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P00359

- G3P3_YEAST

UniProt

P00359 - G3P3_YEAST

Protein

Glyceraldehyde-3-phosphate dehydrogenase 3

Gene

TDH3

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 160 (01 Oct 2014)
      Sequence version 3 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    Catalytic activityi

    D-glyceraldehyde 3-phosphate + phosphate + NAD+ = 3-phospho-D-glyceroyl phosphate + NADH.PROSITE-ProRule annotation

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei33 – 331NADBy similarity
    Binding sitei78 – 781NAD; via carbonyl oxygenBy similarity
    Active sitei150 – 1501NucleophilePROSITE-ProRule annotation
    Sitei177 – 1771Activates thiol group during catalysisBy similarity
    Binding sitei180 – 1801Glyceraldehyde 3-phosphateBy similarity
    Binding sitei232 – 2321Glyceraldehyde 3-phosphateBy similarity
    Binding sitei314 – 3141NADBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi11 – 122NADBy similarity

    GO - Molecular functioni

    1. glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity Source: SGD
    2. NAD binding Source: InterPro
    3. NADP binding Source: InterPro

    GO - Biological processi

    1. apoptotic process Source: SGD
    2. gluconeogenesis Source: SGD
    3. glycolytic process Source: SGD
    4. reactive oxygen species metabolic process Source: SGD

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Glycolysis

    Keywords - Ligandi

    NAD

    Enzyme and pathway databases

    BioCyciYEAST:YGR192C-MONOMER.
    SABIO-RKP00359.
    UniPathwayiUPA00109; UER00184.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Glyceraldehyde-3-phosphate dehydrogenase 3 (EC:1.2.1.12)
    Short name:
    GAPDH 3
    Gene namesi
    Name:TDH3
    Synonyms:GPD3
    Ordered Locus Names:YGR192C
    ORF Names:G7576
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome VII

    Organism-specific databases

    SGDiS000003424. TDH3.

    Subcellular locationi

    Cytoplasm 1 Publication

    GO - Cellular componenti

    1. cytoplasm Source: SGD
    2. fungal-type cell wall Source: SGD
    3. lipid particle Source: SGD
    4. mitochondrion Source: SGD

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 332331Glyceraldehyde-3-phosphate dehydrogenase 3PRO_0000145591Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei302 – 3021Phosphoserine1 Publication

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP00359.
    PaxDbiP00359.
    PeptideAtlasiP00359.
    PRIDEiP00359.

    2D gel databases

    COMPLUYEAST-2DPAGEP00359.
    SWISS-2DPAGEP00359.

    Expressioni

    Gene expression databases

    GenevestigatoriP00359.

    Interactioni

    Subunit structurei

    Homotetramer.1 Publication

    Protein-protein interaction databases

    BioGridi33445. 153 interactions.
    DIPiDIP-4309N.
    IntActiP00359. 100 interactions.
    MINTiMINT-8285236.
    STRINGi4932.YGR192C.

    Structurei

    Secondary structure

    1
    332
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 75
    Helixi11 – 2212
    Beta strandi27 – 326
    Helixi38 – 469
    Turni49 – 513
    Beta strandi58 – 603
    Beta strandi62 – 676
    Beta strandi70 – 756
    Helixi80 – 823
    Turni85 – 895
    Beta strandi91 – 955
    Beta strandi97 – 1004
    Helixi103 – 1119
    Beta strandi115 – 1217
    Beta strandi124 – 1263
    Turni131 – 1333
    Helixi135 – 1373
    Beta strandi144 – 1463
    Helixi150 – 16617
    Beta strandi168 – 17811
    Beta strandi183 – 1875
    Helixi195 – 1973
    Helixi200 – 2023
    Beta strandi205 – 2084
    Helixi211 – 2188
    Helixi220 – 2223
    Beta strandi225 – 23410
    Beta strandi239 – 24911
    Helixi253 – 26513
    Turni266 – 2716
    Beta strandi272 – 2754
    Helixi281 – 2844
    Beta strandi290 – 2945
    Helixi295 – 2973
    Beta strandi299 – 3024
    Beta strandi305 – 3128
    Helixi316 – 33116

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3PYMX-ray2.00A/B1-332[»]
    4IQ8X-ray2.49A1-332[»]
    ProteinModelPortaliP00359.
    SMRiP00359. Positions 1-332.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni149 – 1513Glyceraldehyde 3-phosphate bindingBy similarity
    Regioni209 – 2102Glyceraldehyde 3-phosphate bindingBy similarity

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0057.
    GeneTreeiENSGT00720000108591.
    HOGENOMiHOG000071678.
    KOiK00134.
    OMAiINDIMDI.
    OrthoDBiEOG70W3Q6.

