BRENDA - Enzyme Database show
show all sequences of 1.1.1.45

Dimeric crystal structure of rabbit L-gulonate 3-dehydrogenase/lambda-crystallin: insights into the catalytic mechanism

Asada, Y.; Kuroishi, C.; Ukita, Y.; Sumii, R.; Endo, S.; Matsunaga, T.; Hara, A.; Kunishima, N.; J. Mol. Biol. 401, 906-920 (2010)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
expression of wild-type and mutant enzymes in Escherichia coli strain BL21(DE3) cells
Oryctolagus cuniculus
Crystallization (Commentary)
Crystallization
Organism
purified recombinant enzyme in both apo form and NADH-bound holo form, X-ray diffraction structure determination and analysis at 1.70-1.85 A resolution
Oryctolagus cuniculus
Engineering
Amino acid exchange
Commentary
Organism
D36R
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
Oryctolagus cuniculus
D36R/Q41N
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
Oryctolagus cuniculus
E97Q
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
Oryctolagus cuniculus
Q41N
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
Oryctolagus cuniculus
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.01
-
NAD+
wild-type enzyme, pH 7.0, 25°C
Oryctolagus cuniculus
0.018
-
L-gulonate
with NAD+, wild-type enzyme, pH 7.0, 25°C
Oryctolagus cuniculus
0.028
-
NAD+
mutant enzyme Q41N, pH 7.0, 25°C
Oryctolagus cuniculus
0.054
-
NAD+
mutant enzyme E97Q, pH 7.0, 25°C
Oryctolagus cuniculus
0.12
-
NADP+
mutant enzyme D36R/Q41N, pH 7.0, 25°C
Oryctolagus cuniculus
0.2
-
NADP+
mutant enzyme D36R, pH 7.0, 25°C
Oryctolagus cuniculus
0.67
-
NADP+
wild-type enzyme, pH 7.0, 25°C
Oryctolagus cuniculus
0.86
-
NADP+
mutant enzyme Q41N, pH 7.0, 25°C
Oryctolagus cuniculus
1.3
-
L-gulonate
with NAD+, mutant enzyme Q41N, pH 7.0, 25°C
Oryctolagus cuniculus
1.3
-
NAD+
mutant enzyme D36R, pH 7.0, 25°C
Oryctolagus cuniculus
1.6
-
L-gulonate
with NAD+, mutant enzyme E97Q, pH 7.0, 25°C
Oryctolagus cuniculus
2.4
-
L-gulonate
with NADP+, wild-type enzyme, pH 7.0, 25°C
Oryctolagus cuniculus
2.6
-
L-gulonate
with NADP+, mutant enzyme D36R/Q41N, pH 7.0, 25°C
Oryctolagus cuniculus
2.6
-
NAD+
mutant enzyme D36R/Q41N, pH 7.0, 25°C
Oryctolagus cuniculus
3.3
-
L-gulonate
with NAD+, mutant enzyme D36R/Q41N, pH 7.0, 25°C
Oryctolagus cuniculus
14
-
L-gulonate
with NAD+, mutant enzyme D36R, pH 7.0, 25°C; with NADP+, mutant enzyme Q41N, pH 7.0, 25°C
Oryctolagus cuniculus
18
-
L-gulonate
with NADP+, mutant enzyme D36R, pH 7.0, 25°C
Oryctolagus cuniculus
Molecular Weight [Da]
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
36000
-
2 * 36000, recombinant enzyme, SDS-PAGE
Oryctolagus cuniculus
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
L-gulonate + NAD+
Oryctolagus cuniculus
-
3-dehydro-L-gulonate + NADH + H+
-
-
r
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Oryctolagus cuniculus
P14755
-
-
Purification (Commentary)
Commentary
Organism
recombinant wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) cells
Oryctolagus cuniculus
Reaction
Reaction
Commentary
Organism
L-gulonate + NAD+ = 3-dehydro-L-gulonate + NADH + H+
Cys125, Glu97, and Ser124 are putative coenzyme/substrate-binding residues, catalytic mechanism with induced-fit mechanism upon coenzyme binding and involving a network-based substrate recognition, overview
Oryctolagus cuniculus
Source Tissue
Source Tissue
Commentary
Organism
Textmining
lens
-
Oryctolagus cuniculus
-
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
L-gulonate + NAD+
-
712765
Oryctolagus cuniculus
3-dehydro-L-gulonate + NADH + H+
-
-
-
r
L-gulonate + NAD+
NAD+ is preferred as cofactor
712765
Oryctolagus cuniculus
3-dehydro-L-gulonate + NADH + H+
-
-
-
r
L-gulonate + NADP+
NAD+ is preferred as cofactor
712765
Oryctolagus cuniculus
3-dehydro-L-gulonate + NADPH + H+
-
-
-
r
additional information
active site structure and substrate recognition, importance of the dimeric state of the enzyme, overview
712765
Oryctolagus cuniculus
?
