BRENDA - Enzyme Database
show all sequences of 1.1.2.3

QM/MM study of l-lactate oxidation by flavocytochrome b2

Gillet, N.; Ruiz-Pernia, J.J.; de la Lande, A.; Levy, B.; Lederer, F.; Demachy, I.; Moliner, V.; Phys. Chem. Chem. Phys. 18, 15609-15618 (2016)

Data extracted from this reference:

Engineering
Amino acid exchange
Commentary
Organism
D282N
site-directed mutagenesis, while the wild-type mutant has residue R289 in a distal or a proximal conformation, the mutant shows R289 only in a distal conformation
Saccharomyces cerevisiae
additional information
active site structures of wild-type and mutant enzymes, detailed overview
Saccharomyces cerevisiae
Y254L
site-directed mutagenesis, while the wild-type mutant has residue R289 in a distal or a proximal conformation, the mutant shows R289 only in a distal conformation
Saccharomyces cerevisiae
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
additional information
-
additional information
steady-state kinetics
Saccharomyces cerevisiae
Localization
Localization
Commentary
Organism
GeneOntology No.
Textmining
mitochondrial intermembrane space
-
Saccharomyces cerevisiae
5758
-
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
(S)-lactate + 2 ferricytochrome c
Saccharomyces cerevisiae
the first step of the catalytic cycle consists of the oxidation of L-lactate by the FMN prosthetic group. FMN is later reoxidized by transferring its electrons one by one to the ferric heme. The final electron acceptor is cytochrome c
pyruvate + 2 ferrocytochrome c + 2 H+
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Saccharomyces cerevisiae
P00175
-
-
Reaction
Reaction
Commentary
Organism
(S)-lactate + 2 ferricytochrome c = pyruvate + 2 ferrocytochrome c + 2 H+
the hydride transfer mechanism involves the transfer of the lactate hydroxyl proton to H373 while the substrate aH atom is transferred as a hydride to the flavin mononucleotide (FMN) prosthetic group anchored in the active site
Saccharomyces cerevisiae
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
(S)-lactate + 2 ferricytochrome c
the first step of the catalytic cycle consists of the oxidation of L-lactate by the FMN prosthetic group. FMN is later reoxidized by transferring its electrons one by one to the ferric heme. The final electron acceptor is cytochrome c
743420
Saccharomyces cerevisiae
pyruvate + 2 ferrocytochrome c + 2 H+
-
-
-
?
(S)-lactate + 2 flavocytochrome b2
-
743420
Saccharomyces cerevisiae
pyruvate + 2 ferrocytochrome c + 2 H+
-
-
-
?
Subunits
Subunits
Commentary
Organism
homotetramer
-
Saccharomyces cerevisiae
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
30
-
assay at
Saccharomyces cerevisiae
Turnover Number [1/s]
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
0.51
-
(S)-lactate
mutant Y254L with R289 distal, pH 7.0, 30°C
Saccharomyces cerevisiae
3.9
-
(S)-lactate
mutant D282N with R289 distal, pH 7.0, 30°C
Saccharomyces cerevisiae
270
-
(S)-lactate
wild-type enzyme with R289 distal, pH 7.0, 30°C
Saccharomyces cerevisiae
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7
-
assay at
Saccharomyces cerevisiae
Cofactor
Cofactor
Commentary
Organism
Structure
ferricytochrome c
-
Saccharomyces cerevisiae
flavocytochrome b2
-
Saccharomyces cerevisiae
FMN
each of the four subunits contains a flavin mononucleotide prosthetic group
Saccharomyces cerevisiae
heme
each of the four subunits contains a beta-type heme
Saccharomyces cerevisiae
additional information
FMN and heme groups are localized in two different domains
Saccharomyces cerevisiae
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
ferricytochrome c
-
Saccharomyces cerevisiae
flavocytochrome b2
-
Saccharomyces cerevisiae
FMN
each of the four subunits contains a flavin mononucleotide prosthetic group
Saccharomyces cerevisiae
heme
each of the four subunits contains a beta-type heme
Saccharomyces cerevisiae
additional information
FMN and heme groups are localized in two different domains
Saccharomyces cerevisiae
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
D282N
site-directed mutagenesis, while the wild-type mutant has residue R289 in a distal or a proximal conformation, the mutant shows R289 only in a distal conformation
Saccharomyces cerevisiae
additional information
active site structures of wild-type and mutant enzymes, detailed overview
Saccharomyces cerevisiae
Y254L
site-directed mutagenesis, while the wild-type mutant has residue R289 in a distal or a proximal conformation, the mutant shows R289 only in a distal conformation
Saccharomyces cerevisiae
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
additional information
-
additional information
steady-state kinetics
Saccharomyces cerevisiae
Localization (protein specific)
Localization
Commentary
Organism
GeneOntology No.
