Pyruvate decarboxylase isozyme 3 - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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P26263 (PDC6_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified December 14, 2011. Version 115. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Pyruvate decarboxylase isozyme 3
EC=4.1.1.-
EC=4.1.1.1

Gene names

Name:	PDC6
Ordered Locus Names:	YGR087C

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	563 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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 can not compensate for the other two pyruvate decarboxylases to sustain fermentation. Ref.5 Ref.6 Ref.7 Ref.8 Ref.9 Ref.10 Ref.11
Catalytic activity	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.
Cofactor	Binds 1 magnesium per subunit By similarity. Binds 1 thiamine pyrophosphate per subunit By similarity.
Pathway	Fermentation; ethanol fermentation. Amino-acid degradation; Ehrlich pathway.
Subunit structure	Homotetramer By similarity.
Subcellular location	Cytoplasm Ref.14.
Induction	Expression is very low in the presence of fermentable carbon sources, but is induced, in contrast to PDC5, by ethanol.
Biotechnological use	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). Ref.12
Miscellaneous	Present with 1525 molecules/cell in log phase SD medium. Ref.15
Sequence similarities	Belongs to the TPP enzyme family.

Ontologies

Keywords
Biological process	Branched-chain amino acid catabolism Phenylalanine catabolism Tryptophan catabolism
Cellular component	Cytoplasm
Ligand	Magnesium Metal-binding Thiamine pyrophosphate
Molecular function	Decarboxylase Lyase
PTM	Acetylation Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	L-phenylalanine catabolic process Inferred from electronic annotation. Source: UniProtKB-KW branched chain family amino acid catabolic process Inferred from electronic annotation. Source: UniProtKB-KW ethanol metabolic process Inferred from mutant phenotype Ref.1. Source: SGD tryptophan catabolic process Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cytoplasm Inferred from direct assay Ref.14. Source: SGD
Molecular function	magnesium ion binding Inferred from electronic annotation. Source: InterPro pyruvate decarboxylase activity Inferred from mutant phenotype Ref.1. Source: SGD thiamine pyrophosphate binding Inferred from electronic annotation. Source: InterPro transferase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed By similarity

Chain

2 – 563

562

Pyruvate decarboxylase isozyme 3

PRO_0000090772

Regions

Region

390 – 476

Thiamine pyrophosphate binding By similarity

Sites

Metal binding

444

Magnesium By similarity

Metal binding

471

Magnesium By similarity

Metal binding

473

Magnesium; via carbonyl oxygen By similarity

Binding site

Substrate By similarity

Binding site

115

Substrate By similarity

Binding site

477

Substrate By similarity

Amino acid modifications

Modified residue

N-acetylserine By similarity

Modified residue

294

Phosphothreonine Ref.16

Modified residue

296

Phosphoserine Ref.16

Modified residue

300

Phosphoserine Ref.16

Sequences

Sequence

Length

Mass (Da)

Tools

P26263 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: 83625F09371EBD0F
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FASTA

563

61,580

        10         20         30         40         50         60 
MSEITLGKYL FERLKQVNVN TIFGLPGDFN LSLLDKIYEV DGLRWAGNAN ELNAAYAADG 

        70         80         90        100        110        120 
YARIKGLSVL VTTFGVGELS ALNGIAGSYA EHVGVLHVVG VPSISAQAKQ LLLHHTLGNG 

       130        140        150        160        170        180 
DFTVFHRMSA NISETTSMIT DIATAPSEID RLIRTTFITQ RPSYLGLPAN LVDLKVPGSL 

       190        200        210        220        230        240 
LEKPIDLSLK PNDPEAEKEV IDTVLELIQN SKNPVILSDA CASRHNVKKE TQKLIDLTQF 

       250        260        270        280        290        300 
PAFVTPLGKG SIDEQHPRYG GVYVGTLSKQ DVKQAVESAD LILSVGALLS DFNTGSFSYS 

       310        320        330        340        350        360 
YKTKNVVEFH SDYVKVKNAT FLGVQMKFAL QNLLKVIPDV VKGYKSVPVP TKTPANKGVP 

       370        380        390        400        410        420 
ASTPLKQEWL WNELSKFLQE GDVIISETGT SAFGINQTIF PKDAYGISQV LWGSIGFTTG 

       430        440        450        460        470        480 
ATLGAAFAAE EIDPNKRVIL FIGDGSLQLT VQEISTMIRW GLKPYLFVLN NDGYTIEKLI 

       490        500        510        520        530        540 
HGPHAEYNEI QTWDHLALLP AFGAKKYENH KIATTGEWDA LTTDSEFQKN SVIRLIELKL 

       550        560 
PVFDAPESLI KQAQLTAATN AKQ

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Characterization of PDC6, a third structural gene for pyruvate decarboxylase in Saccharomyces cerevisiae." Hohmann S. J. Bacteriol. 173:7963-7969(1991) [PubMed: 1744053] [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. Kleine K. Nature 387:81-84(1997) [PubMed: 9169869] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases 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: 9341119] [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: 9748245] [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: 10234824] [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: 10753893] [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: 11141278] [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: 12499363] [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: 12902239] [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: 9655924] [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: 9655908] [Abstract] Cited for: REVIEW.
[14]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed: 14562095] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[15]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[16]	"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: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-294; SER-296 AND SER-300, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	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.
PIR	S64382.
RefSeq	NP_011601.1. NM_001181216.1.
3D structure databases
ProteinModelPortal	P26263.
SMR	P26263. Positions 2-563.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-3912N.
IntAct	P26263. 9 interactions.
MINT	MINT-483419.
STRING	P26263.
Proteomic databases
PeptideAtlas	P26263.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YGR087C; YGR087C; YGR087C.
GeneID	852978.
KEGG	sce:YGR087C.
NMPDR	fig\|4932.3.peg.2718.
Organism-specific databases
SGD	S000003319. PDC6.
Phylogenomic databases
eggNOG	fuNOG05694.
GeneTree	EFGT00050000001792.
HOGENOM	HBG479104.
OMA	PINNAIC.
OrthoDB	EOG41NXVF.
Enzyme and pathway databases
BioCyc	MetaCyc:MONOMER-11721.
Gene expression databases
ArrayExpress	P26263.
Genevestigator	P26263.
GermOnline	YGR087C. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR012110. Pyruvt_ip_decrb. IPR012000. Thiamin_PyroP_enz_cen_dom. IPR012001. Thiamin_PyroP_enz_TPP-bd_dom. IPR000399. TPP-bd_CS. IPR011766. TPP_enzyme-bd_C. [Graphical view]
KO	K01568.
PANTHER	PTHR18968:SF4. PTHR18968:SF4. 1 hit.
Pfam	PF02775. TPP_enzyme_C. 1 hit. PF00205. TPP_enzyme_M. 1 hit. PF02776. TPP_enzyme_N. 1 hit. [Graphical view]
PIRSF	PIRSF036565. Pyruvt_ip_decrb. 1 hit.
PROSITE	PS00187. TPP_ENZYMES. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	972780.

Entry information

Entry name

PDC6_YEAST

Accession

Primary (citable) accession number: P26263
Secondary accession number(s): D6VUL9

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 1, 1992
Last sequence update:	January 23, 2007
Last modified:	December 14, 2011
This is version 115 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program

Relevant documents

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

Yeast chromosome VII

Yeast (Saccharomyces cerevisiae) chromosome VII: entries and gene names

PATHWAY comments

Index of metabolic and biosynthesis pathways

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents