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Protein

Pyruvate decarboxylase isozyme 3

Gene

PDC6

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

Minor of three pyruvate decarboxylases (PDC1, PDC5, PDC6) implicated in the nonoxidative conversion of pyruvate to acetaldehyde and carbon dioxide during alcoholic fermentation. Most of the produced acetaldehyde is subsequently reduced to ethanol, but some is required for cytosolic acetyl-CoA production for biosynthetic pathways. The enzyme is also one of five 2-oxo acid decarboxylases (PDC1, PDC5, PDC6, ARO10, and THI3) able to decarboxylate more complex 2-oxo acids (alpha-keto-acids) than pyruvate, which seem mainly involved in amino acid catabolism. Here the enzyme catalyzes the decarboxylation of amino acids, which, in a first step, have been transaminated to the corresponding 2-oxo acids. In a third step, the resulting aldehydes are reduced to alcohols, collectively referred to as fusel oils or alcohols. Its preferred substrates are the transaminated amino acids valine, isoleucine, phenylalanine, and tryptophan, whereas leucine is no substrate. In a side-reaction the carbanionic intermediate (or active aldehyde) generated by decarboxylation or by activation of an aldehyde can react with an aldehyde via condensation (or carboligation) yielding a 2-hydroxy ketone, collectively called acyloins. The expression level of this protein in the presence of fermentable carbon sources is so low that it cannot compensate for the other two pyruvate decarboxylases to sustain fermentation.7 Publications

Catalytic activityi

A 2-oxo acid = an aldehyde + CO2.
3-(indol-3-yl)pyruvate = 2-(indol-3-yl)acetaldehyde + CO2.
Phenylpyruvate = phenylacetaldehyde + CO2.
Pyruvate = Acetaldehyde + CO2.
A 2-oxo acid + an aldehyde = A 2-hydroxy ketone + CO2.
An aldehyde + an aldehyde = A 2-hydroxy ketone.

Cofactori

Protein has several cofactor binding sites:
  • Mg2+By similarityNote: Binds 1 Mg2+ per subunit.By similarity
  • thiamine diphosphateBy similarityNote: Binds 1 thiamine pyrophosphate per subunit.By similarity

Pathwayi: ethanol fermentation

This protein is involved in the pathway ethanol fermentation, which is part of Fermentation.
View all proteins of this organism that are known to be involved in the pathway ethanol fermentation and in Fermentation.

Pathwayi: Ehrlich pathway

This protein is involved in the pathway Ehrlich pathway, which is part of Amino-acid degradation.
View all proteins of this organism that are known to be involved in the pathway Ehrlich pathway and in Amino-acid degradation.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei28 – 281SubstrateBy similarity
Binding sitei115 – 1151SubstrateBy similarity
Metal bindingi444 – 4441MagnesiumBy similarity
Metal bindingi471 – 4711MagnesiumBy similarity
Metal bindingi473 – 4731Magnesium; via carbonyl oxygenBy similarity
Binding sitei477 – 4771SubstrateBy similarity

GO - Molecular functioni

GO - Biological processi

  • aromatic amino acid family catabolic process to alcohol via Ehrlich pathway Source: SGD
  • branched-chain amino acid catabolic process Source: UniProtKB-KW
  • ethanol metabolic process Source: SGD
  • L-phenylalanine catabolic process Source: SGD
  • tryptophan catabolic process Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Biological processi

Branched-chain amino acid catabolism, Phenylalanine catabolism, Tryptophan catabolism

Keywords - Ligandi

Magnesium, Metal-binding, Thiamine pyrophosphate

Enzyme and pathway databases

BioCyciMetaCyc:YGR087C-MONOMER.
YEAST:YGR087C-MONOMER.
BRENDAi4.1.1.1. 984.
UniPathwayiUPA00206.
UPA00866.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyruvate decarboxylase isozyme 3 (EC:4.1.1.1)
Gene namesi
Name:PDC6
Ordered Locus Names:YGR087C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome VII

