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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: Annotation score: 5 out of 5-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 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.9 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

Enzyme regulationi

Allosterically activated by substrate.

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

  • branched-chain-2-oxoacid decarboxylase activity Source: SGD
  • magnesium ion binding Source: InterPro
  • pyruvate decarboxylase activity Source: SGD
  • thiamine pyrophosphate binding Source: InterPro

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
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: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.-, EC:4.1.1.1)
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

GO - Cellular componenti

  • cytoplasm Source: UniProtKB-SubCell
  • nucleus Source: SGD
Complete GO annotation...

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
Initiator methionineiRemovedBy similarity
ChainiPRO_00000907712 – 563Pyruvate decarboxylase isozyme 2Add BLAST562

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineBy similarity1
Cross-linki212Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Modified residuei223PhosphoserineBy similarity1
Cross-linki233Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Modified residuei266PhosphothreonineBy similarity1
Cross-linki332Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki520Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Modified residuei522PhosphothreonineBy similarity1

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiP16467.
PRIDEiP16467.
TopDownProteomicsiP16467.

PTM databases

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. 35 interactors.
DIPiDIP-4603N.
IntActiP16467. 5 interactors.
MINTiMINT-487502.

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.
OMAiHEWLWPR.
OrthoDBiEOG092C29BL.

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.

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.

Cross-referencesi

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.

3D structure databases

ProteinModelPortaliP16467.
SMRiP16467.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31403. 35 interactors.
DIPiDIP-4603N.
IntActiP16467. 5 interactors.
MINTiMINT-487502.

PTM databases

iPTMnetiP16467.

Proteomic databases

MaxQBiP16467.
PRIDEiP16467.
TopDownProteomicsiP16467.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYLR134W; YLR134W; YLR134W.
GeneIDi850825.
KEGGisce:YLR134W.

Organism-specific databases

EuPathDBiFungiDB:YLR134W.
SGDiS000004124. PDC5.

Phylogenomic databases

GeneTreeiENSGT00550000075465.
HOGENOMiHOG000061334.
InParanoidiP16467.
KOiK01568.
OMAiHEWLWPR.
OrthoDBiEOG092C29BL.

Enzyme and pathway databases

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

Miscellaneous databases

PROiP16467.

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...

Entry informationi

Entry nameiPDC5_YEAST
AccessioniPrimary (citable) accession number: P16467
Secondary accession number(s): D6VYC9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1990
Last sequence update: January 23, 2007
Last modified: November 2, 2016
This is version 162 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

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

Keywords - Technical termi

Allosteric enzyme, 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 XII
    Yeast (Saccharomyces cerevisiae) chromosome XII: 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.