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Protein

Pyruvate decarboxylase isozyme 2

Gene

PDC5

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

Functioni

Second most abundant 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 derived from threonine (2-oxobutanoate), norvaline (2-oxopentanoate), valine (3-methyl-2-oxobutanoate, also alpha-keto-isovalerate), isoleucine ((3S)-3-methyl-2-oxopentanoate, also alpha-keto-beta-methylvalerate), phenylalanine (phenylpyruvate), and tryptophan (3-(indol-3-yl)pyruvate), whereas transaminated 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.10 Publications

Miscellaneous

Present with 471316 molecules/cell in log phase SD medium.1 Publication

Catalytic activityi

Pyruvate = acetaldehyde + CO2.1 Publication
3-methyl-2-oxobutanoate = 2-methylpropanal + CO2.1 Publication
(3S)-3-methyl-2-oxopentanoate = 2-methylbutanal + CO2.1 Publication
3-(indol-3-yl)pyruvate = 2-(indol-3-yl)acetaldehyde + CO2.1 Publication
Phenylpyruvate = phenylacetaldehyde + CO2.1 Publication
2-oxobutanoate = 1-propanal + CO2.1 Publication
2-oxopentanoate = butanal + CO2.2 Publications
2 acetaldehyde = acetoin.1 Publication1 Publication
Acetaldehyde + pyruvate = acetoin + CO2.1 Publication1 Publication

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

Enzyme regulationi

Allosterically activated by substrate.

Kineticsi

  1. KM=5.1 mM for pyruvate1 Publication
  2. KM=1.2 mM for 2-oxobutanoate1 Publication
  3. KM=1.5 mM for 2-oxopentanoate1 Publication
  4. KM=0.67 mM for phenylpyruvate1 Publication
  1. Vmax=1.3 µmol/min/mg enzyme for pyruvate1 Publication
  2. Vmax=0.4 µmol/min/mg enzyme for 2-oxobutanoate1 Publication
  3. Vmax=0.4 µmol/min/mg enzyme for 2-oxopentanoate1 Publication
  4. Vmax=68 µmol/min/mg enzyme for phenylpyruvate1 Publication
  5. Vmax=46 µmol/min/mg enzyme for 3-methyl-2-oxobutanoate1 Publication
  6. Vmax=19 µmol/min/mg enzyme for 4-methyl-2-oxopentanoate1 Publication
  7. Vmax=8 µmol/min/mg enzyme for 3-methyl-2-oxopentanoate1 Publication
  8. Vmax=54 µmol/min/mg enzyme for 4-methylthio-2-oxobutanoate1 Publication

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)DescriptionActionsGraphical viewLength
Binding sitei28SubstrateBy similarity1
Binding sitei115SubstrateBy similarity1
Binding sitei157Substrate; allosteric siteBy similarity1
Metal bindingi444MagnesiumBy similarity1
Metal bindingi471MagnesiumBy similarity1
Metal bindingi473Magnesium; via carbonyl oxygenBy similarity1
Binding sitei477SubstrateBy similarity1

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
  • glycolytic fermentation to ethanol Source: SGD
  • L-phenylalanine catabolic process Source: SGD
  • pyruvate metabolic process Source: SGD
  • tryptophan catabolic process Source: SGD

Keywordsi

Molecular functionAllosteric enzyme, Decarboxylase, Lyase
Biological processBranched-chain amino acid catabolism, Phenylalanine catabolism, Tryptophan catabolism
LigandMagnesium, Metal-binding, Thiamine pyrophosphate

Enzyme and pathway databases

BioCyciMetaCyc:YLR134W-MONOMER
YEAST:YLR134W-MONOMER
BRENDAi4.1.1.1 984
SABIO-RKP16467
UniPathwayiUPA00206
UPA00866

Names & Taxonomyi

Protein namesi
Recommended name:
Pyruvate decarboxylase isozyme 2 (EC:4.1.1.-2 Publications, EC:4.1.1.431 Publication, EC:4.1.1.722 Publications, EC:4.1.1.741 Publication)
Alternative name(s):
Thiamine pyrophosphate-dependent 2-oxo-acid decarboxylase
Short name:
2ODC
Gene namesi
Name:PDC5
Ordered Locus Names:YLR134W
ORF Names:L3133, L9606.7
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XII

Organism-specific databases

EuPathDBiFungiDB:YLR134W
SGDiS000004124 PDC5

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

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)DescriptionActionsGraphical viewLength
ChainiPRO_00000907711 – 563Pyruvate decarboxylase isozyme 2Add BLAST563

Proteomic databases

MaxQBiP16467
PaxDbiP16467
PRIDEiP16467
TopDownProteomicsiP16467

PTM databases

CarbonylDBiP16467
iPTMnetiP16467

Expressioni

Inductioni

Protein expression is strongly induced by high concentrations of fermentable carbon sources, under anaerobic growth conditions, and by thiamine limitation, but is repressed by the presence of PDC1 (independent of its catalytic activity) and thiamine.

