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Protein

Pyruvate decarboxylase isozyme 1

Gene

PDC1

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

Major 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-ketoacids) 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.10 Publications

Catalytic activityi

A 2-oxo acid = an aldehyde + CO2.1 Publication
Pyruvate = Acetaldehyde + CO2.1 Publication
Phenylpyruvate = phenylacetaldehyde + CO2.1 Publication
3-(indol-3-yl)pyruvate = 2-(indol-3-yl)acetaldehyde + CO2.1 Publication

Cofactori

Protein has several cofactor binding sites:

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 sitei28Substrate1
Binding sitei115Substrate1
Binding sitei157Substrate; allosteric site1
Metal bindingi444Magnesium1
Metal bindingi471Magnesium1
Metal bindingi473Magnesium; via carbonyl oxygen1
Binding sitei477Substrate1

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
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:MONOMER3O-117.
YEAST:MONOMER3O-117.
BRENDAi4.1.1.1. 984.
SABIO-RKP06169.
UniPathwayiUPA00206.
UPA00866.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyruvate decarboxylase isozyme 1 (EC:4.1.1.-1 Publication, EC:4.1.1.11 Publication, EC:4.1.1.431 Publication, EC:4.1.1.741 Publication)
Gene namesi
Name:PDC1
Ordered Locus Names:YLR044C
ORF Names:L2104
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XII

Organism-specific databases

EuPathDBiFungiDB:YLR044C.
SGDiS000004034. PDC1.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: SGD
  • 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

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi291D → N in PDC1-8; reduces catalytic activity to 10% but retains autoregulatory activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved2 Publications
ChainiPRO_00000907702 – 563Pyruvate decarboxylase isozyme 1Add BLAST562

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserine2 Publications1
Cross-linki212Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Modified residuei223PhosphoserineCombined sources1
Cross-linki233Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Modified residuei266PhosphothreonineCombined sources1
Cross-linki269Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Cross-linki332Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Modified residuei336PhosphothreonineCombined sources1
Modified residuei353PhosphothreonineCombined sources1
Cross-linki484Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Cross-linki505Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Cross-linki520Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Modified residuei522PhosphothreonineCombined sources1
Modified residuei526PhosphoserineCombined sources1

Post-translational modificationi

Cleavage of N-terminal methionine and N-terminal acetylation by NAT1/ARD1.2 Publications

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiP06169.
PRIDEiP06169.
TopDownProteomicsiP06169.

2D gel databases

COMPLUYEAST-2DPAGEP06169.
SWISS-2DPAGEP06169.

PTM databases

iPTMnetiP06169.

Expressioni

Inductioni

Protein expression is strongly induced by high concentrations of fermentable carbon sources and under anaerobic growth conditions and is repressed by ethanol. Protein expression level is also autoregulated through an unknown mechanism.

Interactioni

Subunit structurei

Homotetramer.3 Publications

Protein-protein interaction databases

BioGridi31319. 121 interactors.
DIPiDIP-6773N.
IntActiP06169. 79 interactors.
MINTiMINT-667063.

Structurei

Secondary structure

1563
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 5Combined sources3
Helixi6 – 16Combined sources11
Beta strandi21 – 24Combined sources4
Helixi28 – 30Combined sources3
Helixi31 – 35Combined sources5
Helixi36 – 39Combined sources4
Helixi51 – 65Combined sources15
Beta strandi68 – 73Combined sources6
Helixi76 – 91Combined sources16
Beta strandi95 – 101Combined sources7
Helixi104 – 108Combined sources5
Beta strandi109 – 111Combined sources3
Beta strandi114 – 116Combined sources3
Beta strandi118 – 120Combined sources3
Helixi124 – 130Combined sources7
Beta strandi134 – 138Combined sources5
Turni142 – 144Combined sources3
Helixi145 – 159Combined sources15
Beta strandi163 – 168Combined sources6
Helixi171 – 173Combined sources3
Beta strandi174 – 177Combined sources4
Helixi178 – 182Combined sources5
Helixi194 – 210Combined sources17
Beta strandi212 – 218Combined sources7
Helixi220 – 224Combined sources5
Helixi228 – 238Combined sources11
Beta strandi242 – 244Combined sources3
Turni246 – 250Combined sources5
Beta strandi259 – 262Combined sources4
Helixi265 – 267Combined sources3
Helixi270 – 277Combined sources8
Beta strandi280 – 286Combined sources7
Turni291 – 297Combined sources7
Beta strandi306 – 309Combined sources4
Beta strandi311 – 316Combined sources6
Beta strandi319 – 322Combined sources4
Helixi326 – 340Combined sources15
Turni341 – 343Combined sources3
Helixi367 – 374Combined sources8
Turni375 – 377Combined sources3
Beta strandi383 – 386Combined sources4
Helixi390 – 394Combined sources5
Helixi395 – 397Combined sources3
Beta strandi405 – 407Combined sources3
Turni410 – 412Combined sources3
Helixi417 – 432Combined sources16
Beta strandi438 – 443Combined sources6
Helixi444 – 450Combined sources7
Helixi451 – 453Combined sources3
Helixi454 – 459Combined sources6
Beta strandi465 – 473Combined sources9
Helixi475 – 480Combined sources6
Helixi486 – 488Combined sources3
Helixi495 – 497Combined sources3
Helixi498 – 501Combined sources4
Beta strandi505 – 512Combined sources8
Helixi515 – 522Combined sources8
Turni525 – 528Combined sources4
Beta strandi531 – 539Combined sources9
Helixi547 – 561Combined sources15

