UniProtKB - P06169 (PDC1_YEAST)
Pyruvate decarboxylase isozyme 1
PDC1
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 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.
11 PublicationsMiscellaneous
Catalytic activityi
Cofactori
Protein has several cofactor binding sites:- Mg2+1 PublicationNote: Binds 1 Mg2+ per subunit.1 Publication
- thiamine diphosphate1 PublicationNote: Binds 1 thiamine pyrophosphate per subunit.1 Publication
Activity regulationi
Kineticsi
- KM=2.8 mM for pyruvate1 Publication
- KM=1.0 mM for 2-oxobutanoate1 Publication
- KM=1.5 mM for 2-oxopentanoate1 Publication
- Vmax=1.5 µmol/min/mg enzyme for pyruvate1 Publication
- Vmax=0.5 µmol/min/mg enzyme for 2-oxobutanoate1 Publication
- Vmax=0.4 µmol/min/mg enzyme for 2-oxopentanoate1 Publication
- Vmax=38 µmol/min/mg enzyme for 3-methyl-2-oxobutanoate1 Publication
- Vmax=15 µmol/min/mg enzyme for 4-methyl-2-oxopentanoate1 Publication
- Vmax=9 µmol/min/mg enzyme for 3-methyl-2-oxopentanoate1 Publication
- Vmax=41 µmol/min/mg enzyme for 4-methylthio-2-oxobutanoate1 Publication
: ethanol fermentation Pathwayi
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 key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Binding sitei | 28 | Pyruvate 1; substrate; shared with neighboring subunit1 Publication | 1 | |
Binding sitei | 115 | Pyruvate 1; substrate; shared with neighboring subunitCombined sources1 Publication | 1 | |
Binding sitei | 157 | Pyruvate 2; allosteric activator1 Publication | 1 | |
Binding sitei | 224 | Pyruvate 2; allosteric activatorCombined sources1 Publication | 1 | |
Binding sitei | 390 | Thiamine pyrophosphateCombined sources1 Publication | 1 | |
Metal bindingi | 444 | MagnesiumCombined sources1 Publication | 1 | |
Metal bindingi | 471 | MagnesiumCombined sources1 Publication | 1 | |
Metal bindingi | 473 | Magnesium; via carbonyl oxygenCombined sources1 Publication | 1 | |
Binding sitei | 477 | Pyruvate 1; substrate; shared with neighboring subunit1 Publication | 1 |
GO - Molecular functioni
- branched-chain-2-oxoacid decarboxylase activity Source: SGD
- carboxy-lyase activity Source: GO_Central
- indolepyruvate decarboxylase activity Source: UniProtKB-EC
- magnesium ion binding Source: InterPro
- phenylpyruvate decarboxylase activity Source: UniProtKB-EC
- 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
- regulation of viral genome replication Source: SGD
- tryptophan catabolic process Source: SGD
Keywordsi
Molecular function | Allosteric enzyme, Decarboxylase, Lyase |
Biological process | Branched-chain amino acid catabolism, Phenylalanine catabolism, Tryptophan catabolism |
Ligand | Magnesium, Metal-binding, Thiamine pyrophosphate |
Enzyme and pathway databases
BRENDAi | 4.1.1.1, 984 |
SABIO-RKi | P06169 |
UniPathwayi | UPA00206 UPA00866 |
Names & Taxonomyi
Protein namesi | |
Gene namesi | Name:PDC1 Ordered Locus Names:YLR044C ORF Names:L2104 |
Organismi | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) |
Taxonomic identifieri | 559292 [NCBI] |
Taxonomic lineagei | Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › |
Proteomesi |
|
Organism-specific databases
SGDi | S000004034, PDC1 |
VEuPathDBi | FungiDB:YLR044C |
Subcellular locationi
Cytosol
- cytosol Source: SGD
Nucleus
- nucleus Source: SGD
Other locations
- cytoplasm Source: SGD
- replication compartment Source: SGD
Keywords - Cellular componenti
Cytoplasm, NucleusPathology & Biotechi
Biotechnological usei
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 291 | D → N in PDC1-8; reduces catalytic activity to 10% but retains autoregulatory activity. 1 Publication | 1 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Initiator methioninei | Removed2 Publications | |||
ChainiPRO_0000090770 | 2 – 563 | Pyruvate decarboxylase isozyme 1Add BLAST | 562 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Modified residuei | 2 | N-acetylserine2 Publications | 1 | |
Cross-linki | 212 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources | ||
Modified residuei | 223 | PhosphoserineCombined sources | 1 | |
Cross-linki | 233 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources | ||
Modified residuei | 266 | PhosphothreonineCombined sources | 1 | |
Cross-linki | 269 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources | ||
Cross-linki | 332 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources | ||
Modified residuei | 336 | PhosphothreonineCombined sources | 1 | |
Modified residuei | 353 | PhosphothreonineCombined sources | 1 | |
Cross-linki | 484 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources | ||
Cross-linki | 505 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources | ||
Cross-linki | 520 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources | ||
Modified residuei | 522 | PhosphothreonineCombined sources | 1 | |
Modified residuei | 526 | PhosphoserineCombined sources | 1 |
Post-translational modificationi
Keywords - PTMi
Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugationProteomic databases
MaxQBi | P06169 |
PaxDbi | P06169 |
PRIDEi | P06169 |
TopDownProteomicsi | P06169 |
2D gel databases
COMPLUYEAST-2DPAGEi | P06169 |
SWISS-2DPAGEi | P06169 |
PTM databases
CarbonylDBi | P06169 |
iPTMneti | P06169 |
Expressioni
Inductioni
Interactioni
Subunit structurei
Homotetramer.
