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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)DescriptionActionsGraphical viewLength
    Binding sitei12SubstrateUniRule annotation1
    Binding sitei16ATPUniRule annotation1
    Binding sitei132SubstrateUniRule annotation1
    Binding sitei261ATPUniRule annotation1
    Binding sitei303ATP; via carbonyl oxygenUniRule annotation1
    Binding sitei307ATP; via amide nitrogenUniRule annotation1
    Binding sitei322ATPUniRule annotation1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi12 – 14ATPUniRule annotation3
    Nucleotide bindingi402 – 406ATPUniRule annotation5

    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

    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)DescriptionActionsGraphical viewLength
    ChainiPRO_00000595301 – 497Glycerol kinaseAdd BLAST497

    Interactioni

    Subunit structurei

    Homodimer.2 Publications

    Protein-protein interaction databases

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

    Structurei

    Secondary structure

    1497
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi4 – 10Combined sources7
    Beta strandi12 – 20Combined sources9
    Beta strandi26 – 33Combined sources8
    Helixi48 – 66Combined sources19
    Helixi70 – 72Combined sources3
    Beta strandi73 – 80Combined sources8
    Beta strandi85 – 88Combined sources4
    Beta strandi94 – 96Combined sources3
    Helixi107 – 125Combined sources19
    Helixi134 – 144Combined sources11
    Helixi148 – 153Combined sources6
    Beta strandi158 – 161Combined sources4
    Helixi162 – 171Combined sources10
    Beta strandi175 – 177Combined sources3
    Helixi178 – 181Combined sources4
    Beta strandi184 – 188Combined sources5
    Turni189 – 192Combined sources4
    Helixi196 – 201Combined sources6
    Helixi206 – 208Combined sources3
    Beta strandi211 – 213Combined sources3
    Beta strandi215 – 221Combined sources7
    Helixi224 – 227Combined sources4
    Beta strandi232 – 238Combined sources7
    Helixi239 – 246Combined sources8
    Beta strandi255 – 270Combined sources16
    Beta strandi279 – 287Combined sources9
    Beta strandi290 – 300Combined sources11
    Helixi303 – 311Combined sources9
    Helixi319 – 321Combined sources3
    Helixi322 – 326Combined sources5
    Beta strandi329 – 331Combined sources3
    Beta strandi336 – 338Combined sources3
    Turni346 – 348Combined sources3
    Beta strandi355 – 360Combined sources6
    Helixi366 – 388Combined sources23
    Turni389 – 391Combined sources3
    Beta strandi397 – 401Combined sources5
    Helixi402 – 405Combined sources4
    Helixi407 – 417Combined sources11
    Beta strandi421 – 425Combined sources5
    Helixi429 – 441Combined sources13
    Helixi448 – 452Combined sources5
    Beta strandi457 – 461Combined sources5
    Helixi467 – 482Combined sources16
    Turni483 – 486Combined sources4
    Helixi487 – 490Combined sources4

    3D structure databases

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

    Miscellaneous databases

    EvolutionaryTraceiO93623.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni82 – 83Substrate bindingUniRule annotation2
    Regioni239 – 240Substrate bindingUniRule annotation2

    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)DescriptionActionsGraphical viewLength
    Sequence conflicti25N → D in BAA34909 (PubMed:9930671).Curated1

    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
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2ZF5X-ray2.40O/Y1-497[»]
    ProteinModelPortaliO93623.
    SMRiO93623.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    IntActiO93623. 1 interactor.
    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.
    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: November 2, 2016
    This is version 110 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.