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Protein

D-glycerate 2-kinase

Gene

TM_1585

Organism
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the degradation of serine via 3-hydroxypyruvate. Catalyzes the ATP-dependent phosphorylation of D-glycerate to 2-phosphoglycerate.1 Publication

Catalytic activityi

ATP + D-glycerate = ADP + 2-phospho-D-glycerate.1 Publication

Cofactori

Mg2+1 Publication

Kineticsi

Kcat is 14.4 sec(-1) for phosphorylation of D-glycerate.

  1. KM=0.095 mM for ATP1 Publication
  2. KM=0.15 mM for D-glycerate1 Publication

    GO - Molecular functioni

    • ATP binding Source: UniProtKB-KW
    • glycerate kinase activity Source: GO_Central
    • magnesium ion binding Source: UniProtKB
    • phosphotransferase activity, alcohol group as acceptor Source: UniProtKB

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Kinase, Transferase

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciTMAR243274:GC6P-1626-MONOMER.
    SABIO-RKQ9X1S1.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    D-glycerate 2-kinase (EC:2.7.1.165)
    Short name:
    GCK
    Gene namesi
    Ordered Locus Names:TM_1585
    ORF Names:THEMA_06355, Tmari_1593
    OrganismiThermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
    Taxonomic identifieri243274 [NCBI]
    Taxonomic lineageiBacteriaThermotogaeThermotogalesThermotogaceaeThermotoga
    Proteomesi
    • UP000013901 Componenti: Chromosome
    • UP000008183 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi47 – 471K → A: Very low residual kinase activity. 1 Publication
    Mutagenesisi47 – 471K → R: Significant decrease of the kinase activity with a 180-fold decrease of catalytic efficiency. 1 Publication
    Mutagenesisi325 – 3251R → A or K: Significant decrease of the kinase activity with a 17-fold decrease of catalytic efficiency. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 417417D-glycerate 2-kinasePRO_0000428994Add
    BLAST

    Interactioni

    Subunit structurei

    Homodimer.2 Publications

    Protein-protein interaction databases

    STRINGi243274.TM1585.

    Structurei

    Secondary structure

    1
    417
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi5 – 2016Combined sources
    Helixi24 – 296Combined sources
    Helixi32 – 354Combined sources
    Beta strandi39 – 468Combined sources
    Helixi49 – 6012Combined sources
    Helixi61 – 633Combined sources
    Beta strandi64 – 729Combined sources
    Beta strandi84 – 885Combined sources
    Beta strandi90 – 923Combined sources
    Helixi95 – 10814Combined sources
    Beta strandi116 – 1216Combined sources
    Helixi125 – 1284Combined sources
    Helixi138 – 15013Combined sources
    Helixi155 – 1639Combined sources
    Beta strandi166 – 1683Combined sources
    Turni169 – 1713Combined sources
    Helixi172 – 1776Combined sources
    Beta strandi180 – 1878Combined sources
    Turni195 – 1973Combined sources
    Helixi198 – 2003Combined sources
    Helixi210 – 21910Combined sources
    Helixi226 – 2327Combined sources
    Beta strandi241 – 2499Combined sources
    Helixi251 – 26414Combined sources
    Beta strandi268 – 2769Combined sources
    Helixi280 – 29718Combined sources
    Beta strandi303 – 3119Combined sources
    Helixi325 – 33612Combined sources
    Turni337 – 3393Combined sources
    Beta strandi343 – 3497Combined sources
    Beta strandi355 – 3584Combined sources
    Beta strandi361 – 3655Combined sources
    Helixi368 – 3747Combined sources
    Helixi379 – 3846Combined sources
    Helixi388 – 3947Combined sources
    Beta strandi410 – 4167Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2B8NX-ray2.53A/B1-417[»]
    ProteinModelPortaliQ9X1S1.
    SMRiQ9X1S1. Positions 4-417.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9X1S1.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the glycerate kinase type-1 family.Curated

    Phylogenomic databases

    eggNOGiENOG4105D1Z. Bacteria.
    COG2379. LUCA.
    InParanoidiQ9X1S1.
    KOiK00050.
    OMAiIYEAGHP.
    OrthoDBiEOG6TTVJX.