3 PublicationsProtein-protein interaction databases
BioGRIDi | 31319, 217 interactors |
DIPi | DIP-6773N |
IntActi | P06169, 134 interactors |
MINTi | P06169 |
STRINGi | 4932.YLR044C |
Miscellaneous databases
RNActi | P06169, protein |
Structurei
Secondary structure
3D structure databases
AlphaFoldDBi | P06169 |
SMRi | P06169 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | P06169 |
Family & Domainsi
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 413 – 415 | Thiamine pyrophosphate bindingCombined sources1 Publication | 3 | |
Regioni | 445 – 446 | Thiamine pyrophosphate bindingCombined sources1 Publication | 2 | |
Regioni | 471 – 476 | Thiamine pyrophosphate bindingCombined sources1 Publication | 6 |
Sequence similaritiesi
Phylogenomic databases
eggNOGi | KOG1184, Eukaryota |
GeneTreei | ENSGT00940000176336 |
HOGENOMi | CLU_013748_0_2_1 |
InParanoidi | P06169 |
OMAi | EQRYNDI |
Family and domain databases
InterProi | View 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 |
PANTHERi | PTHR43452, PTHR43452, 1 hit |
Pfami | View protein in Pfam PF02775, TPP_enzyme_C, 1 hit PF00205, TPP_enzyme_M, 1 hit PF02776, TPP_enzyme_N, 1 hit |
PIRSFi | PIRSF036565, Pyruvt_ip_decrb, 1 hit |
SUPFAMi | SSF52467, SSF52467, 1 hit SSF52518, SSF52518, 2 hits |
PROSITEi | View protein in PROSITE PS00187, TPP_ENZYMES, 1 hit |
i Sequence
Sequence statusi: Complete.
: The displayed sequence is further processed into a mature form. Sequence processingi
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
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 55 | A → R in CAA54522 (PubMed:3537965).Curated | 1 | |
Sequence conflicti | 106 | A → S in CAA28380 (PubMed:3537965).Curated | 1 | |
Sequence conflicti | 106 | A → S in CAA54522 (PubMed:3537965).Curated | 1 | |
Sequence conflicti | 106 | A → S in CAA54518 (PubMed:3537965).Curated | 1 | |
Sequence conflicti | 106 | A → S in CAA54521 (PubMed:3537965).Curated | 1 | |
Sequence conflicti | 115 | Missing in CAA28380 (PubMed:3537965).Curated | 1 | |
Sequence conflicti | 143 | A → C in CAA54522 (PubMed:3537965).Curated | 1 | |
Sequence conflicti | 143 | A → C in CAA54518 (PubMed:3537965).Curated | 1 | |
Sequence conflicti | 143 | A → C in CAA54521 (PubMed:3537965).Curated | 1 | |
Sequence conflicti | 145 – 146 | AP → PQ in CAA28380 (PubMed:3537965).Curated | 2 | |
Sequence conflicti | 206 | A → V in CAA28380 (PubMed:3537965).Curated | 1 | |
Sequence conflicti | 208 | V → A in CAA54522 (PubMed:3537965).Curated | 1 | |
Sequence conflicti | 253 | D → S in CAA28380 (PubMed:3537965).Curated | 1 | |
Sequence conflicti | 253 | D → S in CAA54522 (PubMed:3537965).Curated | 1 | |
Sequence conflicti | 253 | D → S in CAA54518 (PubMed:3537965).Curated | 1 | |
Sequence conflicti | 253 | D → S in CAA54521 (PubMed:3537965).Curated | 1 | |
Sequence conflicti | 336 | T → N in CAA28380 (PubMed:3537965).Curated | 1 | |
Sequence conflicti | 336 | T → N in CAA54522 (PubMed:3537965).Curated | 1 | |
Sequence conflicti | 336 | T → N in CAA54518 (PubMed:3537965).Curated | 1 | |
Sequence conflicti | 336 | T → N in CAA54521 (PubMed:3537965).Curated | 1 | |
Sequence conflicti | 538 | I → V in CAA28380 (PubMed:3537965).Curated | 1 | |
Sequence conflicti | 538 | I → V in CAA54522 (PubMed:3537965).Curated | 1 | |
