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Protein

Glyceraldehyde-3-phosphate dehydrogenase

Gene

gap

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

Functioni

Catalyzes the oxidative phosphorylation of glyceraldehyde 3-phosphate (G3P) to 1,3-bisphosphoglycerate (BPG) using the cofactor NAD (PubMed:2271518). The first reaction step involves the formation of a hemiacetal intermediate between G3P and a cysteine residue, and this hemiacetal intermediate is then oxidized to a thioester, with concomitant reduction of NAD to NADH. The reduced NADH is then exchanged with the second NAD, and the thioester is attacked by a nucleophilic inorganic phosphate to produce BPG (By similarity).By similarity1 Publication

Catalytic activityi

D-glyceraldehyde 3-phosphate + phosphate + NAD+ = 3-phospho-D-glyceroyl phosphate + NADH.2 Publications

Kineticsi

  1. KM=440 µM for glyceraldehyde-3-phosphate (at pH 8.0 and 40 degrees Celsius)1 Publication
  2. KM=360 µM for glyceraldehyde-3-phosphate (at pH 8.0 and 50 degrees Celsius)1 Publication
  3. KM=400 µM for glyceraldehyde-3-phosphate (at pH 8.0 and 60 degrees Celsius)1 Publication
  4. KM=18.6 µM for NAD+ (at pH 8.0 and 40 degrees Celsius)1 Publication
  5. KM=37.0 µM for NAD+ (at pH 8.0 and 50 degrees Celsius)1 Publication
  6. KM=78.8 µM for NAD+ (at pH 8.0 and 60 degrees Celsius)1 Publication

    Pathwayi: glycolysis

    This protein is involved in step 1 of the subpathway that synthesizes pyruvate from D-glyceraldehyde 3-phosphate.Curated
    Proteins known to be involved in the 5 steps of the subpathway in this organism are:
    1. Glyceraldehyde-3-phosphate dehydrogenase (gap)
    2. Bifunctional PGK/TIM (pgk/tpi), Phosphoglycerate kinase (Tmari_0689)
    3. Probable 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (apgM), Probable 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (apgM)
    4. Enolase (eno), Enolase (eno)
    5. Pyruvate kinase (pyk), Pyruvate kinase (Tmari_0206)
    This subpathway is part of the pathway glycolysis, which is itself part of Carbohydrate degradation.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyruvate from D-glyceraldehyde 3-phosphate, the pathway glycolysis and in Carbohydrate degradation.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei35 – 351NAD1 Publication
    Binding sitei121 – 1211NAD1 Publication
    Active sitei152 – 1521NucleophileBy similarity
    Sitei179 – 1791Activates thiol group during catalysisBy similarity
    Binding sitei182 – 1821Glyceraldehyde 3-phosphate1 Publication
    Binding sitei183 – 1831NAD1 Publication
    Binding sitei197 – 1971Glyceraldehyde 3-phosphate1 Publication
    Binding sitei233 – 2331Glyceraldehyde 3-phosphate1 Publication
    Binding sitei315 – 3151NAD1 Publication

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi11 – 122NAD1 Publication

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Glycolysis

    Keywords - Ligandi

    NAD, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-401.
    UniPathwayiUPA00109; UER00184.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Glyceraldehyde-3-phosphate dehydrogenase2 Publications (EC:1.2.1.122 Publications)
    Short name:
    GAPDH2 Publications
    Alternative name(s):
    NAD-dependent glyceraldehyde-3-phosphate dehydrogenase1 Publication
    Gene namesi
    Name:gap
    Ordered Locus Names:TM_0688
    OrganismiThermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
    Taxonomic identifieri243274 [NCBI]
    Taxonomic lineageiBacteriaThermotogaeThermotogalesThermotogaceaeThermotoga
    Proteomesi
    • UP000008183 Componenti: Chromosome

    Subcellular locationi

    • Cytoplasm 1 Publication

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methionineiRemoved1 Publication
    Chaini2 – 333332Glyceraldehyde-3-phosphate dehydrogenasePRO_0000145711Add
    BLAST

    Interactioni

    Subunit structurei

    Homotetramer.2 Publications

    Protein-protein interaction databases

    STRINGi243274.TM0688.

