IED Industry Enzyme Database

Detail Information for IndEnz0002007935
IED ID IndEnz0002007935
Enzyme Type ID protease007935
Protein Name Pyruvate dehydrogenase
ubiquinone
EC 1.2.5.1
Pyruvate oxidase
POX
Pyruvate:ubiquinone-8 oxidoreductase
Gene Name poxB b0871 JW0855
Organism Escherichia coli (strain K12)
Taxonomic Lineage cellular organisms Bacteria Proteobacteria Gammaproteobacteria Enterobacterales Enterobacteriaceae Escherichia Escherichia coli Escherichia coli (strain K12)
Enzyme Sequence MKQTVAAYIAKTLESAGVKRIWGVTGDSLNGLSDSLNRMGTIEWMSTRHEEVAAFAAGAEAQLSGELAVCAGSCGPGNLHLINGLFDCHRNHVPVLAIAAHIPSSEIGSGYFQETHPQELFRECSHYCELVSSPEQIPQVLAIAMRKAVLNRGVSVVVLPGDVALKPAPEGATMHWYHAPQPVVTPEEEELRKLAQLLRYSSNIALMCGSGCAGAHKELVEFAGKIKAPIVHALRGKEHVEYDNPYDVGMTGLIGFSSGFHTMMNADTLVLLGTQFPYRAFYPTDAKIIQIDINPASIGAHSKVDMALVGDIKSTLRALLPLVEEKADRKFLDKALEDYRDARKGLDDLAKPSEKAIHPQYLAQQISHFAADDAIFTCDVGTPTVWAARYLKMNGKRRLLGSFNHGSMANAMPQALGAQATEPERQVVAMCGDGGFSMLMGDFLSVVQMKLPVKIVVFNNSVLGFVAMEMKAGGYLTDGTELHDTNFARIAEACGITGIRVEKASEVDEALQRAFSIDGPVLVDVVVAKEELAIPPQIKLEQAKGFSLYMLRAIISGRGDEVIELAKTNWLR
Enzyme Length 572
Uniprot Accession Number P07003
Absorption
Active Site
Activity Regulation ACTIVITY REGULATION: The C-terminus inhibits activity; it has to move for the enzyme to be active (PubMed:18988747). Activated by lipid-binding, which occurs via the C-terminus; detergents also activate the enzyme (PubMed:334770, PubMed:334771, PubMed:2663858, PubMed:18988747). Specifically activated by palmitic acid; 12 (lauric) and 14-carbon (myristic) fatty acids as well as unsaturated 16 and 18-carbon fatty acids also activate the enzyme (PubMed:6385860). Lipid affinity is increased in the presence of pyruvate plus the thiamine pyrophosphate cofactor (PubMed:334770, PubMed:334771, PubMed:2663858, PubMed:18988747). {ECO:0000255|HAMAP-Rule:MF_00850, ECO:0000269|PubMed:18988747, ECO:0000269|PubMed:2663858, ECO:0000269|PubMed:334770, ECO:0000269|PubMed:334771, ECO:0000269|PubMed:6385860}.
Binding Site BINDING 50; /note="Thiamine pyrophosphate"; /evidence="ECO:0000255|HAMAP-Rule:MF_00850, ECO:0000269|PubMed:18988747, ECO:0007744|PDB:3EY9, ECO:0007744|PDB:3EYA"; BINDING 210; /note="FAD"; /evidence="ECO:0000269|PubMed:18988747, ECO:0007744|PDB:3EY9, ECO:0007744|PDB:3EYA"; BINDING 292; /note="FAD"; /evidence="ECO:0000255|HAMAP-Rule:MF_00850, ECO:0000269|PubMed:18988747, ECO:0007744|PDB:3EY9, ECO:0007744|PDB:3EYA"; BINDING 297; /note="FAD"; /evidence="ECO:0000269|PubMed:18988747, ECO:0007744|PDB:3EY9, ECO:0007744|PDB:3EYA"; BINDING 382; /note="Thiamine pyrophosphate"; /evidence="ECO:0000269|PubMed:18988747, ECO:0007744|PDB:3EY9, ECO:0007744|PDB:3EYA"
Calcium Binding
catalytic Activity CATALYTIC ACTIVITY: Reaction=a ubiquinone + H2O + pyruvate = a ubiquinol + acetate + CO2; Xref=Rhea:RHEA:27405, Rhea:RHEA-COMP:9565, Rhea:RHEA-COMP:9566, ChEBI:CHEBI:15361, ChEBI:CHEBI:15377, ChEBI:CHEBI:16389, ChEBI:CHEBI:16526, ChEBI:CHEBI:17976, ChEBI:CHEBI:30089; EC=1.2.5.1; Evidence={ECO:0000255|HAMAP-Rule:MF_00850, ECO:0000269|PubMed:18988747, ECO:0000269|PubMed:2663858, ECO:0000269|PubMed:3527254, ECO:0000269|PubMed:365232, ECO:0000269|PubMed:6286628, ECO:0000269|PubMed:6752142, ECO:0000305|PubMed:5336022};
DNA Binding
EC Number 1.2.5.1
Enzyme Function FUNCTION: A peripheral cell membrane enzyme that catalyzes the oxidative decarboxylation of pyruvate to form acetate and CO(2). It channels electrons from the cytoplasm to the respiratory chain at the cell membrane via ubiquinone (By similarity) (PubMed:18988747, PubMed:2663858, PubMed:365232). The main pathway for acetate production during stationary phase (PubMed:16080684). {ECO:0000255|HAMAP-Rule:MF_00850, ECO:0000269|PubMed:16080684, ECO:0000269|PubMed:18988747, ECO:0000269|PubMed:2663858, ECO:0000269|PubMed:365232}.