-
-
-
-
Subunits
Subunits
Commentary
Organism
dimer
2 * 36000, recombinant enzyme, SDS-PAGE
Oryctolagus cuniculus
More
the enzyme possesses two domains, the N-terminal domain with a Rossmann fold and the C-terminal domain with a helical fold. In the N-terminal domain of the NADH-bound structure exist 11 coenzyme-binding residues and two distinct side-chain conformers of coenzyme binding residue Ser124. Subunit dimerization is mediated by numerous intersubunit interactions, including 22 hydrogen bonds and 104 residue pairs of van der Waals interactions, of which those between two cognate C-terminal domains are predominant. Domain and subunit interface structures, structure comparison with the human enzyme, overview
Oryctolagus cuniculus
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
25
-
assay at
Oryctolagus cuniculus
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7
-
assay at
Oryctolagus cuniculus
Cofactor
Cofactor
Commentary
Organism
Structure
NAD+
cofactor binding mode, overview
Oryctolagus cuniculus
NADH
cofactor binding mode, overview
Oryctolagus cuniculus
NADP+
cofactor binding mode, overview
Oryctolagus cuniculus
NADPH
cofactor binding mode, overview
Oryctolagus cuniculus
Cloned(Commentary) (protein specific)
Commentary
Organism
expression of wild-type and mutant enzymes in Escherichia coli strain BL21(DE3) cells
Oryctolagus cuniculus
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
NAD+
cofactor binding mode, overview
Oryctolagus cuniculus
NADH
cofactor binding mode, overview
Oryctolagus cuniculus
NADP+
cofactor binding mode, overview
Oryctolagus cuniculus
NADPH
cofactor binding mode, overview
Oryctolagus cuniculus
Crystallization (Commentary) (protein specific)
Crystallization
Organism
purified recombinant enzyme in both apo form and NADH-bound holo form, X-ray diffraction structure determination and analysis at 1.70-1.85 A resolution
Oryctolagus cuniculus
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
D36R
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
Oryctolagus cuniculus
D36R/Q41N
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
Oryctolagus cuniculus
E97Q
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
Oryctolagus cuniculus
Q41N
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
Oryctolagus cuniculus
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.01
-
NAD+
wild-type enzyme, pH 7.0, 25°C
Oryctolagus cuniculus
0.018
-
L-gulonate
with NAD+, wild-type enzyme, pH 7.0, 25°C
Oryctolagus cuniculus
0.028
-
NAD+
mutant enzyme Q41N, pH 7.0, 25°C
Oryctolagus cuniculus
0.054
-
NAD+
mutant enzyme E97Q, pH 7.0, 25°C
Oryctolagus cuniculus
0.12
-
NADP+
mutant enzyme D36R/Q41N, pH 7.0, 25°C
Oryctolagus cuniculus
0.2
-
NADP+
mutant enzyme D36R, pH 7.0, 25°C
Oryctolagus cuniculus
0.67
-
NADP+
wild-type enzyme, pH 7.0, 25°C
Oryctolagus cuniculus
0.86
-
NADP+
mutant enzyme Q41N, pH 7.0, 25°C
Oryctolagus cuniculus
1.3
-
L-gulonate
with NAD+, mutant enzyme Q41N, pH 7.0, 25°C
Oryctolagus cuniculus
1.3
-
NAD+
mutant enzyme D36R, pH 7.0, 25°C
Oryctolagus cuniculus
1.6
-
L-gulonate
with NAD+, mutant enzyme E97Q, pH 7.0, 25°C
Oryctolagus cuniculus
2.4
-
L-gulonate
with NADP+, wild-type enzyme, pH 7.0, 25°C
Oryctolagus cuniculus
2.6
-
L-gulonate
with NADP+, mutant enzyme D36R/Q41N, pH 7.0, 25°C
Oryctolagus cuniculus
2.6
-
NAD+