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1PVDX-ray2.30A/B2-556[»]
1PYDX-ray2.40A/B1-556[»]
1QPBX-ray2.40A/B1-563[»]
2VK1X-ray1.71A/B/C/D1-563[»]
2VK8X-ray1.42A/B/C/D1-563[»]
2W93X-ray1.60A/B/C/D1-563[»]
ProteinModelPortaliP06169.
SMRiP06169.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP06169.

Family & Domainsi

Region

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

Sequence similaritiesi

Belongs to the TPP enzyme family.Curated

Phylogenomic databases

GeneTreeiENSGT00550000075465.
InParanoidiP06169.
KOiK01568.
OMAiWPRVGEF.
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.

P06169-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSEITLGKYL FERLKQVNVN TVFGLPGDFN LSLLDKIYEV EGMRWAGNAN
60 70 80 90 100
ELNAAYAADG YARIKGMSCI ITTFGVGELS ALNGIAGSYA EHVGVLHVVG
110 120 130 140 150
VPSISAQAKQ LLLHHTLGNG DFTVFHRMSA NISETTAMIT DIATAPAEID
160 170 180 190 200
RCIRTTYVTQ RPVYLGLPAN LVDLNVPAKL LQTPIDMSLK PNDAESEKEV
210 220 230 240 250
IDTILALVKD AKNPVILADA CCSRHDVKAE TKKLIDLTQF PAFVTPMGKG
260 270 280 290 300
SIDEQHPRYG GVYVGTLSKP EVKEAVESAD LILSVGALLS DFNTGSFSYS
310 320 330 340 350
YKTKNIVEFH SDHMKIRNAT FPGVQMKFVL QKLLTTIADA AKGYKPVAVP
360 370 380 390 400
ARTPANAAVP ASTPLKQEWM WNQLGNFLQE GDVVIAETGT SAFGINQTTF
410 420 430 440 450
PNNTYGISQV LWGSIGFTTG ATLGAAFAAE EIDPKKRVIL FIGDGSLQLT
460 470 480 490 500
VQEISTMIRW GLKPYLFVLN NDGYTIEKLI HGPKAQYNEI QGWDHLSLLP
510 520 530 540 550
TFGAKDYETH RVATTGEWDK LTQDKSFNDN SKIRMIEIML PVFDAPQNLV
560
EQAKLTAATN AKQ
Length:563
Mass (Da):61,495
Last modified:January 23, 2007 - v7
Checksum:i799F85C3AC3FCAB6
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti55A → R in CAA54522 (PubMed:3537965).Curated1
Sequence conflicti106A → S in CAA28380 (PubMed:3537965).Curated1
Sequence conflicti106A → S in CAA54522 (PubMed:3537965).Curated1
Sequence conflicti106A → S in CAA54518 (PubMed:3537965).Curated1
Sequence conflicti106A → S in CAA54521 (PubMed:3537965).Curated1
Sequence conflicti115Missing in CAA28380 (PubMed:3537965).Curated1
Sequence conflicti143A → C in CAA54522 (PubMed:3537965).Curated1
Sequence conflicti143A → C in CAA54518 (PubMed:3537965).Curated1
Sequence conflicti143A → C in CAA54521 (PubMed:3537965).Curated1
Sequence conflicti145 – 146AP → PQ in CAA28380 (PubMed:3537965).Curated2
Sequence conflicti206A → V in CAA28380 (PubMed:3537965).Curated1
Sequence conflicti208V → A in CAA54522 (PubMed:3537965).Curated1
Sequence conflicti253D → S in CAA28380 (PubMed:3537965).Curated1
Sequence conflicti253D → S in CAA54522 (PubMed:3537965).Curated1
Sequence conflicti253D → S in CAA54518 (PubMed:3537965).Curated1
Sequence conflicti253D → S in CAA54521 (PubMed:3537965).Curated1
Sequence conflicti336T → N in CAA28380 (PubMed:3537965).Curated1
Sequence conflicti336T → N in CAA54522 (PubMed:3537965).Curated1
Sequence conflicti336T → N in CAA54518 (PubMed:3537965).Curated1
Sequence conflicti336T → N in CAA54521 (PubMed:3537965).Curated1
Sequence conflicti538I → V in CAA28380 (PubMed:3537965).Curated1
Sequence conflicti538I → V in CAA54522 (PubMed:3537965).Curated1
Sequence conflicti538I → V in CAA54518 (PubMed:3537965).Curated1
Sequence conflicti538I → V in CAA54521 (PubMed:3537965).Curated1
Sequence conflicti545 – 563APQNL…TNAKQ → CSTKLG in CAA28380 (PubMed:3537965).CuratedAdd BLAST19

