BRENDA - Enzyme Database show
show all sequences of 1.1.1.283

Structural insights into the cofactor-assisted substrate recognition of yeast methylglyoxal/isovaleraldehyde reductase Gre2

Guo, P.C.; Bao, Z.Z.; Ma, X.X.; Xia, Q.; Li, W.F.; Biochim. Biophys. Acta 1844, 1486-1492 (2014)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
gene gre2, recombinant expression of His6-tagged type and mutant enzymes in Escherichia coli strain BL21(DE3)
Saccharomyces cerevisiae
Crystallization (Commentary)
Crystallization
Organism
purified recombinant enzyme in apoform and in a complex with NADPH, X-ray diffraction structure determination and analysis at 2.0 A and 2.4 A, respectively
Saccharomyces cerevisiae
Engineering
Amino acid exchange
Commentary
Organism
F132A/V162A
the replacement of Phe132/Val162, with Ala results in the elevation of enzymatic activity toward isovaleraldehyde, probably via enlarging the pocket entrance
Saccharomyces cerevisiae
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
isovaleraldehyde + NADPH + H+
Saccharomyces cerevisiae
catalytic mechanism involving Ser127, Tyr165, and Lys169, overview. The carbonyl oxygen interactswith the side chain of Ser127, Tyr165 through hydrogen bonds (about 2.7 A), giving a distance of 3.0 A between the C4 atom of the nicotinamide and the carbonyl carbon of substrate
isoamyl alcohol + NADP+
-
-
?
methylglyoxal + NADPH + H+
Saccharomyces cerevisiae
-
(S)-lactaldehyde + NADP+
-
-
r
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Saccharomyces cerevisiae
Q12068
-
-
Purification (Commentary)
Commentary
Organism
recombinant His6-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration, followed by ultrafiltration
Saccharomyces cerevisiae
Reaction
Reaction
Commentary
Organism
(S)-lactaldehyde + NADP+ = 2-oxopropanal + NADPH + H+
catalytic mechanism involving Ser127, Tyr165, and Lys169, overview. In the first step, the hydroxyl groups of the Ser127 and Tyr165 residues form hydrogen bonds with the carbonyl oxygen of isovaleraldehyde, stabilizing its position. Subsequently, the hydroxyl group of Tyr165 donates a hydrogen to the carbonyl through deprotonation. Concomitantly, NADPH releases a hydrogen from the B-face of the nicotinamide ring onto the susceptible position of the carbonyl group. Thus, the carbonyl group is reduced to an alcohol group, and the isoamyl alcohol and NADP+ are produced. Upon reduction of the carbonyl group, the hydrogen bond between the side chain of Tyr165 and isoamyl alcohol is broken. With the redox state change, the conformation of NADP+ also may change, accompanied by the opening of the interdomain cleft for the release of the product
Saccharomyces cerevisiae
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
(S)-lactaldehyde + NADP+
-
741962
Saccharomyces cerevisiae
methylglyoxal + NADPH + H+
-
-
-
r
isovaleraldehyde + NADPH + H+
catalytic mechanism involving Ser127, Tyr165, and Lys169, overview. The carbonyl oxygen interactswith the side chain of Ser127, Tyr165 through hydrogen bonds (about 2.7 A), giving a distance of 3.0 A between the C4 atom of the nicotinamide and the carbonyl carbon of substrate
741962
Saccharomyces cerevisiae
isoamyl alcohol + NADP+
-
-
-
?
isovaleraldehyde + NADPH + H+
catalytic mechanism involving Ser127, Tyr165, and Lys169, overview. The carbonyl oxygen interacts with the side chain of Ser127, Tyr165 through hydrogen bonds (about 2.7 A), giving a distance of 3.0 A between the C4 atom of the nicotinamide and the carbonyl carbon of substrate
741962
Saccharomyces cerevisiae
isoamyl alcohol + NADP+
-
-
-
?