Temperature Dependency
PH Dependency
Pathway
nucleotide Binding NP_BIND 234..235; /note="FAD"; /evidence="ECO:0000269|PubMed:18988747, ECO:0007744|PDB:3EY9, ECO:0007744|PDB:3EYA"; NP_BIND 251..254; /note="FAD"; /evidence="ECO:0000255|HAMAP-Rule:MF_00850, ECO:0000269|PubMed:18988747, ECO:0007744|PDB:3EY9, ECO:0007744|PDB:3EYA"; NP_BIND 274..278; /note="FAD"; /evidence="ECO:0000255|HAMAP-Rule:MF_00850, ECO:0000269|PubMed:18988747, ECO:0007744|PDB:3EY9, ECO:0007744|PDB:3EYA"; NP_BIND 311..312; /note="FAD"; /evidence="ECO:0000269|PubMed:18988747, ECO:0007744|PDB:3EY9, ECO:0007744|PDB:3EYA"; NP_BIND 403..404; /note="FAD"; /evidence="ECO:0000269|PubMed:18988747, ECO:0007744|PDB:3EY9, ECO:0007744|PDB:3EYA"
Features Beta strand (28); Binding site (5); Chain (1); Helix (33); Metal binding (3); Mutagenesis (8); Nucleotide binding (5); Region (7); Sequence conflict (4); Site (2); Turn (4)
Keywords 3D-structure;Cell inner membrane;Cell membrane;Direct protein sequencing;FAD;Flavoprotein;Lipid-binding;Magnesium;Membrane;Metal-binding;Nucleotide-binding;Oxidoreductase;Pyruvate;Reference proteome;Thiamine pyrophosphate;Ubiquinone
Interact With Itself
Induction INDUCTION: Activity is maximal in late exponential and early stationary phase (at protein level) (PubMed:8022274, PubMed:16080684). Expression increases at pH 6.0 (PubMed:16080684). Under control of rpoS (at protein level). Transcribed at lower levels during anaerobic growth (PubMed:8022274). {ECO:0000269|PubMed:16080684, ECO:0000269|PubMed:8022274}.
Subcellular Location SUBCELLULAR LOCATION: Cell inner membrane {ECO:0000255|HAMAP-Rule:MF_00850, ECO:0000269|PubMed:365232, ECO:0000305|PubMed:5336022}; Peripheral membrane protein {ECO:0000255|HAMAP-Rule:MF_00850, ECO:0000269|PubMed:365232, ECO:0000305|PubMed:5336022}; Cytoplasmic side {ECO:0000255|HAMAP-Rule:MF_00850, ECO:0000269|PubMed:365232}.
Modified Residue
Post Translational Modification PTM: Activated by limited proteolytic digestion in vitro. This cleavage produces a peptide (alpha-peptide) and mimics the activation of enzyme by phospholipids (PubMed:5336022, PubMed:3902830, PubMed:334770, PubMed:334771). Protease activation and lipid-activation are mutually exclusive. Proteolytic cleavage results in the loss of the high affinity lipid-binding site of the enzyme; the cleaved protein is no longer activated by lipids or detergents (PubMed:334771, PubMed:2663858). The proteolytically cleaved enzyme does not represent a functional cleavage in vivo (PubMed:3527254). {ECO:0000269|PubMed:2663858, ECO:0000269|PubMed:334770, ECO:0000269|PubMed:334771, ECO:0000269|PubMed:3527254, ECO:0000269|PubMed:3902830, ECO:0000269|PubMed:5336022}.
Signal Peptide
Structure 3D X-ray crystallography (2)
Cross Reference PDB 3EY9; 3EYA;
Mapped Pubmed ID 16606699; 16858726; 1832150; 24561554; 6209262;
Motif
Gene Encoded By
Mass 62,011
Kinetics BIOPHYSICOCHEMICAL PROPERTIES: Kinetic parameters: KM=90 mM for pyruvate, non-activated form {ECO:0000269|PubMed:18988747}; KM=12 mM for pyruvate, activated form {ECO:0000269|PubMed:18988747}; Note=kcat is 7 sec(-1) for non-activated, 200 sec(-1) for activated form. {ECO:0000269|PubMed:18988747};
Metal Binding METAL 433; /note="Magnesium"; /evidence="ECO:0000255|HAMAP-Rule:MF_00850, ECO:0000269|PubMed:18988747, ECO:0007744|PDB:3EY9, ECO:0007744|PDB:3EYA"; METAL 460; /note="Magnesium"; /evidence="ECO:0000255|HAMAP-Rule:MF_00850, ECO:0000269|PubMed:18988747, ECO:0007744|PDB:3EY9, ECO:0007744|PDB:3EYA"; METAL 462; /note="Magnesium; via carbonyl oxygen"; /evidence="ECO:0000269|PubMed:18988747, ECO:0007744|PDB:3EY9, ECO:0007744|PDB:3EYA"
Rhea ID RHEA:27405
Cross Reference Brenda 1.2.5.1;