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Information on EC 4.1.1.1 - pyruvate decarboxylase and Organism(s) Kluyveromyces lactis and UniProt Accession Q12629

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EC Tree
     4 Lyases
         4.1 Carbon-carbon lyases
             4.1.1 Carboxy-lyases
                4.1.1.1 pyruvate decarboxylase
IUBMB Comments
A thiamine-diphosphate protein. Also catalyses acyloin formation.
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This record set is specific for:
Kluyveromyces lactis
UNIPROT: Q12629
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The taxonomic range for the selected organisms is: Kluyveromyces lactis
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea
Synonyms
pdc, pyruvate decarboxylase, acetohydroxyacid synthase, yeast pyruvate decarboxylase, pdc1p, p59nc, ifpl730, pyruvate decarboxylase 1, zmpdc, pdc5p, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8-10 nm cytoplasmic filament-associated protein
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alpha-Carboxylase
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alpha-Keto acid carboxylase
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Decarboxylase, pyruvate
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P59NC
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Pyruvic decarboxylase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
a 2-oxo carboxylate = an aldehyde + CO2
show the reaction diagram
catalytic mechanism
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
decarboxylation
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SYSTEMATIC NAME
IUBMB Comments
2-oxo-acid carboxy-lyase (aldehyde-forming)
A thiamine-diphosphate protein. Also catalyses acyloin formation.
CAS REGISTRY NUMBER
COMMENTARY hide
9001-04-1
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
pyruvate
acetaldehyde + CO2
show the reaction diagram
pyruvate
acetaldehyde + CO2
show the reaction diagram
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
pyruvate
acetaldehyde + CO2
show the reaction diagram
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-
-
?
pyruvate
acetaldehyde + CO2
show the reaction diagram
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key enzyme at the branching point of alcoholic fermentation and respiration, expression at high glucose and low oxygen concentration
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?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
thiamine diphosphate
dependent on, bound tightly, but not covalently, at the interface of two monomers, reversible dissociation of the cofactor at pH above 8.0, leads to complete loss of activity
thiamine diphosphate
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mg2+
dependent on, bound tightly, but not covalently, at the interface of two monomers, reversible dissociation of Mg2+ at pH above 8.0, leads to complete loss of activity
Mg2+
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cofactor, requirement
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Pyruvamide
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mixed type inhibitor
pyruvate
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weak substrate inhibition, above 100 mM
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Pyruvamide
the activator pyruvamide arrests the flexible loops comprising residues 106-113 and 292-301, so that two of four active sites become closed
pyruvate
allosteric substrate activation, binding of substrate at a regulatory site induces catalytic activity, accompanied by conformational changes and subunit rearrangements, the structuring of the flexible loop region 105-113 seems to be the crucial step during the substrate activation process
Pyruvamide
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artificial activator
pyruvate
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concentration-dependent substrate activation, minimum at 1.5 mM, mechanism, kinetics
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.24
pyruvate
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pH 6, 30°C
additional information
additional information
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kinetic studies
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
40
pyruvate
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pH 6, 30°C, enzyme monomer
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1200
pyruvate
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pH 6, 30°C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
single gene
SwissProt
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
200000
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about, gel filtration
61500
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4 * 61500, mass spectrometry, SDS-PAGE, 4 * 61821, calculated from the amino acid sequence
61821
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4 * 61500, mass spectrometry, SDS-PAGE, 4 * 61821, calculated from the amino acid sequence
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
tetramer
subunit crystal structure analysis, the subunits are each composed of three domains, the R domain, the PYR domain, and the PP domain, all three domains exhibit typical alpha/beta-topology, the enzyme shows a half-side closed tetramer in presence or absence of any activator, the half-side closed form is predominant for Kluyveromyces lactis pyruvate decarboxylase, the structuring of the flexible loop region 105-113 seems to be the crucial step during the substrate activation process, overview
tetramer
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4 * 61500, mass spectrometry, SDS-PAGE, 4 * 61821, calculated from the amino acid sequence
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant enzyme, 2 mg/ml protein in 50 mM MES, pH 6.45, 5 mM thiamine diphosphate, 1 mM dithiothreitol, and 5 mM MgSO4, or 35 mM sodium citrate, pH 6.45, 1 mM dithiothreitol, 5 mM thiamine diphosphate, and 5 mM MgSO4, in absence of ammonium sulfate, hanging drop vapour diffusion method, 8°C, in a 1:1 mixture with reservoir solution containing 20% w/v PEG 2000/PEG 8000 in crystallization buffer, microcrystals within 3 days, larger crystals within 4 weeks, X-ray diffraction structure determination and analysis at 2.26 A resolution
hanging drop vapor diffusion method, using 20 mM citrate buffer, pH 6.1, 1 mM dithiothreitol, 5 mM thiamine diphosphate, 5 mM MgSO4, 20% (w/v) PEG 2000/PEG 6000 (1:1 ratio)
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D28A
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the mutant is almost catalytically inactive
E477Q
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the mutant is almost catalytically inactive
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
native enzyme by ammonium sulfate fractionation, gel filtration, and anion exchange chromatography to over 95% homogeneity
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant expression
expressed in Hansenula polymorpha
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expressed in Hansenula polymorpha strain NCYC495 leu1-1
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Krieger, F.; Spinka, M.; Golbik, R.; Hubner, G.; Konig, S.
Pyruvate decarboxylase from Kluyveromyces lactis. An enzyme with an extraordinary substrate activation behaviour
Eur. J. Biochem.
269
3256-3263
2002
Kluyveromyces lactis, Kluyveromyces lactis JA-6
Manually annotated by BRENDA team
Kutter, S.; Wille, G.; Relle, S.; Weiss, M.S.; Huebner, G.; Koenig, S.
The crystal structure of pyruvate decarboxylase from Kluyveromyces lactis. Implications for the substrate activation mechanism of this enzyme
FEBS J.
273
4199-4209
2006
Saccharomyces cerevisiae (P06169), Saccharomyces cerevisiae, Kluyveromyces lactis (Q12629), Kluyveromyces lactis
Manually annotated by BRENDA team
Ishchuk, O.P.; Voronovsky, A.Y.; Stasyk, O.V.; Gayda, G.Z.; Gonchar, M.V.; Abbas, C.A.; Sibirny, A.A.
Overexpression of pyruvate decarboxylase in the yeast Hansenula polymorpha results in increased ethanol yield in high-temperature fermentation of xylose
FEMS Yeast Res.
8
1164-1174
2008
Kluyveromyces lactis, Kluyveromyces lactis CBS 2359
Manually annotated by BRENDA team
Kutter, S.; Weiss, M.S.; Wille, G.; Golbik, R.; Spinka, M.; Koenig, S.
Covalently bound substrate at the regulatory site of yeast pyruvate decarboxylases triggers allosteric enzyme activation
J. Biol. Chem.
284
12136-12144
2009
Kluyveromyces lactis, Saccharomyces cerevisiae (P06169), Saccharomyces cerevisiae
Manually annotated by BRENDA team