methylglyoxal + NADPH + H+
-
741962
Saccharomyces cerevisiae
(S)-lactaldehyde + NADP+
-
-
-
r
additional information
the substrate recognition and the catalytic mechanism underlie the stereoselective reduction of Gre2. Analysis of the substrate-binding site using computational simulation and enzymatic activity assays, noticeable induced fit upon NADPH binding, overview. In Gre2, the hydrophobic residues Phe85, Tyr128 and Tyr198 combine with Phe132 and Val162 to form one funneled pocket which consists of one broad pocket entrance and one deep hydrophobic channel. The extended hydrophobic entrance of Gre2 plays a role in accommodating a wide variety of carbonyl compounds, such as diketones, aliphatic and cyclic alpha- and beta-keto esters and aldehydes.The deep hydrophobic channel prefers to identify a substrate with a linear substrate. That is why Gre2 shows high reduction activity to butanal, pentanal and 2,5-hexanedione, as well as some aldehydes
741962
Saccharomyces cerevisiae
?
-
-
-
-
Subunits
Subunits
Commentary
Organism
homodimer
enzyme Gre2 forms a homodimer, each subunit of which contains an N-terminal Rossmann-fold domain and a variable C-terminal domain, which participates in substrate recognition. The induced fit upon binding to the cofactor NADPH makes the two domains shift toward each other, producing an interdomain cleft that better fits the substrate
Saccharomyces cerevisiae
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
30
-
assay at
Saccharomyces cerevisiae
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.5
-
assay at
Saccharomyces cerevisiae
Cofactor
Cofactor
Commentary
Organism
Structure
NADP+
-
Saccharomyces cerevisiae
NADPH
dependent on
Saccharomyces cerevisiae
Cloned(Commentary) (protein specific)
Commentary
Organism
gene gre2, recombinant expression of His6-tagged type and mutant enzymes in Escherichia coli strain BL21(DE3)
Saccharomyces cerevisiae
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
NADP+
-
Saccharomyces cerevisiae
NADPH
dependent on
Saccharomyces cerevisiae
Crystallization (Commentary) (protein specific)
Crystallization
Organism
purified recombinant enzyme in apoform and in a complex with NADPH, X-ray diffraction structure determination and analysis at 2.0 A and 2.4 A, respectively
Saccharomyces cerevisiae
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
F132A/V162A
the replacement of Phe132/Val162, with Ala results in the elevation of enzymatic activity toward isovaleraldehyde, probably via enlarging the pocket entrance
Saccharomyces cerevisiae
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
isovaleraldehyde + NADPH + H+
Saccharomyces cerevisiae
catalytic mechanism involving Ser127, Tyr165, and Lys169, overview. The carbonyl oxygen interactswith the side chain of Ser127, Tyr165 through hydrogen bonds (about 2.7 A), giving a distance of 3.0 A between the C4 atom of the nicotinamide and the carbonyl carbon of substrate
isoamyl alcohol + NADP+
-
-
?
methylglyoxal + NADPH + H+
Saccharomyces cerevisiae
-
(S)-lactaldehyde + NADP+
-
-
r
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant His6-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration, followed by ultrafiltration
Saccharomyces cerevisiae
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
(S)-lactaldehyde + NADP+
-
741962
Saccharomyces cerevisiae
methylglyoxal + NADPH + H+
-
-
-
r
isovaleraldehyde + NADPH + H+
catalytic mechanism involving Ser127, Tyr165, and Lys169, overview. The carbonyl oxygen interactswith the side chain of Ser127, Tyr165 through hydrogen bonds (about 2.7 A), giving a distance of 3.0 A between the C4 atom of the nicotinamide and the carbonyl carbon of substrate
741962
Saccharomyces cerevisiae
isoamyl alcohol + NADP+
-
-
-
?
isovaleraldehyde + NADPH + H+
catalytic mechanism involving Ser127, Tyr165, and Lys169, overview. The carbonyl oxygen interacts with the side chain of Ser127, Tyr165 through hydrogen bonds (about 2.7 A), giving a distance of 3.0 A between the C4 atom of the nicotinamide and the carbonyl carbon of substrate
741962
Saccharomyces cerevisiae
isoamyl alcohol + NADP+
-
-
-
?