    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]
    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.

    P00359-1 [UniParc]FASTAAdd to Basket

    « Hide

    MVRVAINGFG RIGRLVMRIA LSRPNVEVVA LNDPFITNDY AAYMFKYDST    50
    HGRYAGEVSH DDKHIIVDGK KIATYQERDP ANLPWGSSNV DIAIDSTGVF 100
    KELDTAQKHI DAGAKKVVIT APSSTAPMFV MGVNEEKYTS DLKIVSNASC 150
    TTNCLAPLAK VINDAFGIEE GLMTTVHSLT ATQKTVDGPS HKDWRGGRTA 200
    SGNIIPSSTG AAKAVGKVLP ELQGKLTGMA FRVPTVDVSV VDLTVKLNKE 250
    TTYDEIKKVV KAAAEGKLKG VLGYTEDAVV SSDFLGDSHS SIFDASAGIQ 300
    LSPKFVKLVS WYDNEYGYST RVVDLVEHVA KA 332
    Length:332
    Mass (Da):35,747
    Last modified:January 23, 2007 - v3
    Checksum:i6CFFFEE7061BC36F
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti136 – 1361E → V in CAA24607. (PubMed:385592)Curated
    Sequence conflicti136 – 1361E → V in AAA88714. (PubMed:385592)Curated
    Sequence conflicti248 – 2481N → D in CAA24607. (PubMed:385592)Curated
    Sequence conflicti248 – 2481N → D in AAA88714. (PubMed:385592)Curated
    Sequence conflicti287 – 2871D → G in AAS56157. (PubMed:17322287)Curated
    Sequence conflicti329 – 3291V → I in CAA24607. (PubMed:385592)Curated
    Sequence conflicti329 – 3291V → I in AAA88714. (PubMed:385592)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    V01300 Genomic DNA. Translation: CAA24607.1.
    J01324 Genomic DNA. Translation: AAA88714.1.
    X82408 Genomic DNA. Translation: CAA57803.1.
    Z72977 Genomic DNA. Translation: CAA97218.1.
    AY557831 Genomic DNA. Translation: AAS56157.1.
    BK006941 Genomic DNA. Translation: DAA08285.1.
    PIRiS55870. DEBYG2.
    RefSeqiNP_011708.3. NM_001181321.3.

    Genome annotation databases

    EnsemblFungiiYGR192C; YGR192C; YGR192C.
    GeneIDi853106.
    KEGGisce:YGR192C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    V01300 Genomic DNA. Translation: CAA24607.1 .
    J01324 Genomic DNA. Translation: AAA88714.1 .
    X82408 Genomic DNA. Translation: CAA57803.1 .
    Z72977 Genomic DNA. Translation: CAA97218.1 .
    AY557831 Genomic DNA. Translation: AAS56157.1 .
    BK006941 Genomic DNA. Translation: DAA08285.1 .
    PIRi S55870. DEBYG2.
    RefSeqi NP_011708.3. NM_001181321.3.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3PYM X-ray 2.00 A/B 1-332 [» ]
    4IQ8 X-ray 2.49 A 1-332 [» ]
    ProteinModelPortali P00359.
    SMRi P00359. Positions 1-332.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 33445. 153 interactions.
    DIPi DIP-4309N.
    IntActi P00359. 100 interactions.
    MINTi MINT-8285236.
    STRINGi 4932.YGR192C.

    2D gel databases

    COMPLUYEAST-2DPAGE P00359.
    SWISS-2DPAGE P00359.

    Proteomic databases

    MaxQBi P00359.
    PaxDbi P00359.
    PeptideAtlasi P00359.
    PRIDEi P00359.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YGR192C ; YGR192C ; YGR192C .
    GeneIDi 853106.
    KEGGi sce:YGR192C.

    Organism-specific databases

    SGDi S000003424. TDH3.

