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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)DescriptionActionsGraphical viewLength
    Binding sitei35NAD1 Publication1
    Binding sitei121NAD1 Publication1
    Active sitei152NucleophileBy similarity1
    Sitei179Activates thiol group during catalysisBy similarity1
    Binding sitei182Glyceraldehyde 3-phosphate1 Publication1
    Binding sitei183NAD1 Publication1
    Binding sitei197Glyceraldehyde 3-phosphate1 Publication1
    Binding sitei233Glyceraldehyde 3-phosphate1 Publication1
    Binding sitei315NAD1 Publication1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi11 – 12NAD1 Publication2

    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)DescriptionActionsGraphical viewLength
    Initiator methionineiRemoved1 Publication
    ChainiPRO_00001457112 – 333Glyceraldehyde-3-phosphate dehydrogenaseAdd BLAST332

    Interactioni

    Subunit structurei

    Homotetramer.2 Publications

    Protein-protein interaction databases

    STRINGi243274.TM0688.

    Structurei

    Secondary structure

    1333
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi3 – 7Combined sources5
    Helixi11 – 23Combined sources13
    Beta strandi29 – 34Combined sources6
    Helixi39 – 47Combined sources9
    Turni50 – 52Combined sources3
    Beta strandi59 – 61Combined sources3
    Beta strandi63 – 68Combined sources6
    Beta strandi71 – 76Combined sources6
    Helixi81 – 83Combined sources3
    Helixi86 – 89Combined sources4
    Beta strandi93 – 96Combined sources4
    Beta strandi98 – 100Combined sources3
    Helixi104 – 107Combined sources4
    Helixi109 – 112Combined sources4
    Beta strandi116 – 122Combined sources7
    Beta strandi128 – 130Combined sources3
    Turni133 – 135Combined sources3
    Helixi137 – 139Combined sources3
    Beta strandi146 – 148Combined sources3
    Helixi152 – 168Combined sources17
    Beta strandi170 – 180Combined sources11
    Beta strandi185 – 189Combined sources5
    Turni195 – 198Combined sources4
    Helixi201 – 203Combined sources3
    Beta strandi206 – 208Combined sources3
    Helixi212 – 219Combined sources8
    Helixi221 – 223Combined sources3
    Turni224 – 226Combined sources3
    Beta strandi227 – 235Combined sources9
    Beta strandi240 – 250Combined sources11
    Helixi254 – 265Combined sources12
    Turni266 – 272Combined sources7
    Beta strandi273 – 276Combined sources4
    Helixi282 – 285Combined sources4
    Beta strandi291 – 295Combined sources5
    Turni296 – 298Combined sources3
    Beta strandi300 – 302Combined sources3
    Turni303 – 305Combined sources3
    Beta strandi306 – 313Combined sources8
    Helixi317 – 329Combined sources13
    Helixi330 – 332Combined sources3

    3D structure databases

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

    Miscellaneous databases

    EvolutionaryTraceiP17721.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni151 – 153Glyceraldehyde 3-phosphate binding1 Publication3
    Regioni210 – 211Glyceraldehyde 3-phosphate binding1 Publication2

    Sequence similaritiesi

    Phylogenomic databases

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

    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
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1HDGX-ray2.50O/Q2-333[»]
    ProteinModelPortaliP17721.
    SMRiP17721.
    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.

    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...

    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: November 2, 2016
    This is version 145 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.