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X04675 Genomic DNA. Translation: CAA28380.1.
X77316 Genomic DNA. Translation: CAA54522.1.
X94607 Genomic DNA. Translation: CAA64291.1.
Z73216 Genomic DNA. Translation: CAA97573.1.
Z73217 Genomic DNA. Translation: CAA97575.1.
X77312 Genomic DNA. Translation: CAA54518.1.
X77315 Genomic DNA. Translation: CAA54521.1.
BK006945 Genomic DNA. Translation: DAA09362.1.
PIRiS64871. DCBYP.
RefSeqiNP_013145.1. NM_001181931.1.

Genome annotation databases

EnsemblFungiiYLR044C; YLR044C; YLR044C.
GeneIDi850733.
KEGGisce:YLR044C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X04675 Genomic DNA. Translation: CAA28380.1.
X77316 Genomic DNA. Translation: CAA54522.1.
X94607 Genomic DNA. Translation: CAA64291.1.
Z73216 Genomic DNA. Translation: CAA97573.1.
Z73217 Genomic DNA. Translation: CAA97575.1.
X77312 Genomic DNA. Translation: CAA54518.1.
X77315 Genomic DNA. Translation: CAA54521.1.
BK006945 Genomic DNA. Translation: DAA09362.1.
PIRiS64871. DCBYP.
RefSeqiNP_013145.1. NM_001181931.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1PVDX-ray2.30A/B2-556[»]
1PYDX-ray2.40A/B1-556[»]
1QPBX-ray2.40A/B1-563[»]
2VK1X-ray1.71A/B/C/D1-563[»]
2VK8X-ray1.42A/B/C/D1-563[»]
2W93X-ray1.60A/B/C/D1-563[»]
ProteinModelPortaliP06169.
SMRiP06169.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31319. 121 interactors.
DIPiDIP-6773N.
IntActiP06169. 79 interactors.
MINTiMINT-667063.

PTM databases

iPTMnetiP06169.

2D gel databases

COMPLUYEAST-2DPAGEP06169.
SWISS-2DPAGEP06169.

Proteomic databases

MaxQBiP06169.
PRIDEiP06169.
TopDownProteomicsiP06169.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYLR044C; YLR044C; YLR044C.
GeneIDi850733.
KEGGisce:YLR044C.

Organism-specific databases

EuPathDBiFungiDB:YLR044C.
SGDiS000004034. PDC1.

Phylogenomic databases

GeneTreeiENSGT00550000075465.
InParanoidiP06169.
KOiK01568.
OMAiWPRVGEF.
OrthoDBiEOG092C29BL.

Enzyme and pathway databases

UniPathwayiUPA00206.
UPA00866.
BioCyciMetaCyc:MONOMER3O-117.
YEAST:MONOMER3O-117.
BRENDAi4.1.1.1. 984.
SABIO-RKP06169.

Miscellaneous databases

EvolutionaryTraceiP06169.
PROiP06169.

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 nameiPDC1_YEAST
AccessioniPrimary (citable) accession number: P06169
Secondary accession number(s): D6VY46
, O00042, Q07991, Q12682, Q12686, Q12687
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 1, 1988
Last sequence update: January 23, 2007
Last modified: November 2, 2016
This is version 188 of the entry and version 7 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 8966 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Allosteric enzyme, 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 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.