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Protein

Glycerol kinase

Gene

glpK

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 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. It also catalyzes the phosphorylation of dihydroxyacetone, L-glyceraldehyde and D-glyceraldehyde. It uses only ATP.UniRule annotation3 Publications

Catalytic activityi

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

Enzyme regulationi

Activity of this regulatory enzyme is affected by several metabolites. The non-competitive allosteric inhibition by fructose 1,6-bisphosphate (FBP) causes alterations in the quaternary structure of the enzyme. FBP inhibition requires that the enzyme exist only in a tetrameric state. Salt such as KCl reduces the affinity of the tetrameric form of the enzyme for FBP. Unphosphorylated phosphocarrier protein EIIA-Glc (III-Glc), an integral component of the bacterial phosphotransferase (PTS) system, also inhibits non-competitively and allostericaly the activity. Unlike FBP, both the dimer and the tetramer appear to be fully sensitive to enzyme EIIA-Glc inhibition. Zn(+2) greatly enhances the inhibitory potency of EIIA-Glc. Both allosteric regulatory agents is strongly pH dependent, with maximal inhibition occurring at pH 6.5.8 Publications

Kineticsi

  1. KM=1.3 µM for glycerol4 Publications
  2. KM=400 µM for D-glyceraldehyde4 Publications
  3. KM=500 µM for dihydroxyacetone4 Publications
  4. KM=3 mM for L-glyceraldehyde4 Publications
  5. KM=4 mM for ATP4 Publications

    pH dependencei

    Optimum pH is 9.8.4 Publications

    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 sitei14SubstrateUniRule annotation1 Publication1
    Binding sitei18ATP1
    Binding sitei136SubstrateUniRule annotation1 Publication1
    Binding sitei268ATP1
    Binding sitei311ATP; via carbonyl oxygen1
    Binding sitei315ATP; via amide nitrogen1
    Binding sitei330ATP1
    Metal bindingi479Zinc; shared with EIIA-Glc1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi14 – 16ATP3
    Nucleotide bindingi412 – 416ATP5

    GO - Molecular functioni

    • ATP binding Source: UniProtKB-HAMAP
    • glycerol kinase activity Source: UniProtKB
    • metal ion binding Source: EcoCyc
    • zinc ion binding Source: UniProtKB

    GO - Biological processi

    • cellular response to DNA damage stimulus Source: EcoliWiki
    • glycerol-3-phosphate metabolic process Source: UniProtKB-HAMAP
    • glycerol catabolic process Source: UniProtKB-UniPathway
    • glycerol metabolic process Source: UniProtKB
    • phosphorylation Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Kinase, Transferase

    Keywords - Biological processi

    Glycerol metabolism

    Keywords - Ligandi

    ATP-binding, Metal-binding, Nucleotide-binding, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:GLYCEROL-KIN-MONOMER.
    ECOL316407:JW3897-MONOMER.
    MetaCyc:GLYCEROL-KIN-MONOMER.
    BRENDAi2.7.1.30. 2026.
    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:b3926, JW3897
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10398. glpK.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: UniProtKB
    Complete GO annotation...