methylglyoxal + NADPH + H+
-
741962
Saccharomyces cerevisiae
(S)-lactaldehyde + NADP+
-
-
-
r
additional information
the substrate recognition and the catalytic mechanism underlie the stereoselective reduction of Gre2. Analysis of the substrate-binding site using computational simulation and enzymatic activity assays, noticeable induced fit upon NADPH binding, overview. In Gre2, the hydrophobic residues Phe85, Tyr128 and Tyr198 combine with Phe132 and Val162 to form one funneled pocket which consists of one broad pocket entrance and one deep hydrophobic channel. The extended hydrophobic entrance of Gre2 plays a role in accommodating a wide variety of carbonyl compounds, such as diketones, aliphatic and cyclic alpha- and beta-keto esters and aldehydes.The deep hydrophobic channel prefers to identify a substrate with a linear substrate. That is why Gre2 shows high reduction activity to butanal, pentanal and 2,5-hexanedione, as well as some aldehydes
741962
Saccharomyces cerevisiae
?
-
-
-
-
Subunits (protein specific)
Subunits
Commentary
Organism
homodimer
enzyme Gre2 forms a homodimer, each subunit of which contains an N-terminal Rossmann-fold domain and a variable C-terminal domain, which participates in substrate recognition. The induced fit upon binding to the cofactor NADPH makes the two domains shift toward each other, producing an interdomain cleft that better fits the substrate
Saccharomyces cerevisiae
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
30
-
assay at
Saccharomyces cerevisiae
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.5
-
assay at
Saccharomyces cerevisiae
General Information
General Information
Commentary
Organism
evolution
the enzyme belongs to the short-chain dehydrogenase/reductase (SDR) superfamily, which includes various oxidoreductases, some isomerases and lyases
Saccharomyces cerevisiae
additional information
Gre2 forms a homodimer, each subunit of which contains an N-terminal Rossmann-fold domain and a variable C-terminal domain, which participates in substrate recognition. The induced fit upon binding to the cofactor NADPH makes the two domains shift toward each other, producing an interdomain cleft that better fits the substrate. The substrate-binding pocket structure determines the stringent substrate stereoselectivity for catalysis
Saccharomyces cerevisiae
physiological function
the Saccharomyces cerevisiae enzyme serves as a versatile enzyme that catalyzes the stereoselective reduction of a broad range of substrates including aliphatic and aromatic ketones, diketones, as well as aldehydes, using NADPH as the cofactor
Saccharomyces cerevisiae
General Information (protein specific)
General Information
Commentary
Organism
evolution
the enzyme belongs to the short-chain dehydrogenase/reductase (SDR) superfamily, which includes various oxidoreductases, some isomerases and lyases
Saccharomyces cerevisiae
additional information
Gre2 forms a homodimer, each subunit of which contains an N-terminal Rossmann-fold domain and a variable C-terminal domain, which participates in substrate recognition. The induced fit upon binding to the cofactor NADPH makes the two domains shift toward each other, producing an interdomain cleft that better fits the substrate. The substrate-binding pocket structure determines the stringent substrate stereoselectivity for catalysis
Saccharomyces cerevisiae
physiological function
the Saccharomyces cerevisiae enzyme serves as a versatile enzyme that catalyzes the stereoselective reduction of a broad range of substrates including aliphatic and aromatic ketones, diketones, as well as aldehydes, using NADPH as the cofactor
Saccharomyces cerevisiae
Other publictions for EC 1.1.1.283
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)
736122
Akita
Molecular cloning and characte ...
Kluyveromyces marxianus, Kluyveromyces marxianus DMB1
FEMS Microbiol. Lett.
362
fnv116
2015
-
-
1
-
-
-
-
4
-
-
3
-
-
9
-
-
-
-
-
-
11
-
26
1
2
-
2
4
1
-
-
2
-
-
-
-
-
2
4
-
-
-
-
-
-
4
-
-
4
-
-
-
-
-
-
-
11
-
26
2
2
-
4
4
2
-
-
-
-
-
-
-
-
-
737753
Guo
Structural insights into the c ...
Saccharomyces cerevisiae
Biochim. Biophys. Acta
1844
1486-1492
2014
-
-
1
1
-
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
741962
Guo
Structural insights into the ...
Saccharomyces cerevisiae
Biochim. Biophys. Acta
1844
1486-1492
2014
-
-
1
1
1
-
-
-
-
-
-
2
-
2
-
-
1
1
-
-
-
-
5
1
1
-
-
-
1
-
-
2
-
-
-
-
-
1
2
1
1
-
-
-
-
-
-
-
-
2
-
-
-
1
-
-
-
-
5
1
1
-
-
-
1
-
-
-
-
3
3
-
-
-
710768
Breicha
Crystallization and preliminar ...