Textmining
mitochondrial intermembrane space
-
Saccharomyces cerevisiae
5758
-
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
(S)-lactate + 2 ferricytochrome c
Saccharomyces cerevisiae
the first step of the catalytic cycle consists of the oxidation of L-lactate by the FMN prosthetic group. FMN is later reoxidized by transferring its electrons one by one to the ferric heme. The final electron acceptor is cytochrome c
pyruvate + 2 ferrocytochrome c + 2 H+
-
-
?
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
(S)-lactate + 2 ferricytochrome c
the first step of the catalytic cycle consists of the oxidation of L-lactate by the FMN prosthetic group. FMN is later reoxidized by transferring its electrons one by one to the ferric heme. The final electron acceptor is cytochrome c
743420
Saccharomyces cerevisiae
pyruvate + 2 ferrocytochrome c + 2 H+
-
-
-
?
(S)-lactate + 2 flavocytochrome b2
-
743420
Saccharomyces cerevisiae
pyruvate + 2 ferrocytochrome c + 2 H+
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
homotetramer
-
Saccharomyces cerevisiae
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
30
-
assay at
Saccharomyces cerevisiae
Turnover Number [1/s] (protein specific)
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
0.51
-
(S)-lactate
mutant Y254L with R289 distal, pH 7.0, 30°C
Saccharomyces cerevisiae
3.9
-
(S)-lactate
mutant D282N with R289 distal, pH 7.0, 30°C
Saccharomyces cerevisiae
270
-
(S)-lactate
wild-type enzyme with R289 distal, pH 7.0, 30°C
Saccharomyces cerevisiae
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7
-
assay at
Saccharomyces cerevisiae
General Information
General Information
Commentary
Organism
additional information
molecular dynamics simulations using a hybrid quantum mechanics/molecular mechanics (QM/MM) scheme to study the mechanism of L-lactate oxidation by flavocytochrome b2. Simulation results highlight the influence of the environment on the catalytic mechanism by describing a step-wise process in the wild-type enzyme with R289 in a distal position and a concerted mechanism for the other systems. Structure analysis of pyruvate in the Fcb2 active site pocket with R289 in the distal conformation. Residue Y254 plays a role in the catalytic process by stabilizing the product of the first proton transfer from substrate to H373, while residue D282 is expected to stabilize the imidazolium ion in transition and product states by electrostatic interactions and hydrogen bonding with the Hdelta of H373. Active site structures of wild-type and mutant enzymes, detailed overview
Saccharomyces cerevisiae
General Information (protein specific)
General Information
Commentary
Organism
additional information
molecular dynamics simulations using a hybrid quantum mechanics/molecular mechanics (QM/MM) scheme to study the mechanism of L-lactate oxidation by flavocytochrome b2. Simulation results highlight the influence of the environment on the catalytic mechanism by describing a step-wise process in the wild-type enzyme with R289 in a distal position and a concerted mechanism for the other systems. Structure analysis of pyruvate in the Fcb2 active site pocket with R289 in the distal conformation. Residue Y254 plays a role in the catalytic process by stabilizing the product of the first proton transfer from substrate to H373, while residue D282 is expected to stabilize the imidazolium ion in transition and product states by electrostatic interactions and hydrogen bonding with the Hdelta of H373. Active site structures of wild-type and mutant enzymes, detailed overview
Saccharomyces cerevisiae
Other publictions for EC 1.1.2.3
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
743420
Gillet
QM/MM study of l-lactate oxid ...
Saccharomyces cerevisiae
Phys. Chem. Chem. Phys.
