Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Glyceraldehyde-3-phosphate dehydrogenase 1

Gene

gapA1

Organism
Staphylococcus aureus (strain MRSA252)
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. 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.1 Publication

Catalytic activityi

D-glyceraldehyde 3-phosphate + phosphate + NAD+ = 3-phospho-D-glyceroyl phosphate + NADH.1 Publication

Kineticsi

Kcat is 70 sec(-1) for dehydrogenase activity.1 Publication

Manual assertion based on experiment ini

  • Ref.2
    "Crystal structure of glyceraldehyde-3-phosphate dehydrogenase 1 from methicillin-resistant Staphylococcus aureus MRSA252 provides novel insights into substrate binding and catalytic mechanism."
    Mukherjee S., Dutta D., Saha B., Das A.K.
    J. Mol. Biol. 401:949-968(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF MUTANT SER-151 IN COMPLEX WITH GLYCERALDEHYDE-3-PHOSPHATE AND NAD, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF CYS-151 AND HIS-178, ACTIVE SITE, SUBUNIT.

  1. KM=0.31 mM for G3P1 Publication
  2. KM=316 mM for NAD1 Publication

    pH dependencei

    Optimum pH is 8.7.1 Publication

    Temperature dependencei

    Optimum temperature is 25 degrees Celsius.1 Publication

    Pathwayi: glycolysis

    This protein is involved in step 1 of the subpathway that synthesizes pyruvate from D-glyceraldehyde 3-phosphate.1 Publication
    Proteins known to be involved in the 5 steps of the subpathway in this organism are:
    1. Glyceraldehyde-3-phosphate dehydrogenase 1 (gapA1), Glyceraldehyde-3-phosphate dehydrogenase 2 (gapA2)
    2. Phosphoglycerate kinase (pgk)
    3. 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (gpmI), 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase (gpmA)
    4. Enolase (eno)
    5. Pyruvate kinase (pyk)
    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 sitei34NAD2 Publications1
    Binding sitei120NAD2 Publications1
    Active sitei151Nucleophile1 Publication1
    Sitei178Activates thiol group during catalysis1 Publication1
    Binding sitei181Glyceraldehyde 3-phosphate1 Publication1
    Binding sitei198Glyceraldehyde 3-phosphateBy similarity1
    Binding sitei234Glyceraldehyde 3-phosphate1 Publication1
    Binding sitei316NAD1 Publication1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi12 – 13NAD2 Publications2

    GO - Molecular functioni

    • glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity Source: UniProtKB
    • NAD binding Source: UniProtKB
    • NADP binding Source: InterPro

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Glycolysis

    Keywords - Ligandi

    NAD, Nucleotide-binding

    Enzyme and pathway databases

    BRENDAi1.2.1.12. 3352.
    UniPathwayiUPA00109; UER00184.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Glyceraldehyde-3-phosphate dehydrogenase 11 Publication (EC:1.2.1.121 Publication)
    Short name:
    GAPDH 11 Publication
    Alternative name(s):
    NAD-dependent glyceraldehyde-3-phosphate dehydrogenase1 Publication
    Gene namesi
    Name:gapA1
    Synonyms:gap, gapA
    Ordered Locus Names:SAR0828
    OrganismiStaphylococcus aureus (strain MRSA252)
    Taxonomic identifieri282458 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesStaphylococcaceaeStaphylococcus

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi151C → S: Loss of dehydrogenase activity. 1 Publication1
    Mutagenesisi178H → N: Loss of dehydrogenase activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001456851 – 336Glyceraldehyde-3-phosphate dehydrogenase 1Add BLAST336

    Interactioni

    Subunit structurei

    Homotetramer.2 Publications

    Structurei

    Secondary structure

    1336
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi3 – 8Combined sources6
    Helixi12 – 22Combined sources11
    Beta strandi27 – 33Combined sources7
    Helixi38 – 46Combined sources9
    Turni49 – 51Combined sources3
    Beta strandi58 – 61Combined sources4
    Beta strandi64 – 67Combined sources4
    Beta strandi70 – 75Combined sources6
    Helixi80 – 82Combined sources3
    Turni85 – 89Combined sources5
    Beta strandi91 – 95Combined sources5
    Beta strandi97 – 99Combined sources3
    Helixi103 – 111Combined sources9
    Beta strandi115 – 121Combined sources7
    Beta strandi124 – 126Combined sources3
    Turni132 – 134Combined sources3
    Helixi136 – 138Combined sources3
    Beta strandi144 – 147Combined sources4
    Helixi151 – 167Combined sources17
    Beta strandi169 – 179Combined sources11
    Beta strandi186 – 188Combined sources3
    Turni196 – 199Combined sources4
    Helixi202 – 204Combined sources3
    Beta strandi207 – 210Combined sources4
    Turni213 – 216Combined sources4
    Helixi217 – 219Combined sources3
    Helixi222 – 224Combined sources3
    Beta strandi227 – 236Combined sources10
    Beta strandi241 – 253Combined sources13
    Helixi256 – 265Combined sources10
    Beta strandi269 – 274Combined sources6
    Helixi280 – 283Combined sources4
    Beta strandi289 – 293Combined sources5
    Helixi294 – 296Combined sources3
    Beta strandi298 – 302Combined sources5
    Beta strandi305 – 314Combined sources10
    Helixi318 – 334Combined sources17

