BRENDA - Enzyme Database show
show all sequences of 1.1.1.215

Crystallization and structural analysis of 2-hydroxyacid dehydrogenase from Ketogulonicigenium vulgare

Han, X.; Xiong, X.; Hu, X.; Li, M.; Zhang, W.; Liu, X.; Biotechnol. Lett. 36, 295-300 (2014)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
recombinant overexpression of C-terminally His6-tagged enzyme in Escherichia coli
Ketogulonicigenium vulgare
Crystallization (Commentary)
Crystallization
Organism
purified recombinant enzyme, sitting drop vapour diffusion method, mixing of 0.001 ml of 30 mg/ml protein in 25 mM Tris/HCl, pH 8.0, 0.3 M NaCl, and 1 mM dithiothreitol, with 0.001 ml of reservoir solution containing 23% w/v PEG 3350, 0.2 M MgCl2, and 0.1 M HEPES, pH 7.0, and equilibration against 0.1 ml of reservoir solution, 20C, X-ray diffraction structure determination and analysis at 1.64 A resolution, molecular replacement and modeling
Ketogulonicigenium vulgare
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.05
-
NADPH
recombinant His6-tagged enzyme, pH and temperature not specified in the publication
Ketogulonicigenium vulgare
0.11
-
NADH
recombinant His6-tagged enzyme, pH and temperature not specified in the publication
Ketogulonicigenium vulgare
2.6
-
2-dehydro-L-gluconate
recombinant His6-tagged enzyme, pH and temperature not specified in the publication
Ketogulonicigenium vulgare
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
2-dehydro-L-gluconate + NADPH + H+
Ketogulonicigenium vulgare
-
L-idonate + NADP+
-
-
?
2-dehydro-L-gluconate + NADPH + H+
Ketogulonicigenium vulgare Y25
-
L-idonate + NADP+
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Ketogulonicigenium vulgare
-
-
-
Ketogulonicigenium vulgare Y25
-
-
-
Purification (Commentary)
Commentary
Organism
recombinant His6-tagged enzyme from Escherichia coli by nickel affinity and anion exchange chromatography, followed by gel filtration
Ketogulonicigenium vulgare
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
2-dehydro-L-gluconate + NADH + H+
-
742168
Ketogulonicigenium vulgare
L-idonate + NAD+
-
-
-
?
2-dehydro-L-gluconate + NADH + H+
-
742168
Ketogulonicigenium vulgare Y25
L-idonate + NAD+
-
-
-
?
2-dehydro-L-gluconate + NADPH + H+
-
742168
Ketogulonicigenium vulgare
L-idonate + NADP+
-
-
-
?
2-dehydro-L-gluconate + NADPH + H+
-
742168
Ketogulonicigenium vulgare Y25
L-idonate + NADP+
-
-
-
?
Subunits
Subunits
Commentary
Organism
More
the enzyme shows a structure consisting of two-compact domains separated by a deep active cleft. This typical topology is conserved in other 2-HDH. The smaller domain is the substrate binding domain or catalytic domain, which is formed from N-terminal residues 2-102 and C-terminal residues 288-317. It is folded into a five-stranded parallel beta-sheet flanked by five alpha-helices, forming a modified Rossmann topology. The larger domain is responsible for binding the cofactor and contains a conserved [GXGXXG (X17) D] motif that is characteristic of the NAD(P)H/NAD(P)+-binding region. It consists of residues 103-287, forming a seven-stranded parallel beta-sheet flanked by seven alpha-helices. A two-stranded hinge connects the two domains showing flexibility during catalysis
Ketogulonicigenium vulgare
Cofactor
Cofactor
Commentary
Organism
Structure
additional information
the larger enzyme domain is responsible for binding the cofactor and contains a conserved [GXGXXG (X17) D] motif that is characteristic of the NAD(P)H/NAD(P)+-binding region. It consists of residues 103-287, forming a seven-stranded parallel beta-sheet flanked by seven alpha-helices
Ketogulonicigenium vulgare
NADH
-
Ketogulonicigenium vulgare
NADPH
-
Ketogulonicigenium vulgare
Cloned(Commentary) (protein specific)
Commentary
Organism
recombinant overexpression of C-terminally His6-tagged enzyme in Escherichia coli
Ketogulonicigenium vulgare
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
additional information
the larger enzyme domain is responsible for binding the cofactor and contains a conserved [GXGXXG (X17) D] motif that is characteristic of the NAD(P)H/NAD(P)+-binding region. It consists of residues 103-287, forming a seven-stranded parallel beta-sheet flanked by seven alpha-helices
Ketogulonicigenium vulgare
NADH
-
Ketogulonicigenium vulgare
NADPH
-
Ketogulonicigenium vulgare
Crystallization (Commentary) (protein specific)
Crystallization
Organism
purified recombinant enzyme, sitting drop vapour diffusion method, mixing of 0.001 ml of 30 mg/ml protein in 25 mM Tris/HCl, pH 8.0, 0.3 M NaCl, and 1 mM dithiothreitol, with 0.001 ml of reservoir solution containing 23% w/v PEG 3350, 0.2 M MgCl2, and 0.1 M HEPES, pH 7.0, and equilibration against 0.1 ml of reservoir solution, 20C, X-ray diffraction structure determination and analysis at 1.64 A resolution, molecular replacement and modeling
Ketogulonicigenium vulgare
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.05
-
NADPH
recombinant His6-tagged enzyme, pH and temperature not specified in the publication
Ketogulonicigenium vulgare
0.11
-
NADH
recombinant His6-tagged enzyme, pH and temperature not specified in the publication
Ketogulonicigenium vulgare
2.6
-
2-dehydro-L-gluconate
recombinant His6-tagged enzyme, pH and temperature not specified in the publication
Ketogulonicigenium vulgare
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
2-dehydro-L-gluconate + NADPH + H+
Ketogulonicigenium vulgare
-
L-idonate + NADP+
-
-
?