Organism-specific databases

EuPathDBiFungiDB:YGR087C.
SGDiS000003319. PDC6.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Biotechnological usei

Fusel oils and acyloins are important flavor and aroma compounds in yeast-fermented products contributing to the quality of beverages and food, e.g. fusel oils in whiskey, contrary to common believe, seem to alleviate hangover. In general they are desirable at low concentrations, whereas high concentrations may spoil the product. By adjusting growth conditions and substrate their production is sought to be influenced. Due to their broad substrate tolerance pyruvate decarboxylases are important biocatalysts for chemoenzymatic syntheses, both by fermentation and in vitro, e.g. in the production of ephedrine, vitamin E, or phenylethanol (rose flavor).1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedBy similarity
Chaini2 – 563562Pyruvate decarboxylase isozyme 3PRO_0000090772Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserineBy similarity
Modified residuei223 – 2231PhosphoserineBy similarity
Modified residuei266 – 2661PhosphothreonineBy similarity
Modified residuei353 – 3531PhosphothreonineBy similarity
Modified residuei522 – 5221PhosphothreonineBy similarity

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiP26263.
PeptideAtlasiP26263.
TopDownProteomicsiP26263.

PTM databases

iPTMnetiP26263.

Expressioni

Inductioni

Expression is very low in the presence of fermentable carbon sources, but is induced, in contrast to PDC5, by ethanol.

Interactioni

Subunit structurei

Homotetramer.By similarity

Protein-protein interaction databases

BioGridi33329. 28 interactions.
DIPiDIP-3912N.
MINTiMINT-483419.

Structurei

3D structure databases

ProteinModelPortaliP26263.
SMRiP26263. Positions 2-563.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni390 – 47687Thiamine pyrophosphate bindingBy similarityAdd
BLAST

Sequence similaritiesi

Belongs to the TPP enzyme family.Curated

Phylogenomic databases

GeneTreeiENSGT00550000075465.
HOGENOMiHOG000061334.
InParanoidiP26263.
KOiK01568.
OMAiNKVPEYM.
OrthoDBiEOG779P6S.

Family and domain databases

Gene3Di3.40.50.1220. 1 hit.
3.40.50.970. 2 hits.
InterProiIPR029035. DHS-like_NAD/FAD-binding_dom.
IPR029061. THDP-binding.
IPR012000. Thiamin_PyroP_enz_cen_dom.
IPR012001. Thiamin_PyroP_enz_TPP-bd_dom.
IPR000399. TPP-bd_CS.
IPR012110. TPP_enzyme.
IPR011766. TPP_enzyme-bd_C.
[Graphical view]
PANTHERiPTHR18968:SF4. PTHR18968:SF4. 1 hit.
PfamiPF02775. TPP_enzyme_C. 1 hit.
PF00205. TPP_enzyme_M. 1 hit.
PF02776. TPP_enzyme_N. 1 hit.
[Graphical view]
PIRSFiPIRSF036565. Pyruvt_ip_decrb. 1 hit.
SUPFAMiSSF52467. SSF52467. 1 hit.
SSF52518. SSF52518. 2 hits.
PROSITEiPS00187. TPP_ENZYMES. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P26263-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSEITLGKYL FERLKQVNVN TIFGLPGDFN LSLLDKIYEV DGLRWAGNAN
60 70 80 90 100
ELNAAYAADG YARIKGLSVL VTTFGVGELS ALNGIAGSYA EHVGVLHVVG
110 120 130 140 150
VPSISAQAKQ LLLHHTLGNG DFTVFHRMSA NISETTSMIT DIATAPSEID
160 170 180 190 200
RLIRTTFITQ RPSYLGLPAN LVDLKVPGSL LEKPIDLSLK PNDPEAEKEV
210 220 230 240 250
IDTVLELIQN SKNPVILSDA CASRHNVKKE TQKLIDLTQF PAFVTPLGKG
260 270 280 290 300
SIDEQHPRYG GVYVGTLSKQ DVKQAVESAD LILSVGALLS DFNTGSFSYS
310 320 330 340 350
YKTKNVVEFH SDYVKVKNAT FLGVQMKFAL QNLLKVIPDV VKGYKSVPVP
360 370 380 390 400
TKTPANKGVP ASTPLKQEWL WNELSKFLQE GDVIISETGT SAFGINQTIF
410 420 430 440 450
PKDAYGISQV LWGSIGFTTG ATLGAAFAAE EIDPNKRVIL FIGDGSLQLT
460 470 480 490 500
VQEISTMIRW GLKPYLFVLN NDGYTIEKLI HGPHAEYNEI QTWDHLALLP
510 520 530 540 550
AFGAKKYENH KIATTGEWDA LTTDSEFQKN SVIRLIELKL PVFDAPESLI
560
KQAQLTAATN AKQ
Length:563
Mass (Da):61,580
Last modified:January 23, 2007 - v3
Checksum:i83625F09371EBD0F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X55905 Genomic DNA. Translation: CAA39398.1.
Z72872 Genomic DNA. Translation: CAA97089.1.
Z72873 Genomic DNA. Translation: CAA97091.1.
X66843 Genomic DNA. Translation: CAA47319.1.
BK006941 Genomic DNA. Translation: DAA08180.1.
PIRiS64382.
RefSeqiNP_011601.3. NM_001181216.3.