mutant enzyme D36R/Q41N, pH 7.0, 25°C
Oryctolagus cuniculus
3.3
-
L-gulonate
with NAD+, mutant enzyme D36R/Q41N, pH 7.0, 25°C
Oryctolagus cuniculus
14
-
L-gulonate
with NAD+, mutant enzyme D36R, pH 7.0, 25°C; with NADP+, mutant enzyme Q41N, pH 7.0, 25°C
Oryctolagus cuniculus
18
-
L-gulonate
with NADP+, mutant enzyme D36R, pH 7.0, 25°C
Oryctolagus cuniculus
Molecular Weight [Da] (protein specific)
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
36000
-
2 * 36000, recombinant enzyme, SDS-PAGE
Oryctolagus cuniculus
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
L-gulonate + NAD+
Oryctolagus cuniculus
-
3-dehydro-L-gulonate + NADH + H+
-
-
r
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) cells
Oryctolagus cuniculus
Source Tissue (protein specific)
Source Tissue
Commentary
Organism
Textmining
lens
-
Oryctolagus cuniculus
-
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
L-gulonate + NAD+
-
712765
Oryctolagus cuniculus
3-dehydro-L-gulonate + NADH + H+
-
-
-
r
L-gulonate + NAD+
NAD+ is preferred as cofactor
712765
Oryctolagus cuniculus
3-dehydro-L-gulonate + NADH + H+
-
-
-
r
L-gulonate + NADP+
NAD+ is preferred as cofactor
712765
Oryctolagus cuniculus
3-dehydro-L-gulonate + NADPH + H+
-
-
-
r
additional information
active site structure and substrate recognition, importance of the dimeric state of the enzyme, overview
712765
Oryctolagus cuniculus
?
-
-
-
-
Subunits (protein specific)
Subunits
Commentary
Organism
dimer
2 * 36000, recombinant enzyme, SDS-PAGE
Oryctolagus cuniculus
More
the enzyme possesses two domains, the N-terminal domain with a Rossmann fold and the C-terminal domain with a helical fold. In the N-terminal domain of the NADH-bound structure exist 11 coenzyme-binding residues and two distinct side-chain conformers of coenzyme binding residue Ser124. Subunit dimerization is mediated by numerous intersubunit interactions, including 22 hydrogen bonds and 104 residue pairs of van der Waals interactions, of which those between two cognate C-terminal domains are predominant. Domain and subunit interface structures, structure comparison with the human enzyme, overview
Oryctolagus cuniculus
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
25
-
assay at
Oryctolagus cuniculus
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7
-
assay at
Oryctolagus cuniculus
General Information
General Information
Commentary
Organism
physiological function
L-gulonate 3-dehydrogenase is a bifunctional dimeric protein that functions not only as an NAD+-dependent enzyme in the uronate cycle but also as a taxon-specific lambda-crystallin in rabbit lens
Oryctolagus cuniculus
General Information (protein specific)
General Information
Commentary
Organism
physiological function
L-gulonate 3-dehydrogenase is a bifunctional dimeric protein that functions not only as an NAD+-dependent enzyme in the uronate cycle but also as a taxon-specific lambda-crystallin in rabbit lens
Oryctolagus cuniculus
Other publictions for EC 1.1.1.45
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)
712765
Asada
Dimeric crystal structure of r ...
Oryctolagus cuniculus
J. Mol. Biol.
401
906-920
2010
-
-
1
1
4
-
-
17
-
-
1
1
-
2
-
-
1
1
-
2
-
-
4
2
1
-
-
-
1
-
-
4
-
-
-
-
-
1
4
1
4
-
-
-
-
17
-
-
1
1
-
-
-
1
-
2
-
-
4
2
1
-
-
-
1
-
-
-
-
1
1
-
-
-
695345
Asada
Crystallization and preliminar ...
