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

  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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei34 – 341NAD2 Publications
    Binding sitei120 – 1201NAD2 Publications
    Active sitei151 – 1511Nucleophile1 Publication
    Sitei178 – 1781Activates thiol group during catalysis1 Publication
    Binding sitei181 – 1811Glyceraldehyde 3-phosphate1 Publication
    Binding sitei198 – 1981Glyceraldehyde 3-phosphateBy similarity
    Binding sitei234 – 2341Glyceraldehyde 3-phosphate1 Publication
    Binding sitei316 – 3161NAD1 Publication

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi12 – 132NAD2 Publications

    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

    BioCyciSAUR282458:GJA5-831-MONOMER.
    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)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi151 – 1511C → S: Loss of dehydrogenase activity. 1 Publication
    Mutagenesisi178 – 1781H → N: Loss of dehydrogenase activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 336336Glyceraldehyde-3-phosphate dehydrogenase 1PRO_0000145685Add
    BLAST

    Proteomic databases

    PRIDEiQ6GIL8.

    Interactioni

    Subunit structurei

    Homotetramer.2 Publications

    Structurei

    Secondary structure

    1
    336
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 86Combined sources
    Helixi12 – 2211Combined sources
    Beta strandi27 – 337Combined sources
    Helixi38 – 469Combined sources
    Turni49 – 513Combined sources
    Beta strandi58 – 614Combined sources
    Beta strandi64 – 674Combined sources
    Beta strandi70 – 756Combined sources
    Helixi80 – 823Combined sources
    Turni85 – 895Combined sources
    Beta strandi91 – 955Combined sources
    Beta strandi97 – 993Combined sources
    Helixi103 – 1119Combined sources
    Beta strandi115 – 1217Combined sources
    Beta strandi124 – 1263Combined sources
    Turni132 – 1343Combined sources
    Helixi136 – 1383Combined sources
    Beta strandi144 – 1474Combined sources
    Helixi151 – 16717Combined sources
    Beta strandi169 – 17911Combined sources
    Beta strandi186 – 1883Combined sources
    Turni196 – 1994Combined sources
    Helixi202 – 2043Combined sources
    Beta strandi207 – 2104Combined sources
    Turni213 – 2164Combined sources
    Helixi217 – 2193Combined sources
    Helixi222 – 2243Combined sources
    Beta strandi227 – 23610Combined sources
    Beta strandi241 – 25313Combined sources
    Helixi256 – 26510Combined sources
    Beta strandi269 – 2746Combined sources
    Helixi280 – 2834Combined sources
    Beta strandi289 – 2935Combined sources
    Helixi294 – 2963Combined sources
    Beta strandi298 – 3025Combined sources
    Beta strandi305 – 31410Combined sources
    Helixi318 – 33417Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    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. Positions 1-336.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ6GIL8.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni150 – 1523Glyceraldehyde 3-phosphate binding1 Publication
    Regioni211 – 2122Glyceraldehyde 3-phosphate binding1 Publication

    Sequence similaritiesi

    Phylogenomic databases

    HOGENOMiHOG000071678.
    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.

    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.
    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
    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. Positions 1-336.
    ModBaseiSearch...
    MobiDBiSearch...

    Proteomic databases

    PRIDEiQ6GIL8.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

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

    Phylogenomic databases

    HOGENOMiHOG000071678.
    KOiK00134.
    OMAiFVRVLSW.
    OrthoDBiEOG66TG3S.

    Enzyme and pathway databases

    UniPathwayiUPA00109; UER00184.
    BioCyciSAUR282458:GJA5-831-MONOMER.
    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...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: MRSA252.
    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.
      Strain: MRSA252.
    3. "Crystal structure of Staphylococcal GAPDH1 in a hexagonal space group."
      Roychowdhury A., Mukherjee S., Dutta D., Das A.K.
      Submitted (DEC-2011) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (3.19 ANGSTROMS) IN COMPLEX WITH NAD, SUBUNIT.
      Strain: MRSA252.

    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: March 16, 2016
    This is version 87 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.