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Protein

Glyceraldehyde-3-phosphate dehydrogenase 3

Gene

TDH3

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

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

Pathway: glycolysis

This protein is involved in step 1 of the subpathway that synthesizes pyruvate from D-glyceraldehyde 3-phosphate.
Proteins known to be involved in the 5 steps of the subpathway in this organism are:
  1. Glyceraldehyde-3-phosphate dehydrogenase 1 (TDH1), Glyceraldehyde-3-phosphate dehydrogenase 2 (TDH2), Glyceraldehyde-3-phosphate dehydrogenase 3 (TDH3)
  2. Phosphoglycerate kinase (PGK1)
  3. Phosphoglycerate mutase 2 (GPM2), Phosphoglycerate mutase 3 (GPM3), Phosphoglycerate mutase 1 (GPM1)
  4. Enolase 2 (ENO2), Enolase-related protein 2 (ERR2), Enolase-related protein 1 (ERR1), Enolase-related protein 3 (ERR3), Enolase 1 (ENO1)
  5. Pyruvate kinase 2 (PYK2), Pyruvate kinase 1 (CDC19)
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 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

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

GO - Biological processi

  • apoptotic process Source: SGD
  • gluconeogenesis Source: SGD
  • glycolytic process Source: SGD
  • reactive oxygen species metabolic process Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Glycolysis

Keywords - Ligandi

NAD

Enzyme and pathway databases

BioCyciYEAST:YGR192C-MONOMER.
ReactomeiREACT_275254. Glycolysis.
REACT_286539. Gluconeogenesis.
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 Componenti: Chromosome VII

Organism-specific databases

EuPathDBiFungiDB:YGR192C.
SGDiS000003424. TDH3.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: SGD
  • fungal-type cell wall Source: SGD
  • lipid particle Source: SGD
  • mitochondrion Source: SGD
Complete GO annotation...

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.

Interactioni

Subunit structurei

Homotetramer.1 Publication

Protein-protein interaction databases

BioGridi33445. 159 interactions.
DIPiDIP-4309N.
IntActiP00359. 102 interactions.
MINTiMINT-8285236.
STRINGi4932.YGR192C.

Structurei

Secondary structure

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

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
GeneTreeiENSGT00760000119172.
HOGENOMiHOG000071678.
InParanoidiP00359.
KOiK00134.
OMAiDFLGDSH.
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

        10         20         30         40         50
MVRVAINGFG RIGRLVMRIA LSRPNVEVVA LNDPFITNDY AAYMFKYDST
60 70 80 90 100
HGRYAGEVSH DDKHIIVDGK KIATYQERDP ANLPWGSSNV DIAIDSTGVF
110 120 130 140 150
KELDTAQKHI DAGAKKVVIT APSSTAPMFV MGVNEEKYTS DLKIVSNASC
160 170 180 190 200
TTNCLAPLAK VINDAFGIEE GLMTTVHSLT ATQKTVDGPS HKDWRGGRTA
210 220 230 240 250
SGNIIPSSTG AAKAVGKVLP ELQGKLTGMA FRVPTVDVSV VDLTVKLNKE
260 270 280 290 300
TTYDEIKKVV KAAAEGKLKG VLGYTEDAVV SSDFLGDSHS SIFDASAGIQ
310 320 330
LSPKFVKLVS WYDNEYGYST RVVDLVEHVA KA
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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

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

Protein-protein interaction databases

BioGridi33445. 159 interactions.
DIPiDIP-4309N.
IntActiP00359. 102 interactions.
MINTiMINT-8285236.
STRINGi4932.YGR192C.

2D gel databases

COMPLUYEAST-2DPAGEP00359.
SWISS-2DPAGEP00359.

Proteomic databases

MaxQBiP00359.
PaxDbiP00359.
PeptideAtlasiP00359.
PRIDEiP00359.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YGR192C.
SGDiS000003424. TDH3.

Phylogenomic databases

eggNOGiCOG0057.
GeneTreeiENSGT00760000119172.
HOGENOMiHOG000071678.
InParanoidiP00359.
KOiK00134.
OMAiDFLGDSH.
OrthoDBiEOG70W3Q6.

Enzyme and pathway databases

UniPathwayiUPA00109; UER00184.
BioCyciYEAST:YGR192C-MONOMER.
ReactomeiREACT_275254. Glycolysis.
REACT_286539. Gluconeogenesis.
SABIO-RKP00359.

Miscellaneous databases

NextBioi973112.
PROiP00359.

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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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: June 24, 2015
This is version 168 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

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 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.