Sequence conflicti | 538 | I → V in CAA54518 (PubMed:3537965).Curated | 1 | |
Sequence conflicti | 538 | I → V in CAA54521 (PubMed:3537965).Curated | 1 | |
Sequence conflicti | 545 – 563 | APQNL…TNAKQ → CSTKLG in CAA28380 (PubMed:3537965).CuratedAdd BLAST | 19 |
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 |
PIRi | S64871, DCBYP |
RefSeqi | NP_013145.1, NM_001181931.1 |
Genome annotation databases
EnsemblFungii | YLR044C_mRNA; YLR044C; YLR044C |
GeneIDi | 850733 |
KEGGi | sce:YLR044C |
Similar proteinsi
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 |
PIRi | S64871, DCBYP |
RefSeqi | NP_013145.1, NM_001181931.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
1PVD | X-ray | 2.30 | A/B | 2-556 | [»] | |
1PYD | X-ray | 2.40 | A/B | 1-556 | [»] | |
1QPB | X-ray | 2.40 | A/B | 1-563 | [»] | |
2VK1 | X-ray | 1.71 | A/B/C/D | 1-563 | [»] | |
2VK8 | X-ray | 1.42 | A/B/C/D | 1-563 | [»] | |
2W93 | X-ray | 1.60 | A/B/C/D | 1-563 | [»] | |
AlphaFoldDBi | P06169 | |||||
SMRi | P06169 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 31319, 217 interactors |
DIPi | DIP-6773N |
IntActi | P06169, 134 interactors |
MINTi | P06169 |
STRINGi | 4932.YLR044C |
PTM databases
CarbonylDBi | P06169 |
iPTMneti | P06169 |
2D gel databases
COMPLUYEAST-2DPAGEi | P06169 |
SWISS-2DPAGEi | P06169 |
Proteomic databases
MaxQBi | P06169 |
PaxDbi | P06169 |
PRIDEi | P06169 |
TopDownProteomicsi | P06169 |
Genome annotation databases
EnsemblFungii | YLR044C_mRNA; YLR044C; YLR044C |
GeneIDi | 850733 |
KEGGi | sce:YLR044C |
Organism-specific databases
SGDi | S000004034, PDC1 |
VEuPathDBi | FungiDB:YLR044C |
Phylogenomic databases
eggNOGi | KOG1184, Eukaryota |
GeneTreei | ENSGT00940000176336 |
HOGENOMi | CLU_013748_0_2_1 |
InParanoidi | P06169 |
OMAi | EQRYNDI |
Enzyme and pathway databases
UniPathwayi | UPA00206 UPA00866 |
BRENDAi | 4.1.1.1, 984 |
SABIO-RKi | P06169 |
Miscellaneous databases
EvolutionaryTracei | P06169 |
PROi | PR:P06169 |
RNActi | P06169, protein |
Family and domain databases
InterProi | View 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 |
PANTHERi | PTHR43452, PTHR43452, 1 hit |
Pfami | View protein in Pfam PF02775, TPP_enzyme_C, 1 hit PF00205, TPP_enzyme_M, 1 hit PF02776, TPP_enzyme_N, 1 hit |
PIRSFi | PIRSF036565, Pyruvt_ip_decrb, 1 hit |
SUPFAMi | SSF52467, SSF52467, 1 hit SSF52518, SSF52518, 2 hits |
PROSITEi | View protein in PROSITE PS00187, TPP_ENZYMES, 1 hit |
MobiDBi | Search... |
Entry informationi
Entry namei | PDC1_YEAST | |
Accessioni | P06169Primary (citable) accession number: P06169 Secondary accession number(s): D6VY46 Q12687 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | January 1, 1988 |
Last sequence update: | January 23, 2007 | |
Last modified: | May 25, 2022 | |
This is version 228 of the entry and version 7 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Fungal Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Direct protein sequencing, Reference proteomeDocuments
- Yeast
Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD - Yeast chromosome XII
Yeast (Saccharomyces cerevisiae) chromosome XII: entries and gene names - PATHWAY comments
Index of metabolic and biosynthesis pathways - PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families