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Protein

Glycerol kinase

Gene

glpK

Organism
Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Key enzyme in the regulation of glycerol uptake and metabolism. Catalyzes the phosphorylation of glycerol to yield sn-glycerol 3-phosphate. Can utilize other nucleoside triphosphates (GTP, CTP, UTP AND ITP) as a phosphoryl donor.UniRule annotation1 Publication

Catalytic activityi

ATP + glycerol = ADP + sn-glycerol 3-phosphate.UniRule annotation1 Publication

Kineticsi

Kcat is 940 (sec-1) for glycerol (at pH 7.5 and 80 degrees Celsius).

  1. KM=15.4 µM for ATP (at pH 7.5 and 80 degrees Celsius)1 Publication
  2. KM=111 µM for glycerol (at pH 7.5 and 80 degrees Celsius)1 Publication

    pH dependencei

    Optimum pH is 8.0. It is highly thermosatble.1 Publication

    Temperature dependencei

    Optimum temperature is 80 degrees Celsius.1 Publication

    Pathwayi: glycerol degradation via glycerol kinase pathway

    This protein is involved in step 1 of the subpathway that synthesizes sn-glycerol 3-phosphate from glycerol.UniRule annotation
    Proteins known to be involved in this subpathway in this organism are:
    1. Glycerol kinase (glpK)
    This subpathway is part of the pathway glycerol degradation via glycerol kinase pathway, which is itself part of Polyol metabolism.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes sn-glycerol 3-phosphate from glycerol, the pathway glycerol degradation via glycerol kinase pathway and in Polyol metabolism.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei12 – 121SubstrateUniRule annotation
    Binding sitei16 – 161ATPUniRule annotation
    Binding sitei132 – 1321SubstrateUniRule annotation
    Binding sitei261 – 2611ATPUniRule annotation
    Binding sitei303 – 3031ATP; via carbonyl oxygenUniRule annotation
    Binding sitei307 – 3071ATP; via amide nitrogenUniRule annotation
    Binding sitei322 – 3221ATPUniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi12 – 143ATPUniRule annotation
    Nucleotide bindingi402 – 4065ATPUniRule annotation

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Kinase, Transferase

    Keywords - Biological processi

    Glycerol metabolism

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciTKOD69014:GH72-1417-MONOMER.
    BRENDAi2.7.1.30. 5246.
    UniPathwayiUPA00618; UER00672.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Glycerol kinaseUniRule annotation (EC:2.7.1.30UniRule annotation)
    Alternative name(s):
    ATP:glycerol 3-phosphotransferaseUniRule annotation
    GlycerokinaseUniRule annotation
    Short name:
    GKUniRule annotation
    Gene namesi
    Name:glpKUniRule annotation
    Ordered Locus Names:TK1396
    OrganismiThermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
    Taxonomic identifieri69014 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaeThermococcus
    Proteomesi
    • UP000000536 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 497497Glycerol kinasePRO_0000059530Add
    BLAST

    Interactioni

    Subunit structurei

    Homodimer.2 Publications

    Protein-protein interaction databases

    IntActiO93623. 1 interaction.
    MINTiMINT-8376983.
    STRINGi69014.TK1396.

    Structurei

    Secondary structure

    1
    497
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi4 – 107Combined sources
    Beta strandi12 – 209Combined sources
    Beta strandi26 – 338Combined sources
    Helixi48 – 6619Combined sources
    Helixi70 – 723Combined sources
    Beta strandi73 – 808Combined sources
    Beta strandi85 – 884Combined sources
    Beta strandi94 – 963Combined sources
    Helixi107 – 12519Combined sources
    Helixi134 – 14411Combined sources
    Helixi148 – 1536Combined sources
    Beta strandi158 – 1614Combined sources
    Helixi162 – 17110Combined sources
    Beta strandi175 – 1773Combined sources
    Helixi178 – 1814Combined sources
    Beta strandi184 – 1885Combined sources
    Turni189 – 1924Combined sources
    Helixi196 – 2016Combined sources
    Helixi206 – 2083Combined sources
    Beta strandi211 – 2133Combined sources
    Beta strandi215 – 2217Combined sources
    Helixi224 – 2274Combined sources
    Beta strandi232 – 2387Combined sources
    Helixi239 – 2468Combined sources
    Beta strandi255 – 27016Combined sources
    Beta strandi279 – 2879Combined sources
    Beta strandi290 – 30011Combined sources
    Helixi303 – 3119Combined sources
    Helixi319 – 3213Combined sources
    Helixi322 – 3265Combined sources
    Beta strandi329 – 3313Combined sources
    Beta strandi336 – 3383Combined sources
    Turni346 – 3483Combined sources
    Beta strandi355 – 3606Combined sources
    Helixi366 – 38823Combined sources
    Turni389 – 3913Combined sources
    Beta strandi397 – 4015Combined sources
    Helixi402 – 4054Combined sources
    Helixi407 – 41711Combined sources
    Beta strandi421 – 4255Combined sources
    Helixi429 – 44113Combined sources
    Helixi448 – 4525Combined sources
    Beta strandi457 – 4615Combined sources
    Helixi467 – 48216Combined sources
    Turni483 – 4864Combined sources
    Helixi487 – 4904Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2ZF5X-ray2.40O/Y1-497[»]
    ProteinModelPortaliO93623.
    SMRiO93623. Positions 1-494.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO93623.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni82 – 832Substrate bindingUniRule annotation
    Regioni239 – 2402Substrate bindingUniRule annotation

    Sequence similaritiesi

    Belongs to the FGGY kinase family.UniRule annotation

    Phylogenomic databases

    eggNOGiarCOG00024. Archaea.
    COG0554. LUCA.
    HOGENOMiHOG000222134.
    InParanoidiO93623.
    KOiK00864.
    OMAiPMEIFAT.