18
15609-15618
2016
-
-
-
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3
-
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1
1
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1
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1
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1
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2
1
1
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3
1
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5
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5
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3
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1
1
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1
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2
1
1
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3
1
-
-
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-
1
1
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-
-
743494
Engqvist
Glycolate oxidase3, a glycola ...
Arabidopsis thaliana, Saccharomyces cerevisiae
Plant Physiol.
169
1042-1061
2015
-
-
1
-
2
-
-
1
2
-
-
2
-
4
-
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2
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3
1
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1
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3
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1
3
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2
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1
2
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2
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2
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3
1
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1
-
-
-
-
-
4
4
-
1
1
743862
Karkovska
L-Lactate-selective microbial ...
Ogataea angusta
Talanta
144
1195-1200
2015
-
1
1
-
1
-
-
-
-
-
-
-
-
4
-
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1
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2
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1
1
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1
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1
1
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1
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1
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2
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-
1
1
-
-
-
1
-
-
-
-
-
-
-
-
-
743847
Smutok
Flavocytochrome b2-based enzy ...
Ogataea angusta, Ogataea angusta tr1
ScientificWorldJournal
2013
461284
2013
-
1
-
-
-
-
-
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1
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-
4
-
4
-
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1
-
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1
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6
1
1
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1
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4
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1
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4
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1
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4
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1
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1
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6
1
1
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-
1
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-
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-
1
1
-
-
-
722066
Smutok
Chromate-reducing activity of ...
Ogataea angusta, Ogataea angusta C-105
Chemosphere
83
449-454
2011
-
1
-
-
-
-
-
1
-
-
-
4
-
6
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1
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1
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8
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1
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1
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2
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1
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2
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1
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4
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1
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1
-
8
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1
-
-
-
1
-
-
-
-
-
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722153
Lederer
Another look at the interactio ...
Saccharomyces cerevisiae
Eur. Biophys. J.
40
1283-1299
2011
-
-
-
1
-
-
-
13
2
-
-
1
-
5
-
-
-
1
-
-
-
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1
1
1
-
-
5
1
-
-
4
-
-
-
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-
4
1
-
-
-
-
-
13
2
-
-
1
-
-
-
-
-
-
-
-
1
1
1
-
-
5
1
-
-
-
-
-
-
-
-
-
695890
Mowat
Flavin-containing heme enzymes ...
Saccharomyces cerevisiae
Arch. Biochem. Biophys.
493
37-52
2010
-
-
-
-
4
-
-
-
-
-
1
1
-
1
-
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1
1
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2
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2
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4
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1
1
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-
1
1
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-
-
-
-
-
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1
1
1
1
-
-
712523
Sakai
Functional replacement of yeas ...
Saccharomyces cerevisiae, Saccharomyces cerevisiae D273-10B/A1
J. Biosci. Bioeng.
110
269-272
2010
-
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1
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1
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2
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3
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1
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2
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1
2
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2
1
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712759
Diep Le
Structural evidence for the fu ...
Saccharomyces cerevisiae
J. Mol. Biol.
400
518-530
2010
-
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1
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2
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1
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3
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1
1
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2
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2
1
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2
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1
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1
1
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721242
Arzi
-
Flavocytochrome b2 activity in ...
Satureja hortensis
Acta Hortic.
853
369-378
2010
-
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1
2
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1
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1
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1
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1
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2
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2
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2
2
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1
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1
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2
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1
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1
1
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696302
Le
Interdomain contacts in flavoc ...
Saccharomyces cerevisiae
Biochemistry
48
10803-10809
2009
-
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-
14
-
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15
1
1
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1
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2
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4
1
1
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26
1
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3
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3
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14
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15
1
1
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1
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4
1
1
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26
1
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1
1
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-
696507
Shkil
Bioelectrochemical detection o ...
Saccharomyces cerevisiae
Bioelectrochemistry
76
175-179
2009
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1
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1
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1
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1
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5
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1
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1
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1
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1
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1
1
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1
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1
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1
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1
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1
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1
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697905
Tabacchi
L-lactate dehydrogenation in f ...
Saccharomyces cerevisiae
FEBS J.
276
2368-2380
2009
-
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1
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1
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1
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1
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1
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1
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3
1
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700066
Dmitruk
Construction of flavocytochrom ...
Ogataea angusta
Microbiology
77
213-218
2008
-
1
1
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1
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4
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1
1
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1
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1
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1
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672749
Hao
Pseudomonas stutzeri as a nove ...