    Family and domain databases

    Gene3Di3.40.1480.10. 1 hit.
    InterProiIPR007835. MOFRL.
    IPR025286. MOFRL_assoc_dom.
    [Graphical view]
    PfamiPF13660. DUF4147. 1 hit.
    PF05161. MOFRL. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q9X1S1-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MFDPESLKKL AIEIVKKSIE AVFPDRAVKE TLPKLNLDRV ILVAVGKAAW
    60 70 80 90 100
    RMAKAAYEVL GKKIRKGVVV TKYGHSEGPI DDFEIYEAGH PVPDENTIKT
    110 120 130 140 150
    TRRVLELVDQ LNENDTVLFL LSGGGSSLFE LPLEGVSLEE IQKLTSALLK
    160 170 180 190 200
    SGASIEEINT VRKHLSQVKG GRFAERVFPA KVVALVLSDV LGDRLDVIAS
    210 220 230 240 250
    GPAWPDSSTS EDALKVLEKY GIETSESVKR AILQETPKHL SNVEIHLIGN
    260 270 280 290 300
    VQKVCDEAKS LAKEKGFNAE IITTSLDCEA REAGRFIASI MKEVKFKDRP
    310 320 330 340 350
    LKKPAALIFG GETVVHVKGN GIGGRNQELA LSAAIALEGI EGVILCSAGT
    360 370 380 390 400
    DGTDGPTDAA GGIVDGSTAK TLKAMGEDPY QYLKNNDSYN ALKKSGALLI
    410
    TGPTGTNVND LIIGLIV
    Length:417
    Mass (Da):44,722
    Last modified:November 1, 1999 - v1
    Checksum:iFEE01EC89CC8E445
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE000512 Genomic DNA. Translation: AAD36652.1.
    CP004077 Genomic DNA. Translation: AGL50517.1.
    CP007013 Genomic DNA. Translation: AHD18518.1.
    PIRiA72236.
    RefSeqiNP_229385.1. NC_000853.1.
    WP_004082016.1. NZ_CP011107.1.

    Genome annotation databases

    EnsemblBacteriaiAAD36652; AAD36652; TM_1585.
    AGL50517; AGL50517; Tmari_1593.
    AHD18518; AHD18518; THEMA_06355.
    GeneIDi897953.
    KEGGitma:TM1585.
    tmi:THEMA_06355.
    tmm:Tmari_1593.
    tmw:THMA_1620.
    PATRICi23938134. VBITheMar51294_1604.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE000512 Genomic DNA. Translation: AAD36652.1.
    CP004077 Genomic DNA. Translation: AGL50517.1.
    CP007013 Genomic DNA. Translation: AHD18518.1.
    PIRiA72236.
    RefSeqiNP_229385.1. NC_000853.1.
    WP_004082016.1. NZ_CP011107.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2B8NX-ray2.53A/B1-417[»]
    ProteinModelPortaliQ9X1S1.
    SMRiQ9X1S1. Positions 4-417.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi243274.TM1585.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAD36652; AAD36652; TM_1585.
    AGL50517; AGL50517; Tmari_1593.
    AHD18518; AHD18518; THEMA_06355.
    GeneIDi897953.
    KEGGitma:TM1585.
    tmi:THEMA_06355.
    tmm:Tmari_1593.
    tmw:THMA_1620.
    PATRICi23938134. VBITheMar51294_1604.

    Phylogenomic databases

    eggNOGiENOG4105D1Z. Bacteria.
    COG2379. LUCA.
    InParanoidiQ9X1S1.
    KOiK00050.
    OMAiIYEAGHP.
    OrthoDBiEOG6TTVJX.

    Enzyme and pathway databases

    BioCyciTMAR243274:GC6P-1626-MONOMER.
    SABIO-RKQ9X1S1.

    Miscellaneous databases

    EvolutionaryTraceiQ9X1S1.

    Family and domain databases

    Gene3Di3.40.1480.10. 1 hit.
    InterProiIPR007835. MOFRL.
    IPR025286. MOFRL_assoc_dom.
    [Graphical view]
    PfamiPF13660. DUF4147. 1 hit.
    PF05161. MOFRL. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099.
    4. "Glycerate 2-kinase of Thermotoga maritima and genomic reconstruction of related metabolic pathways."
      Yang C., Rodionov D.A., Rodionova I.A., Li X., Osterman A.L.
      J. Bacteriol. 190:1773-1782(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, COFACTOR, MUTAGENESIS OF LYS-47 AND ARG-325, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
    5. Cited for: X-RAY CRYSTALLOGRAPHY (2.53 ANGSTROMS), SUBUNIT.

    Entry informationi

    Entry nameiGCK_THEMA
    AccessioniPrimary (citable) accession number: Q9X1S1
    Secondary accession number(s): G4FFX3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 14, 2014
    Last sequence update: November 1, 1999
    Last modified: February 17, 2016
    This is version 92 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, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. 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.