Oryctolagus cuniculus
Acta Crystallogr. Sect. F
64
228-230
2008
-
-
1
1
-
-
-
-
-
-
1
-
-
2
-
-
1
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
1
-
-
-
-
-
-
-
-
1
-
-
-
-
1
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
669147
Ishikura
Structural and functional char ...
Oryctolagus cuniculus
J. Biochem.
137
303-314
2005
-
-
1
-
6
-
5
19
1
-
3
-
-
3
-
-
1
-
-
2
2
-
5
1
-
-
-
-
1
-
-
2
-
1
2
-
-
1
2
-
6
-
2
5
-
19
1
-
3
-
-
-
-
1
-
2
2
-
5
1
-
-
-
-
1
-
-
1
-
-
-
-
-
-
286146
Goode
Accumulation of xylitol in the ...
Bos taurus, Rattus norvegicus
FEBS Lett.
395
174-178
1996
-
2
-
-
-
-
-
-
-
-
2
2
-
2
-
-
-
-
-
2
-
-
4
-
-
-
-
-
-
-
-
4
-
-
-
-
2
-
4
-
-
-
-
-
-
-
-
-
2
2
-
-
-
-
-
2
-
-
4
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
286911
Menotti-Raymond
Further characterization of L- ...
Drosophila melanogaster
Biochim. Biophys. Acta
841
15-21
1985
-
-
-
-
-
-
-
-
-
-
1
1
-
3
-
1
1
-
-
-
2
-
2
1
-
-
-
-
-
-
-
2
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
-
1
1
-
-
1
1
-
-
2
-
2
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
286910
Cannistraro
Subunit structure and kinetic ...
Drosophila melanogaster
Biochim. Biophys. Acta
569
1-5
1979
-
-
-
-
-
1
2
4
-
-
3
1
-
2
-
-
-
-
-
-
1
-
3
1
-
-
-
2
1
-
-
3
-
-
-
-
-
-
3
-
-
1
-
2
-
4
-
-
3
1
-
-
-
-
-
-
1
-
3
1
-
-
-
2
1
-
-
-
-
-
-
-
-
-
286909
Borack
-
Organ distribution of Drosophi ...
Drosophila melanogaster
Experientia
30
31
1974
-
-
-
-
-
-
-
-
-
-
-
1
-
1
-
-
-
-
-
4
-
-
2
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
4
-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
286908
Koundakjian
3-Hydroxy acid dehydrogenases ...
Ovis aries
Biochem. J.
127
449-452
1972
-
-
-
-
-
-
-
-
1
-
-
-
-
1
-
-
-
-
-
4
-
-
1
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
2
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
4
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
286907
Borack
Drosophila beta-L-hydroxy acid ...
Drosophila melanogaster
J. Biol. Chem.
246
5345-5350
1970
-
-
-
-
-
-
-
3
-
-
1
1
-
1
-
-
1
-
-
-
1
-
4
-
-
-
-
-
1
1
-
2
-
-
-
-
-
-
2
-
-
-
-
-
-
3
-
-
1
1
-
-
-
1
-
-
1
-
4
-
-
-
-
-
1
1
-
-
-
-
-
-
-
-
286906
Dworsky
-
L-3-Aldonic acid dehydrogenase ...
Schwanniomyces occidentalis
Acta Biochim. Pol.
9
269-277
1964
-
-
-
-
-
-
3
4
-
-
-
1
-
1
-
-
1
-
-
-
-
-
5
-
-
-
1
-
1
-
-
1
-
-
-
-
-
-
1
-
-
-
-
3
-
4
-
-
-
1
-
-
-
1
-
-
-
-
5
-
-
-
1
-
1
-
-
-
-
-
-
-
-
-
286905
Smiley
-
Purification and properties of ...
Sus scrofa
J. Biol. Chem.
236
357-364
1961
1
-
-
-
-
-
2
8
1
1
-
1
-
1
-
-
1
-
-
1
-
1
16
-
-
-
-
-
2
2
-
2
-
-
-
1
-
-
2
-
-
-
-
2
-
8
1
1
-
1
-
-
-
1
-
1
-
1
16
-
-
-
-
-
2
2
-
-
-
-
-
-
-
-