    Phylogenomic databases

    eggNOGi COG0057.
    GeneTreei ENSGT00720000108591.
    HOGENOMi HOG000071678.
    KOi K00134.
    OMAi INDIMDI.
    OrthoDBi EOG70W3Q6.

    Enzyme and pathway databases

    UniPathwayi UPA00109 ; UER00184 .
    BioCyci YEAST:YGR192C-MONOMER.
    SABIO-RK P00359.

    Miscellaneous databases

    NextBioi 973112.
    PROi P00359.

    Gene expression databases

    Genevestigatori P00359.

    Family and domain databases

    Gene3Di 3.40.50.720. 1 hit.
    InterProi IPR020831. 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 ]
    PANTHERi PTHR10836. PTHR10836. 1 hit.
    Pfami PF02800. Gp_dh_C. 1 hit.
    PF00044. Gp_dh_N. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF000149. GAP_DH. 1 hit.
    PRINTSi PR00078. G3PDHDRGNASE.
    SMARTi SM00846. Gp_dh_N. 1 hit.
    [Graphical view ]
    TIGRFAMsi TIGR01534. GAPDH-I. 1 hit.
    PROSITEi PS00071. GAPDH. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The primary structure of a glyceraldehyde-3-phosphate dehydrogenase gene from Saccharomyces cerevisiae."
      Holland J.P., Holland M.J.
      J. Biol. Chem. 254:9839-9845(1979) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "The complete sequence of a 9037 bp DNA fragment of the right arm of Saccharomyces cerevisiae chromosome VII."
      Arroyo J., Garcia-Gonzalez M., Garcia-Saez M.I., Sanchez M., Nombela C.
      Yeast 11:587-591(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    3. "The nucleotide sequence of Saccharomyces cerevisiae chromosome VII."
      Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L., Coblenz A., Coglievina M., Coissac E.
      , Defoor E., Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K., Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M., Zollner A., Kleine K.
      Nature 387:81-84(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    4. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    5. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    6. "Glyceraldehyde 3-phosphate dehydrogenase: Amino acid sequence of enzyme from baker's yeast."
      Jones G.M., Harris J.I.
      FEBS Lett. 22:185-189(1972) [PubMed] [Europe PMC] [Abstract]
      Cited for: PARTIAL PROTEIN SEQUENCE OF 2-332, CLEAVAGE OF INITIATOR METHIONINE.
    7. Cited for: PROTEIN SEQUENCE OF 47-58.
      Strain: ATCC 204508 / S288c.
    8. "Gene linkage of two-dimensional polyacrylamide gel electrophoresis resolved proteins from isogene families in Saccharomyces cerevisiae by microsequencing of in-gel trypsin generated peptides."
      Norbeck J., Blomberg A.
      Electrophoresis 16:149-156(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: PARTIAL PROTEIN SEQUENCE.
      Strain: ATCC 38531 / Y41 and ATCC 44827 / SKQ2N.
    9. "Yeast mitochondrial dehydrogenases are associated in a supramolecular complex."
      Grandier-Vazeille X., Bathany K., Chaignepain S., Camougrand N., Manon S., Schmitter J.-M.
      Biochemistry 40:9758-9769(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION.
    10. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    11. "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry."
      Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.
      Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    12. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
      Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
      Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-302, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    13. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
      Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
      Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    14. "Sites of ubiquitin attachment in Saccharomyces cerevisiae."
      Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.
      Proteomics 12:236-240(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    15. "Structure of GAPDH 3 from S.cerevisiae at 2.0 A resolution."
      Garcia-Saez I., Kozielski F., Job D., Boscheron C.
      Submitted (DEC-2010) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS).
    16. "Preliminary crystallographic analysis of glyceraldehyde-3-phosphate dehydrogenase 3 from Saccharomyces cerevisiae."
      Liu Q., Wang H., Liu H., Teng M., Li X.
      Acta Crystallogr. F 68:978-980(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.49 ANGSTROMS), SUBUNIT.

    Entry informationi

    Entry nameiG3P3_YEAST
    AccessioniPrimary (citable) accession number: P00359
    Secondary accession number(s): D6VUX4, Q6Q5P9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 21, 1986
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 160 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    There are three genes for G3PDH in yeast.
    Present with 169000 molecules/cell in log phase SD medium.1 Publication

    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
    4. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    5. Yeast chromosome VII
      Yeast (Saccharomyces cerevisiae) chromosome VII: entries and gene names

    External Data

    Dasty 3