Pseudomonas stutzeri
Biotechnol. Lett.
29
105-110
2007
-
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1
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1
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1
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685107
Boubacar
Flavocytochrome b2: reactivity ...
Saccharomyces cerevisiae
Biochemistry
46
13080-13088
2007
-
-
1
-
1
-
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1
-
-
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3
-
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1
2
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1
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1
1
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1
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1
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1
2
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685150
Cenas
Potentiometric and further kin ...
Saccharomyces cerevisiae
Biochemistry
46
4661-4670
2007
-
-
1
-
1
-
6
18
-
-
-
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4
-
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1
1
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19
-
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1
4
-
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-
1
1
-
1
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6
4
18
-
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1
1
-
-
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19
-
-
-
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-
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685174
Tsai
Mechanistic and structural stu ...
Saccharomyces cerevisiae
Biochemistry
46
7844-7851
2007
-
-
1
1
1
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4
-
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2
-
-
-
-
-
-
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1
1
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1
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4
1
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685700
Smutok
Permeabilized cells of flavocy ...
Ogataea angusta
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675858
Smutok
-
Screening of yeasts producing ...
Ogataea angusta, Ogataea angusta 356, Ogataea angusta K-105, Saccharomyces cerevisiae, Saccharomyces cerevisiae IZR-106, Saccharomyces cerevisiae IZR-42
Microbiology
75
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655069
Smutok
A novel L-lactate-selective bi ...
Ogataea angusta
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1285-1290
2005
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654138
Keyhani
-
Expression of L-lactate dehydr ...
Crocus sativus
Acta Hortic.
650
109-117
2004
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654766
Mowat
Altered substrate specificity ...
Saccharomyces cerevisiae
Biochemistry
43
9519-9526
2004
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654235
Gaida
-
A new method of visualization ...
Ogataea angusta
Appl. Biochem. Microbiol.
39
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2003
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654520
Le
Epitope mapping for the monocl ...
Saccharomyces cerevisiae
Biochem. J.
373
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2003
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14
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654690
Sobrado
Solvent and primary deuterium ...
Saccharomyces cerevisiae
Biochemistry
42
15208-15214
2003
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348078
Cunane
Crystallographic study of the ...
Saccharomyces cerevisiae
Biochemistry
41
4264-4272
2002
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656765
Keyhani
Catalytic properties of three ...
Crocus sativus
Mol. Biol. Rep.
29
163-166
2002
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3
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348077
Gondry
The catalytic role of tyrosine ...
Saccharomyces cerevisiae
Eur. J. Biochem.
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2001
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348076
Mowat
Kinetic and crystallographic s ...
Saccharomyces cerevisiae
Biochemistry
39
3266-3275
2000
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1
1
1
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5
11
1
1
1
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4
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8
1
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3
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6
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5
6
11
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3
8
1
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3
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348075
Sinclair
Re-design of Saccharomyces cer ...
Saccharomyces cerevisiae
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5
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348073
Sharp
Deletions in the interdomain h ...
Saccharomyces cerevisiae
Biochemistry
35
891-899
1996
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348074
Daff
New insights into the catalyti ...
Saccharomyces cerevisiae
Biochemistry
35
6345-6350
1996
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3
1
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696188
Daff
Interaction of cytochrome c wi ...
Saccharomyces cerevisiae
Biochemistry
35
6351-6357
1996
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2
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2
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1
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348071
Gaume
Mutation to glutamine of histi ...
Saccharomyces cerevisiae
Biochimie
77
621-630
1995
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1
1
3
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2
4
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2
4
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2
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348072
Tegoni
X-ray structure of two complex ...
Saccharomyces cerevisiae
Biochemistry
34
9840-9850
1995
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1
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1
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4
3
1
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3
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4
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3
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3
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1
4
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3
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696075
Balme
Isolation and characterization ...
Saccharomyces cerevisiae
Biochem. J.
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601-605
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3
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1
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1
1
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3
-
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348069
Balme
On the rate of proton exchange ...
Saccharomyces cerevisiae
Protein Sci.
3
109-117
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1
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2
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4
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1
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1
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1
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1
4
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3
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1
4
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348070
Daff
-
Strategic manipulation of the ...