    Structurei

    Secondary structure

    1
    333
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 75Combined sources
    Helixi11 – 2313Combined sources
    Beta strandi29 – 346Combined sources
    Helixi39 – 479Combined sources
    Turni50 – 523Combined sources
    Beta strandi59 – 613Combined sources
    Beta strandi63 – 686Combined sources
    Beta strandi71 – 766Combined sources
    Helixi81 – 833Combined sources
    Helixi86 – 894Combined sources
    Beta strandi93 – 964Combined sources
    Beta strandi98 – 1003Combined sources
    Helixi104 – 1074Combined sources
    Helixi109 – 1124Combined sources
    Beta strandi116 – 1227Combined sources
    Beta strandi128 – 1303Combined sources
    Turni133 – 1353Combined sources
    Helixi137 – 1393Combined sources
    Beta strandi146 – 1483Combined sources
    Helixi152 – 16817Combined sources
    Beta strandi170 – 18011Combined sources
    Beta strandi185 – 1895Combined sources
    Turni195 – 1984Combined sources
    Helixi201 – 2033Combined sources
    Beta strandi206 – 2083Combined sources
    Helixi212 – 2198Combined sources
    Helixi221 – 2233Combined sources
    Turni224 – 2263Combined sources
    Beta strandi227 – 2359Combined sources
    Beta strandi240 – 25011Combined sources
    Helixi254 – 26512Combined sources
    Turni266 – 2727Combined sources
    Beta strandi273 – 2764Combined sources
    Helixi282 – 2854Combined sources
    Beta strandi291 – 2955Combined sources
    Turni296 – 2983Combined sources
    Beta strandi300 – 3023Combined sources
    Turni303 – 3053Combined sources
    Beta strandi306 – 3138Combined sources
    Helixi317 – 32913Combined sources
    Helixi330 – 3323Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1HDGX-ray2.50O/Q2-333[»]
    ProteinModelPortaliP17721.
    SMRiP17721. Positions 2-333.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP17721.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni151 – 1533Glyceraldehyde 3-phosphate binding1 Publication
    Regioni210 – 2112Glyceraldehyde 3-phosphate binding1 Publication

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105C17. Bacteria.
    COG0057. LUCA.
    InParanoidiP17721.
    KOiK00134.
    OMAiFVRVLSW.
    OrthoDBiEOG66TG3S.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    InterProiIPR020831. GlycerAld/Erythrose_P_DH.
    IPR020830. GlycerAld_3-P_DH_AS.
    IPR020829. GlycerAld_3-P_DH_cat.
    IPR020828. GlycerAld_3-P_DH_NAD(P)-bd.
    IPR006424. Glyceraldehyde-3-P_DH_1.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view]
    PANTHERiPTHR10836. PTHR10836. 1 hit.
    PfamiPF02800. Gp_dh_C. 1 hit.
    PF00044. Gp_dh_N. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000149. GAP_DH. 1 hit.
    PRINTSiPR00078. G3PDHDRGNASE.
    SMARTiSM00846. Gp_dh_N. 1 hit.
    [Graphical view]
    SUPFAMiSSF51735. SSF51735. 1 hit.
    TIGRFAMsiTIGR01534. GAPDH-I. 1 hit.
    PROSITEiPS00071. GAPDH. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P17721-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MARVAINGFG RIGRLVYRII YERKNPDIEV VAINDLTDTK TLAHLLKYDS
    60 70 80 90 100
    VHKKFPGKVE YTENSLIVDG KEIKVFAEPD PSKLPWKDLG VDFVIESTGV
    110 120 130 140 150
    FRNREKAELH LQAGAKKVII TAPAKGEDIT VVIGCNEDQL KPEHTIISCA
    160 170 180 190 200
    SCTTNSIAPI VKVLHEKFGI VSGMLTTVHS YTNDQRVLDL PHKDLRRARA
    210 220 230 240 250
    AAVNIIPTTT GAAKAVALVV PEVKGKLDGM AIRVPTPDGS ITDLTVLVEK
    260 270 280 290 300
    ETTVEEVNAV MKEATEGRLK GIIGYNDEPI VSSDIIGTTF SGIFDATITN
    310 320 330
    VIGGKLVKVA SWYDNEYGYS NRVVDTLELL LKM
    Length:333
    Mass (Da):36,425
    Last modified:January 23, 2007 - v2
    Checksum:i12B77104AB5E1CD0
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X72629 Genomic DNA. Translation: CAA51205.1.
    AE000512 Genomic DNA. Translation: AAD35770.1.
    PIRiS33325. DEHGGT.
    RefSeqiNP_228497.1. NC_000853.1.
    WP_004081074.1. NZ_CP011107.1.