Interactioni

Subunit structurei

Homotetramer.

Protein-protein interaction databases

BioGridi31403, 51 interactors
DIPiDIP-4603N
IntActiP16467, 12 interactors
MINTiP16467
STRINGi4932.YLR134W

Structurei

3D structure databases

ProteinModelPortaliP16467
SMRiP16467
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni390 – 476Thiamine pyrophosphate bindingBy similarityAdd BLAST87

Sequence similaritiesi

Belongs to the TPP enzyme family.Curated

Phylogenomic databases

GeneTreeiENSGT00550000075465
HOGENOMiHOG000061334
InParanoidiP16467
KOiK01568
OrthoDBiEOG092C29BL

Family and domain databases

InterProiView protein in InterPro
IPR029035 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
PfamiView protein in Pfam
PF02775 TPP_enzyme_C, 1 hit
PF00205 TPP_enzyme_M, 1 hit
PF02776 TPP_enzyme_N, 1 hit
PIRSFiPIRSF036565 Pyruvt_ip_decrb, 1 hit
SUPFAMiSSF52467 SSF52467, 1 hit
SSF52518 SSF52518, 2 hits
PROSITEiView protein in PROSITE
PS00187 TPP_ENZYMES, 1 hit

Sequencei

Sequence statusi: Complete.

P16467-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSEITLGKYL FERLSQVNCN TVFGLPGDFN LSLLDKLYEV KGMRWAGNAN
60 70 80 90 100
ELNAAYAADG YARIKGMSCI ITTFGVGELS ALNGIAGSYA EHVGVLHVVG
110 120 130 140 150
VPSISSQAKQ LLLHHTLGNG DFTVFHRMSA NISETTAMIT DIANAPAEID
160 170 180 190 200
RCIRTTYTTQ RPVYLGLPAN LVDLNVPAKL LETPIDLSLK PNDAEAEAEV
210 220 230 240 250
VRTVVELIKD AKNPVILADA CASRHDVKAE TKKLMDLTQF PVYVTPMGKG
260 270 280 290 300
AIDEQHPRYG GVYVGTLSRP EVKKAVESAD LILSIGALLS DFNTGSFSYS
310 320 330 340 350
YKTKNIVEFH SDHIKIRNAT FPGVQMKFAL QKLLDAIPEV VKDYKPVAVP
360 370 380 390 400
ARVPITKSTP ANTPMKQEWM WNHLGNFLRE GDIVIAETGT SAFGINQTTF
410 420 430 440 450
PTDVYAIVQV LWGSIGFTVG ALLGATMAAE ELDPKKRVIL FIGDGSLQLT
460 470 480 490 500
VQEISTMIRW GLKPYIFVLN NNGYTIEKLI HGPHAEYNEI QGWDHLALLP
510 520 530 540 550
TFGARNYETH RVATTGEWEK LTQDKDFQDN SKIRMIEVML PVFDAPQNLV
560
KQAQLTAATN AKQ
Length:563
Mass (Da):61,912
Last modified:January 23, 2007 - v4
Checksum:iDCA06A73E18DD819
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti35D → N in CAA33709 (PubMed:2185016).Curated1
Sequence conflicti143A → R in CAA33709 (PubMed:2185016).Curated1
Sequence conflicti207L → F in CAA33709 (PubMed:2185016).Curated1
Sequence conflicti222A → C in CAA33709 (PubMed:2185016).Curated1
Sequence conflicti341V → A in CAA33709 (PubMed:2185016).Curated1
Sequence conflicti373H → Q in CAA33709 (PubMed:2185016).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X15668 Genomic DNA Translation: CAA33709.1
X91258 Genomic DNA Translation: CAA62647.1
Z73306 Genomic DNA Translation: CAA97705.1
U53881 Genomic DNA Translation: AAB82395.1
BK006945 Genomic DNA Translation: DAA09445.1
PIRiS59324
RefSeqiNP_013235.1, NM_001182021.1

Genome annotation databases

EnsemblFungiiYLR134W; YLR134W; YLR134W
GeneIDi850825
KEGGisce:YLR134W

Similar proteinsi

Entry informationi

Entry nameiPDC5_YEAST
AccessioniPrimary (citable) accession number: P16467
Secondary accession number(s): D6VYC9
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 1, 1990
Last sequence update: January 23, 2007
Last modified: May 23, 2018
This is version 177 of the entry and version 4 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

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