Saccharomyces cerevisiae
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1
9
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5
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1
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1
1
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3
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4
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1
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1
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1
9
-
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5
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348068
Silvestrini
Expression in Escherichia coli ...
Wickerhamomyces anomalus
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295
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1
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3
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1
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1
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-
3
-
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-
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-
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348067
Brunt
Isolation and characterization ...
Saccharomyces cerevisiae
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1
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3
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1
1
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1
1
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-
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1
1
1
1
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1
-
-
-
-
3
-
-
-
-
-
-
-
1
-
-
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-
-
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348065
Lederer
-
On some aspects of the catalys ...
Saccharomyces cerevisiae
Flavins and Flavoproteins (Proc. Int. Symp. , 10th, Meeting Date 1990, Curti, B. , Ronchi S. , Zanetti, G. , eds. ) de Gruyter, Berlin, New York
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1
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2
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1
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1
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4
-
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4
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3
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1
3
1
2
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4
-
1
-
1
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-
-
4
-
-
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-
4
-
-
-
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348064
Genet
The carbanion of nitroethane i ...
Saccharomyces cerevisiae
Biochem. J.
266
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-
-
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3
1
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3
-
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1
2
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1
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3
2
1
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1
-
1
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-
-
-
3
-
-
-
-
-
-
-
-
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-
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-
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348066
Tegoni
Inhibition of L-lactate: cytoc ...
Saccharomyces cerevisiae, Wickerhamomyces anomalus
Eur. J. Biochem.
190
329-342
1990
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-
-
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2
4
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2
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2
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7
-
-
-
-
-
-
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2
1
-
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-
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-
2
-
-
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2
1
4
-
2
-
2
-
-
-
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-
-
7
-
-
-
-
-
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699506
Xia
Molecular structure of flavocy ...
Saccharomyces cerevisiae
J. Mol. Biol.
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1990
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-
-
1
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1
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2
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2
1
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-
-
1
-
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348063
Black
Structural basis for the kinet ...
Saccharomyces cerevisiae, Wickerhamomyces anomalus
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1989
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-
2
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2
1
2
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5
-
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2
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2
2
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2
1
2
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5
-
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-
-
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348062
Ghrir
Primary structure of flavocyto ...
Saccharomyces cerevisiae
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1984
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-
-
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1
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1
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3
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1
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1
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1
-
1
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1
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-
-
3
-
-
-
-
-
-
-
-
-
-
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-
-
-
-
348060
Blazy
A standard high-yield purifica ...
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1
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1
1
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1
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1
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1
1
2
1
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1
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1
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1
-
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1
1
1
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1
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1
1
2
1
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348061
Labeyrie
Flavocytochrome b 2 or L-lacta ...
Saccharomyces cerevisiae, Wickerhamomyces anomalus
Methods Enzymol.
53
238-256
1978
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-
-
1
-
1
6
4
-
2
5
2
-
3
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-
2
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-
-
-
2
5
2
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1
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6
7
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6
1
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1
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6
7
4
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2
5
2
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2
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2
5
2
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1
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287801
Hatefi
-
Metal-containing flavoprotein ...
Saccharomyces cerevisiae, Wickerhamomyces anomalus
The Enzymes, 3rd Ed. (Boyer, P. D. , ed. )
13
175-297
1976
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2
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2
3
2
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2
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6
2
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8
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8
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2
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2
3
2
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6
2
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348058
Jacq
Cytochrome b2 from bakers yeas ...
Saccharomyces cerevisiae
Eur. J. Biochem.
41
311-320
1974
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-
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1
2
1
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2
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1
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1
3
1
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3
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3
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1
2
1
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1
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1
3
1
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348057
Guiard
Yeast L-lactate dehydrogenase ...
Saccharomyces cerevisiae
Eur. J. Biochem.
34
241-247
1973
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1
1
1
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1
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1
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3
1
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2
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2
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1
1
1
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1
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-
3
1
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348056
Pritchard
An NAD+-independent L-lactate ...
Rhizopus oryzae
Biochim. Biophys. Acta
250
25-34
1971
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1
1
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1
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1
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1
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1
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3
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4
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1
1
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2
2
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2
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1
2
1
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1
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1
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1
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3
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4
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1
1
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