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi59S → W: Abolishes inhibition of GK by FBP via disruption of the dimer-tetramer assembly reaction. Inhibition by EIIA-Glc is unchanged compared to wild type. The activity of this mutant is significantly higher than wild-type, and the Michaelis constants are increased slightly compared to wild-type. 1 Publication1
    Mutagenesisi66A → T: Although it completely abolishes FBP regulation and disruptes dimer-tetramer equilibrium, the crystal structure is essentially identical to the symmetric tetramer found in the FBP-bound form of the enzyme. 1 Publication1
    Mutagenesisi231G → D: Displays an increased enzymatic activity and a decreased allosteric regulation by FBP compared to wild-type. It displays a dimer form and is resistant to tetramer formation in the presence of FBP, whereas wild-type dimers are converted into inactive tetramers in the presence of FBP. 1 Publication1
    Mutagenesisi237R → A: Drastically reduces inhibition of GK by FBP and lowers, but did not eliminate, the ability of FBP to promote tetramer association. 1 Publication1
    Mutagenesisi305G → S in glpK22; abolishes glucose control of glycerol utilization. 1
    Mutagenesisi475I → D: It decreases Vmax to about 10% of the wild-type value and the affinity for substrate is increased about two- to fourfold. This mutation decreases the catalytic activity in a manner that is analogous to that obtained upon EIIA-Glc binding. It increases the affinity for FBP about fivefold. 1 Publication1
    Mutagenesisi480R → D: It decreases Vmax to about 10% of the wild-type value and the affinity for substrate is increased about two- to fourfold. This mutation decreases the catalytic activity in a manner that is analogous to that obtained upon EIIA-Glc binding. Regulation by FBP is not affected by this substitution. No inhibition by EIIA-Glc is observed, which is consistent with a decrease in affinity for EIIA-Glc of about 250-fold. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Initiator methionineiRemoved2 Publications
    ChainiPRO_00000594512 – 502Glycerol kinaseAdd BLAST501

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei233N6-malonyllysine1 Publication1

    Proteomic databases

    EPDiP0A6F3.
    PaxDbiP0A6F3.
    PRIDEiP0A6F3.

    2D gel databases

    SWISS-2DPAGEP0A6F3.

    Expressioni

    Inductioni

    By L-alpha-glycerol 3-phosphate.1 Publication

    Interactioni

    Subunit structurei

    Homotetramer and homodimer (in equilibrium). Heterodimer with EIIA-Glc (crr). Binds 1 zinc ion per glycerol kinase EIIA-Glc dimer. The zinc ion is important for dimerization.UniRule annotation9 Publications

    Protein-protein interaction databases

    BioGridi4263162. 380 interactors.
    DIPiDIP-36011N.
    IntActiP0A6F3. 15 interactors.
    STRINGi511145.b3926.

    Structurei

    Secondary structure

    1502
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi6 – 12Combined sources7
    Beta strandi14 – 22Combined sources9
    Beta strandi24 – 26Combined sources3
    Beta strandi28 – 35Combined sources8
    Beta strandi41 – 44Combined sources4
    Helixi50 – 68Combined sources19
    Helixi72 – 74Combined sources3
    Beta strandi75 – 82Combined sources8
    Beta strandi87 – 91Combined sources5
    Turni92 – 94Combined sources3
    Beta strandi97 – 99Combined sources3
    Helixi110 – 118Combined sources9
    Turni119 – 121Combined sources3
    Helixi122 – 129Combined sources8
    Helixi138 – 148Combined sources11
    Beta strandi149 – 151Combined sources3
    Helixi152 – 157Combined sources6
    Turni158 – 160Combined sources3
    Beta strandi161 – 164Combined sources4
    Helixi166 – 174Combined sources9
    Turni175 – 177Combined sources3
    Beta strandi181 – 183Combined sources3
    Helixi184 – 187Combined sources4
    Beta strandi190 – 194Combined sources5
    Turni195 – 198Combined sources4
    Helixi202 – 208Combined sources7
    Helixi212 – 214Combined sources3
    Beta strandi217 – 219Combined sources3
    Beta strandi221 – 228Combined sources8
    Beta strandi231 – 235Combined sources5
    Beta strandi238 – 245Combined sources8
    Helixi246 – 253Combined sources8
    Beta strandi262 – 275Combined sources14
    Beta strandi284 – 286Combined sources3
    Beta strandi288 – 293Combined sources6
    Turni295 – 297Combined sources3
    Beta strandi299 – 308Combined sources10
    Helixi311 – 319Combined sources9
    Beta strandi326 – 328Combined sources3
    Helixi330 – 334Combined sources5
    Beta strandi337 – 339Combined sources3
    Beta strandi344 – 346Combined sources3
    Helixi348 – 350Combined sources3
    Turni354 – 356Combined sources3
    Beta strandi363 – 368Combined sources6
    Helixi374 – 400Combined sources27
    Beta strandi405 – 411Combined sources7
    Helixi412 – 415Combined sources4
    Helixi417 – 427Combined sources11
    Beta strandi429 – 435Combined sources7
    Helixi439 – 451Combined sources13
    Beta strandi454 – 456Combined sources3
    Helixi458 – 460Combined sources3
    Turni461 – 463Combined sources3
    Beta strandi467 – 471Combined sources5
    Helixi477 – 494Combined sources18

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1BO5X-ray3.20O/Z2-502[»]
    1BOTX-ray3.05O/Z2-502[»]
    1BU6X-ray2.37O/X/Y/Z2-502[»]
    1BWFX-ray3.00O/Y2-502[»]
    1GLAX-ray2.60G2-502[»]
    1GLBX-ray2.60G2-502[»]
    1GLCX-ray2.65G2-502[»]
    1GLDX-ray2.93G2-502[»]
    1GLEX-ray2.94G2-502[»]
    1GLFX-ray2.62O/X/Y/Z2-502[»]
    1GLJX-ray3.00O/Y2-502[»]
    1GLLX-ray3.00O/Y2-502[»]
    3EZWX-ray2.00A/B/C/D/E/F/G/H2-501[»]
    ProteinModelPortaliP0A6F3.
    SMRiP0A6F3.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0A6F3.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni84 – 85Substrate binding2
    Regioni234 – 236Allosteric FBP inhibitor binding3
    Regioni246 – 247Substrate binding2

    Sequence similaritiesi

    Belongs to the FGGY kinase family.UniRule annotation

    Phylogenomic databases

    eggNOGiENOG4107QVN. Bacteria.
    COG0554. LUCA.
    HOGENOMiHOG000222134.
    InParanoidiP0A6F3.
    KOiK00864.
    OMAiPMEIFAT.
    PhylomeDBiP0A6F3.

    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.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P0A6F3-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MTEKKYIVAL DQGTTSSRAV VMDHDANIIS VSQREFEQIY PKPGWVEHDP
    60 70 80 90 100
    MEIWATQSST LVEVLAKADI SSDQIAAIGI TNQRETTIVW EKETGKPIYN
    110 120 130 140 150
    AIVWQCRRTA EICEHLKRDG LEDYIRSNTG LVIDPYFSGT KVKWILDHVE
    160 170 180 190 200
    GSRERARRGE LLFGTVDTWL IWKMTQGRVH VTDYTNASRT MLFNIHTLDW
    210 220 230 240 250
    DDKMLEVLDI PREMLPEVRR SSEVYGQTNI GGKGGTRIPI SGIAGDQQAA
    260 270 280 290 300
    LFGQLCVKEG MAKNTYGTGC FMLMNTGEKA VKSENGLLTT IACGPTGEVN
    310 320 330 340 350
    YALEGAVFMA GASIQWLRDE MKLINDAYDS EYFATKVQNT NGVYVVPAFT
    360 370 380 390 400
    GLGAPYWDPY ARGAIFGLTR GVNANHIIRA TLESIAYQTR DVLEAMQADS
    410 420 430 440 450
    GIRLHALRVD GGAVANNFLM QFQSDILGTR VERPEVREVT ALGAAYLAGL
    460 470 480 490 500
    AVGFWQNLDE LQEKAVIERE FRPGIETTER NYRYAGWKKA VKRAMAWEEH

