfkB_CS.
    IPR011611. PfkB_dom.
    IPR002139. Ribokinase.
    IPR029056. Ribokinase-like.
    [Graphical view]
    PfamiPF00294. PfkB. 1 hit.
    [Graphical view]
    PRINTSiPR00990. RIBOKINASE.
    SUPFAMiSSF53613. SSF53613. 1 hit.
    PROSITEiPS00584. PFKB_KINASES_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Complete genome sequence of Thermus thermophilus HB8."
      Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T., Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.
      Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: HB8 / ATCC 27634 / DSM 579.
    2. "Structure of Thermus thermophilus 2-Keto-3-deoxygluconate kinase: evidence for recognition of an open chain substrate."
      Ohshima N., Inagaki E., Yasuike K., Takio K., Tahirov T.H.
      J. Mol. Biol. 340:477-489(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) IN COMPLEX WITH 2-KETO-3-DEOXYGLUCONATE AND ATP, FUNCTION, CATALYTIC ACTIVITY, ACTIVE SITE, BIOPHYSICOCHEMICAL PROPERTIES, REACTION MECHANISM, SUBUNIT.

    Entry informationi

    Entry nameiKDGK_THET8
    AccessioniPrimary (citable) accession number: Q53W83
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 26, 2013
    Last sequence update: May 24, 2005
    Last modified: November 11, 2015
    This is version 79 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, Plasmid, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    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.