    Family and domain databases

    HAMAPiMF_00186. Glycerol_kin. 1 hit.
    InterProiIPR000577. Carb_kinase_FGGY.
    IPR018485. Carb_kinase_FGGY_C.
    IPR018483. Carb_kinase_FGGY_CS.
    IPR018484. Carb_kinase_FGGY_N.
    IPR005999. Glycerol_kin.
    [Graphical view]
    PfamiPF02782. FGGY_C. 1 hit.
    PF00370. FGGY_N. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000538. GlpK. 1 hit.
    TIGRFAMsiTIGR01311. glycerol_kin. 1 hit.
    PROSITEiPS00933. FGGY_KINASES_1. 1 hit.
    PS00445. FGGY_KINASES_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    O93623-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MEKFVLSLDE GTTSARAIIF DRESNIHGIG QYEFPQHYPR PGWVEHNPEE
    60 70 80 90 100
    IWDAQLRAIK DAIQSARIEP NQIAAIGVTN QRETTLVWDK DGKPLYNAIV
    110 120 130 140 150
    WQCRRTAEMV EEIKREYGTM IKEKTGLVPD AYFSASKLKW LLDNVPGLRE
    160 170 180 190 200
    KAEKGEVMFG TVDTFLIYRL TGEHVTDYSN ASRTMLFNIK KLDWDDELLE
    210 220 230 240 250
    LFDIPESVLP EVRESSEVYG YTKKELLGAE IPVSGDAGDQ QAALFGQAAF
    260 270 280 290 300
    EAGMVKATYG TGSFILVNTD KMVLYSDNLL TTIAWGLNGR VSYALEGSIF
    310 320 330 340 350
    VTGAAVQWLR DGIKIIKHAS ETEELATKLE SNEGVYFVPA FVGLGAPYWD
    360 370 380 390 400
    QFARGIIIGI TRGTGREHLA RATLEAIAYL TRDVVDEMEK LVQIKELRVD
    410 420 430 440 450
    GGATANDFLM QFQADILNRK VIRPVVKETT ALGAAYLAGL AVDYWADTRE
    460 470 480 490
    IAELWKAERI FEPKMDEKTR ERLYKGWKEA VKRAMGWAKV VDSAKSN
    Length:497
    Mass (Da):55,904
    Last modified:March 29, 2005 - v2
    Checksum:i7B55049D629CABA3
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti25 – 251N → D in BAA34909 (PubMed:9930671).Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB012099 Genomic DNA. Translation: BAA34909.1.
    AP006878 Genomic DNA. Translation: BAD85585.1.
    PIRiT43888.
    RefSeqiWP_011250347.1. NC_006624.1.

    Genome annotation databases

    EnsemblBacteriaiBAD85585; BAD85585; TK1396.
    GeneIDi3234882.
    KEGGitko:TK1396.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB012099 Genomic DNA. Translation: BAA34909.1.
    AP006878 Genomic DNA. Translation: BAD85585.1.
    PIRiT43888.
    RefSeqiWP_011250347.1. NC_006624.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2ZF5X-ray2.40O/Y1-497[»]
    ProteinModelPortaliO93623.
    SMRiO93623. Positions 1-494.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    IntActiO93623. 1 interaction.
    MINTiMINT-8376983.
    STRINGi69014.TK1396.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiBAD85585; BAD85585; TK1396.
    GeneIDi3234882.
    KEGGitko:TK1396.

    Phylogenomic databases

    eggNOGiarCOG00024. Archaea.
    COG0554. LUCA.
    HOGENOMiHOG000222134.
    InParanoidiO93623.
    KOiK00864.
    OMAiPMEIFAT.

    Enzyme and pathway databases

    UniPathwayiUPA00618; UER00672.
    BioCyciTKOD69014:GH72-1417-MONOMER.
    BRENDAi2.7.1.30. 5246.

    Miscellaneous databases

    EvolutionaryTraceiO93623.

    Family and domain databases

    HAMAPiMF_00186. Glycerol_kin. 1 hit.
    InterProiIPR000577. Carb_kinase_FGGY.
    IPR018485. Carb_kinase_FGGY_C.
    IPR018483. Carb_kinase_FGGY_CS.
    IPR018484. Carb_kinase_FGGY_N.
    IPR005999. Glycerol_kin.
    [Graphical view]
    PfamiPF02782. FGGY_C. 1 hit.
    PF00370. FGGY_N. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000538. GlpK. 1 hit.
    TIGRFAMsiTIGR01311. glycerol_kin. 1 hit.
    PROSITEiPS00933. FGGY_KINASES_1. 1 hit.
    PS00445. FGGY_KINASES_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiGLPK_THEKO
    AccessioniPrimary (citable) accession number: O93623
    Secondary accession number(s): Q5JGZ4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 30, 2000
    Last sequence update: March 29, 2005
    Last modified: September 7, 2016
    This is version 108 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    It is not sensitive to fructose-1,6-bisphosphate (FBP).1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, 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.