    DE
    Length:502
    Mass (Da):56,231
    Last modified:January 23, 2007 - v2
    Checksum:i854B61EA4648AB80
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M18393 Genomic DNA. Translation: AAA23913.1.
    M55990 Genomic DNA. Translation: AAA23887.1.
    L19201 Genomic DNA. Translation: AAB03058.1.
    U00096 Genomic DNA. Translation: AAC76908.1.
    AP009048 Genomic DNA. Translation: BAE77384.1.
    X15054 Genomic DNA. Translation: CAA33154.1.
    U41468 Genomic DNA. Translation: AAB60196.1.
    PIRiA27339. KIECGL.
    RefSeqiNP_418361.1. NC_000913.3.
    WP_000136788.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC76908; AAC76908; b3926.
    BAE77384; BAE77384; BAE77384.
    GeneIDi948423.
    KEGGiecj:JW3897.
    eco:b3926.
    PATRICi32123365. VBIEscCol129921_4043.

    Cross-referencesi

    Web resourcesi

    Worthington enzyme manual

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M18393 Genomic DNA. Translation: AAA23913.1.
    M55990 Genomic DNA. Translation: AAA23887.1.
    L19201 Genomic DNA. Translation: AAB03058.1.
    U00096 Genomic DNA. Translation: AAC76908.1.
    AP009048 Genomic DNA. Translation: BAE77384.1.
    X15054 Genomic DNA. Translation: CAA33154.1.
    U41468 Genomic DNA. Translation: AAB60196.1.
    PIRiA27339. KIECGL.
    RefSeqiNP_418361.1. NC_000913.3.
    WP_000136788.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1BO5X-ray3.20O/Z2-502[»]
    1BOTX-ray3.05O/Z2-502[»]
    1BU6X-ray2.37O/X/Y/Z2-502[»]
    1BWFX-ray3.00O/Y2-502[»]
    1GLAX-ray2.60G2-502[»]
    1GLBX-ray2.60G2-502[»]
    1GLCX-ray2.65G2-502[»]
    1GLDX-ray2.93G2-502[»]
    1GLEX-ray2.94G2-502[»]
    1GLFX-ray2.62O/X/Y/Z2-502[»]
    1GLJX-ray3.00O/Y2-502[»]
    1GLLX-ray3.00O/Y2-502[»]
    3EZWX-ray2.00A/B/C/D/E/F/G/H2-501[»]
    ProteinModelPortaliP0A6F3.
    SMRiP0A6F3.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4263162. 380 interactors.
    DIPiDIP-36011N.
    IntActiP0A6F3. 15 interactors.
    STRINGi511145.b3926.

    2D gel databases

    SWISS-2DPAGEP0A6F3.

    Proteomic databases

    EPDiP0A6F3.
    PaxDbiP0A6F3.
    PRIDEiP0A6F3.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC76908; AAC76908; b3926.
    BAE77384; BAE77384; BAE77384.
    GeneIDi948423.
    KEGGiecj:JW3897.
    eco:b3926.
    PATRICi32123365. VBIEscCol129921_4043.

    Organism-specific databases

    EchoBASEiEB0393.
    EcoGeneiEG10398. glpK.

    Phylogenomic databases

    eggNOGiENOG4107QVN. Bacteria.
    COG0554. LUCA.
    HOGENOMiHOG000222134.
    InParanoidiP0A6F3.
    KOiK00864.
    OMAiPMEIFAT.
    PhylomeDBiP0A6F3.

    Enzyme and pathway databases

    UniPathwayiUPA00618; UER00672.
    BioCyciEcoCyc:GLYCEROL-KIN-MONOMER.
    ECOL316407:JW3897-MONOMER.
    MetaCyc:GLYCEROL-KIN-MONOMER.
    BRENDAi2.7.1.30. 2026.

    Miscellaneous databases

    EvolutionaryTraceiP0A6F3.
    PROiP0A6F3.

    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_ECOLI
    AccessioniPrimary (citable) accession number: P0A6F3
    Secondary accession number(s): P08859, Q2M8M2, Q59381
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 29, 2005
    Last sequence update: January 23, 2007
    Last modified: November 2, 2016
    This is version 103 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Allosteric enzyme, Complete proteome, Direct protein sequencing, 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. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. 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.