Genome annotation databases

EnsemblFungiiYGR087C; YGR087C; YGR087C.
GeneIDi852978.
KEGGisce:YGR087C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X55905 Genomic DNA. Translation: CAA39398.1.
Z72872 Genomic DNA. Translation: CAA97089.1.
Z72873 Genomic DNA. Translation: CAA97091.1.
X66843 Genomic DNA. Translation: CAA47319.1.
BK006941 Genomic DNA. Translation: DAA08180.1.
PIRiS64382.
RefSeqiNP_011601.3. NM_001181216.3.

3D structure databases

ProteinModelPortaliP26263.
SMRiP26263. Positions 2-563.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi33329. 28 interactions.
DIPiDIP-3912N.
MINTiMINT-483419.

PTM databases

iPTMnetiP26263.

Proteomic databases

MaxQBiP26263.
PeptideAtlasiP26263.
TopDownProteomicsiP26263.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYGR087C; YGR087C; YGR087C.
GeneIDi852978.
KEGGisce:YGR087C.

Organism-specific databases

EuPathDBiFungiDB:YGR087C.
SGDiS000003319. PDC6.

Phylogenomic databases

GeneTreeiENSGT00550000075465.
HOGENOMiHOG000061334.
InParanoidiP26263.
KOiK01568.
OMAiNKVPEYM.
OrthoDBiEOG779P6S.

Enzyme and pathway databases

UniPathwayiUPA00206.
UPA00866.
BioCyciMetaCyc:YGR087C-MONOMER.
YEAST:YGR087C-MONOMER.
BRENDAi4.1.1.1. 984.

Miscellaneous databases

PROiP26263.