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3HQ4X-ray2.20O/P/Q/R1-336[»]
    3K73X-ray2.50O/P/Q/R1-336[»]
    3K9QX-ray2.50O/P/Q/R1-336[»]
    3KSDX-ray2.20O/P/Q/R1-336[»]
    3KSZX-ray2.60O/P/Q/R1-336[»]
    3KV3X-ray2.50O/P/Q/R1-336[»]
    3L4SX-ray2.20O/P/Q/R1-336[»]
    3L6OX-ray2.20O/P/Q/R1-336[»]
    3LC1X-ray2.00O/P/Q/R1-336[»]
    3LC2X-ray2.80O/P/Q/R1-336[»]
    3LC7X-ray2.50O/P/Q/R1-336[»]
    3LVFX-ray1.70O/P/Q/R1-336[»]
    3VAZX-ray3.19A/B/O/P/Q/R1-336[»]
    ProteinModelPortaliQ6GIL8.
    SMRiQ6GIL8.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ6GIL8.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni150 – 152Glyceraldehyde 3-phosphate binding1 Publication3
    Regioni211 – 212Glyceraldehyde 3-phosphate binding1 Publication2

    Sequence similaritiesi

    Phylogenomic databases

    HOGENOMiHOG000071678.
    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.

    Q6GIL8-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MAVKVAINGF GRIGRLAFRR IQEVEGLEVV AVNDLTDDDM LAHLLKYDTM
    60 70 80 90 100
    QGRFTGEVEV VDGGFRVNGK EVKSFSEPDA SKLPWKDLNI DVVLECTGFY
    110 120 130 140 150
    TDKDKAQAHI EAGAKKVLIS APATGDLKTI VFNTNHQELD GSETVVSGAS
    160 170 180 190 200
    CTTNSLAPVA KVLNDDFGLV EGLMTTIHAY TGDQNTQDAP HRKGDKRRAR
    210 220 230 240 250
    AAAENIIPNS TGAAKAIGKV IPEIDGKLDG GAQRVPVATG SLTELTVVLE
    260 270 280 290 300
    KQDVTVEQVN EAMKNASNES FGYTEDEIVS SDVVGMTYGS LFDATQTRVM
    310 320 330
    SVGDRQLVKV AAWYDNEMSY TAQLVRTLAY LAELSK
    Length:336
    Mass (Da):36,281
    Last modified:July 19, 2004 - v1
    Checksum:i37A6CEA9376779E5
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    BX571856 Genomic DNA. Translation: CAG39837.1.
    RefSeqiWP_000279414.1. NC_002952.2.

    Genome annotation databases

    EnsemblBacteriaiCAG39837; CAG39837; SAR0828.
    GeneIDi28381664.
    KEGGisar:SAR0828.
    PATRICi19545193. VBIStaAur71814_0829.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    BX571856 Genomic DNA. Translation: CAG39837.1.
    RefSeqiWP_000279414.1. NC_002952.2.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3HQ4X-ray2.20O/P/Q/R1-336[»]
    3K73X-ray2.50O/P/Q/R1-336[»]
    3K9QX-ray2.50O/P/Q/R1-336[»]
    3KSDX-ray2.20O/P/Q/R1-336[»]
    3KSZX-ray2.60O/P/Q/R1-336[»]
    3KV3X-ray2.50O/P/Q/R1-336[»]
    3L4SX-ray2.20O/P/Q/R1-336[»]
    3L6OX-ray2.20O/P/Q/R1-336[»]
    3LC1X-ray2.00O/P/Q/R1-336[»]
    3LC2X-ray2.80O/P/Q/R1-336[»]
    3LC7X-ray2.50O/P/Q/R1-336[»]
    3LVFX-ray1.70O/P/Q/R1-336[»]
    3VAZX-ray3.19A/B/O/P/Q/R1-336[»]
    ProteinModelPortaliQ6GIL8.
    SMRiQ6GIL8.
    ModBaseiSearch...
    MobiDBiSearch...

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCAG39837; CAG39837; SAR0828.
    GeneIDi28381664.
    KEGGisar:SAR0828.
    PATRICi19545193. VBIStaAur71814_0829.

    Phylogenomic databases

    HOGENOMiHOG000071678.
    KOiK00134.
    OMAiFVRVLSW.

    Enzyme and pathway databases

    UniPathwayiUPA00109; UER00184.
    BRENDAi1.2.1.12. 3352.

    Miscellaneous databases

    EvolutionaryTraceiQ6GIL8.

    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 nameiG3P1_STAAR
    AccessioniPrimary (citable) accession number: Q6GIL8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 1, 2005
    Last sequence update: July 19, 2004
    Last modified: November 2, 2016
    This is version 90 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

    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.