    Genome annotation databases

    EnsemblBacteriaiAAD35770; AAD35770; TM_0688.
    GeneIDi898355.
    KEGGitma:TM0688.
    PATRICi23936294. VBITheMar51294_0700.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X72629 Genomic DNA. Translation: CAA51205.1.
    AE000512 Genomic DNA. Translation: AAD35770.1.
    PIRiS33325. DEHGGT.
    RefSeqiNP_228497.1. NC_000853.1.
    WP_004081074.1. NZ_CP011107.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1HDGX-ray2.50O/Q2-333[»]
    ProteinModelPortaliP17721.
    SMRiP17721. Positions 2-333.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi243274.TM0688.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAD35770; AAD35770; TM_0688.
    GeneIDi898355.
    KEGGitma:TM0688.
    PATRICi23936294. VBITheMar51294_0700.

    Phylogenomic databases

    eggNOGiENOG4105C17. Bacteria.
    COG0057. LUCA.
    InParanoidiP17721.
    KOiK00134.
    OMAiFVRVLSW.
    OrthoDBiEOG66TG3S.

    Enzyme and pathway databases

    UniPathwayiUPA00109; UER00184.
    BioCyciMetaCyc:MONOMER-401.

    Miscellaneous databases

    EvolutionaryTraceiP17721.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    InterProiIPR020831. GlycerAld/Erythrose_P_DH.
    IPR020830. GlycerAld_3-P_DH_AS.
    IPR020829. GlycerAld_3-P_DH_cat.
    IPR020828. GlycerAld_3-P_DH_NAD(P)-bd.
    IPR006424. Glyceraldehyde-3-P_DH_1.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view]
    PANTHERiPTHR10836. PTHR10836. 1 hit.
    PfamiPF02800. Gp_dh_C. 1 hit.
    PF00044. Gp_dh_N. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000149. GAP_DH. 1 hit.
    PRINTSiPR00078. G3PDHDRGNASE.
    SMARTiSM00846. Gp_dh_N. 1 hit.
    [Graphical view]
    SUPFAMiSSF51735. SSF51735. 1 hit.
    TIGRFAMsiTIGR01534. GAPDH-I. 1 hit.
    PROSITEiPS00071. GAPDH. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Functional expression of D-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic eubacterium Thermotoga maritima in Escherichia coli. Authenticity and kinetic properties of the recombinant enzyme."
      Tomschy A., Glockhuber R., Jaenicke R.
      Eur. J. Biochem. 214:43-50(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CATALYTIC ACTIVITY, SUBCELLULAR LOCATION.
      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. "Complete amino-acid sequence of glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic eubacterium Thermotoga maritima."
      Schultes V., Deutzmann R., Jaenicke R.
      Eur. J. Biochem. 192:25-31(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-333.
      Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099.
    4. "Extremely thermostable D-glyceraldehyde-3-phosphate dehydrogenase from the eubacterium Thermotoga maritima."
      Wrba A., Schweiger A., Schultes V., Jaenicke R., Zavodszky P.
      Biochemistry 29:7584-7592(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
      Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099.
    5. "The crystal structure of holo-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic bacterium Thermotoga maritima at 2.5-A resolution."
      Korndoerfer I., Steipe B., Huber R., Tomschy A., Jaenicke R.
      J. Mol. Biol. 246:511-521(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH NAD AND SUBSTRATE ANALOG, SUBUNIT.

    Entry informationi

    Entry nameiG3P_THEMA
    AccessioniPrimary (citable) accession number: P17721
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1990
    Last sequence update: January 23, 2007
    Last modified: June 8, 2016
    This is version 142 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, 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.