Family and domain databases

Gene3Di3.40.50.1220. 1 hit.
3.40.50.970. 2 hits.
InterProiIPR029035. DHS-like_NAD/FAD-binding_dom.
IPR029061. THDP-binding.
IPR012000. Thiamin_PyroP_enz_cen_dom.
IPR012001. Thiamin_PyroP_enz_TPP-bd_dom.
IPR000399. TPP-bd_CS.
IPR012110. TPP_enzyme.
IPR011766. TPP_enzyme-bd_C.
[Graphical view]
PANTHERiPTHR18968:SF4. PTHR18968:SF4. 1 hit.
PfamiPF02775. TPP_enzyme_C. 1 hit.
PF00205. TPP_enzyme_M. 1 hit.
PF02776. TPP_enzyme_N. 1 hit.
[Graphical view]
PIRSFiPIRSF036565. Pyruvt_ip_decrb. 1 hit.
SUPFAMiSSF52467. SSF52467. 1 hit.
SSF52518. SSF52518. 2 hits.
PROSITEiPS00187. TPP_ENZYMES. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Characterization of PDC6, a third structural gene for pyruvate decarboxylase in Saccharomyces cerevisiae."
    Hohmann S.
    J. Bacteriol. 173:7963-7969(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], EXPRESSION LEVEL.
  2. "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.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. Hohmann S.
    Submitted (APR-1992) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-159.
  5. "A 13C nuclear magnetic resonance investigation of the metabolism of leucine to isoamyl alcohol in Saccharomyces cerevisiae."
    Dickinson J.R., Lanterman M.M., Danner D.J., Pearson B.M., Sanz P., Harrison S.J., Hewlins M.J.
    J. Biol. Chem. 272:26871-26878(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: ROLE IN AMINO ACID CATABOLISM.
  6. "An investigation of the metabolism of valine to isobutyl alcohol in Saccharomyces cerevisiae."
    Dickinson J.R., Harrison S.J., Hewlins M.J.
    J. Biol. Chem. 273:25751-25756(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: ROLE IN VALINE CATABOLISM.
  7. "Growth requirements of pyruvate-decarboxylase-negative Saccharomyces cerevisiae."
    Flikweert M.T., de Swaaf M., van Dijken J.P., Pronk J.T.
    FEMS Microbiol. Lett. 174:73-79(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CYTOSOLIC ACETYL-COA PRODUCTION.
  8. "An investigation of the metabolism of isoleucine to active Amyl alcohol in Saccharomyces cerevisiae."
    Dickinson J.R., Harrison S.J., Dickinson J.A., Hewlins M.J.
    J. Biol. Chem. 275:10937-10942(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: ROLE IN ISOLEUCINE CATABOLISM.
  9. "Generation of odorous acyloins by yeast pyruvate decarboxylases and their occurrence in sherry and soy sauce."
    Neuser F., Zorn H., Berger R.G.
    J. Agric. Food Chem. 48:6191-6195(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, GENERATION OF ACYLOINS.
  10. "The catabolism of amino acids to long chain and complex alcohols in Saccharomyces cerevisiae."
    Dickinson J.R., Salgado L.E., Hewlins M.J.
    J. Biol. Chem. 278:8028-8034(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: ROLE IN PHENYLALANINE; TRYPTOPHAN AND LEUCINE CATABOLISM.
  11. "Identification and characterization of phenylpyruvate decarboxylase genes in Saccharomyces cerevisiae."
    Vuralhan Z., Morais M.A., Tai S.L., Piper M.D., Pronk J.T.
    Appl. Environ. Microbiol. 69:4534-4541(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, AROMATIC AMINO ACIDS AS NITROGEN SOURCE.
  12. "Application of alpha-keto acid decarboxylases in biotransformations."
    Iding H., Siegert P., Mesch K., Pohl M.
    Biochim. Biophys. Acta 1385:307-322(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW, BIOTECHNOLOGICAL RELEVANCE.
  13. "Thiamin metabolism and thiamin diphosphate-dependent enzymes in the yeast Saccharomyces cerevisiae: genetic regulation."
    Hohmann S., Meacock P.A.
    Biochim. Biophys. Acta 1385:201-219(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.
  14. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  15. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiPDC6_YEAST
AccessioniPrimary (citable) accession number: P26263
Secondary accession number(s): D6VUL9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 1992
Last sequence update: January 23, 2007
Last modified: June 8, 2016
This is version 152 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 1525 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome VII
    Yeast (Saccharomyces cerevisiae) chromosome VII: entries and gene names

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.