Saccharomyces cerevisiae
Acta Crystallogr. Sect. F
66
838-841
2010
-
-
1
1
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
692329
Greig
A comparative study of methylg ...
Leishmania major, Leishmania major Friedlin, Trypanosoma brucei, Trypanosoma cruzi
FEBS J.
276
376-386
2009
-
-
-
-
-
-
-
-
-
-
-
-
-
8
-
-
-
-
-
-
3
-
4
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
3
-
4
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
686820
Hauser
A transcriptome analysis of is ...
Saccharomyces cerevisiae
FEMS Yeast Res.
7
84-92
2007
-
-
-
-
1
-
-
-
-
-
-
1
-
1
-
-
-
-
-
-
-
-
3
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
1
-
1
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
3
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
670170
Xu
Methylglyoxal detoxification b ...
Synechococcus sp.
Microbiology
152
2013-2021
2006
-
-
-
-
-
-
-
11
-
-
-
-
-
3
-
-
-
-
-
-
17
-
18
-
-
-
-
11
1
-
1
1
-
-
-
-
-
-
1
-
-
-
-
-
-
11
-
-
-
-
-
-
-
-
-
-
17
-
18
-
-
-
-
11
1
-
1
-
-
-
-
-
-
-
739760
Warringer
Involvement of yeast YOL151W/G ...
Saccharomyces cerevisiae
Yeast
23
389-398
2006
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
1
-
-
-
657418
Chen
Associating protein activities ...
Saccharomyces cerevisiae
Yeast
20
545-554
2003
-
-
1
-
-
-
-
-
-
-
-
-
-
1
-
-
1
-
-
-
1
-
1
-
-
-
-
-
-
-
-
1
-
-
-
-
-
1
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
1
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
738443
Rodriguez
Highly stereoselective reagent ...
Saccharomyces cerevisiae
J. Am. Chem. Soc.
123
1547-1555
2001
-
1
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
6
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
6
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
207977
Inoue
-
Purification and characterizat ...
Cyberlindnera mrakii
J. Ferment. Bioeng.
71
134-136
1991
-
-
-
-
-
-
3
2
-
-
1
1
-
1
-
-
-
-
-
-
1
-
1
1
-
-
-
-
-
-
-
1
-
-
-
-
-
-
1
-
-
-
-
3
-
2
-
-
1
1
-
-
-
-
-
-
1
-
1
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
207974
Inoue
Metabolism of 2-oxoaldehyde in ...
Aspergillus niger
Eur. J. Biochem.
171
213-218
1988
3
-
-
-
-
-
17
7
-
1
3
1
-
1
-
-
1
1
-
-
2
1
6
1
-
-
-
-
2
-
-
1
-
-
-
3
-
-
1
-
-
-
-
17
-
7
-
1
3
1
-
-
-
1
-
-
2
1
6
1
-
-
-
-
2
-
-
-
-
-
-
-
-
-
207973
Murata
-
Metabolism of alpha-ketoglutar ...
Saccharomyces cerevisiae
J. Ferment. Technol.
64
1-4
1986
-
-
-
-
-
-
-
-
-
-
-
1
-
1
-
-
-
1
-
-
-
-
1
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
207971
Murata
Metabolism of 2-oxoaldehyde in ...
Saccharomyces cerevisiae
Eur. J. Biochem.
151
631-636
1985
6
-
-
-
-
-
8
3
-
-
1
1
-
1
-
1
1
-
-
-
1
1
4
-
-
-
-
-
-
-
-
-
-
-
-
6
-
-
-
-
-
-
-
8
-
3
-
-
1
1
-
-
1
1
-
-
1
1
4
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
207972
Murata
Phenotypic character of the me ...
Saccharomyces cerevisiae
Appl. Environ. Microbiol.
50
1200-1207
1985
-
-
1
-
-
-
-
-
-
-
-
1
-
1
-
-
-
1
-
-
-
-
1
-
-
-
-
-
-
-
-
1
-
-
-
-
-
1
1
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-