2-dehydro-L-gluconate + NADPH + H+
Ketogulonicigenium vulgare Y25
-
L-idonate + NADP+
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant His6-tagged enzyme from Escherichia coli by nickel affinity and anion exchange chromatography, followed by gel filtration
Ketogulonicigenium vulgare
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
2-dehydro-L-gluconate + NADH + H+
-
742168
Ketogulonicigenium vulgare
L-idonate + NAD+
-
-
-
?
2-dehydro-L-gluconate + NADH + H+
-
742168
Ketogulonicigenium vulgare Y25
L-idonate + NAD+
-
-
-
?
2-dehydro-L-gluconate + NADPH + H+
-
742168
Ketogulonicigenium vulgare
L-idonate + NADP+
-
-
-
?
2-dehydro-L-gluconate + NADPH + H+
-
742168
Ketogulonicigenium vulgare Y25
L-idonate + NADP+
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
More
the enzyme shows a structure consisting of two-compact domains separated by a deep active cleft. This typical topology is conserved in other 2-HDH. The smaller domain is the substrate binding domain or catalytic domain, which is formed from N-terminal residues 2-102 and C-terminal residues 288-317. It is folded into a five-stranded parallel beta-sheet flanked by five alpha-helices, forming a modified Rossmann topology. The larger domain is responsible for binding the cofactor and contains a conserved [GXGXXG (X17) D] motif that is characteristic of the NAD(P)H/NAD(P)+-binding region. It consists of residues 103-287, forming a seven-stranded parallel beta-sheet flanked by seven alpha-helices. A two-stranded hinge connects the two domains showing flexibility during catalysis
Ketogulonicigenium vulgare
General Information
General Information
Commentary
Organism
additional information
the amino acid residues Arg234, Glu263 and His 279 form the active site of enzyme HDH. Residues Arg234, Ala210, Thr211, and Arg212, which are located on top of the catalytic triad, act as a size filter to jointly determine the substrate specificity
Ketogulonicigenium vulgare
physiological function
the enzyme catalyzes the bioconversion of 2-dehydro-L-gulonic acid to L-idonate, which plays a negative role in the manufacture of vitamin C. The primary biochemical function of HDH from Ketogulonicigenium vulgare is C=O bond oxidation-reduction, cf. EC 1.1.1.272
Ketogulonicigenium vulgare
General Information (protein specific)
General Information
Commentary
Organism
additional information
the amino acid residues Arg234, Glu263 and His 279 form the active site of enzyme HDH. Residues Arg234, Ala210, Thr211, and Arg212, which are located on top of the catalytic triad, act as a size filter to jointly determine the substrate specificity
Ketogulonicigenium vulgare
physiological function
the enzyme catalyzes the bioconversion of 2-dehydro-L-gulonic acid to L-idonate, which plays a negative role in the manufacture of vitamin C. The primary biochemical function of HDH from Ketogulonicigenium vulgare is C=O bond oxidation-reduction, cf. EC 1.1.1.272
Ketogulonicigenium vulgare
Other publictions for EC 1.1.1.215
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)
740963
Li
Overexpression of membrane-bou ...
Gluconobacter oxydans, Gluconobacter oxydans 621H
Microb. Cell Fact.
15
121
2016
-
1
1
-
1
-
-
-
1
-
-
4
-
4
-
-
-
-
-
-
-
-
4
-
-
-
-
-
-
-
-
1
-
-
-
-
1
1
1
-
1
-
-
-
-
-
1
-
-
4
-
-
-
-
-
-
-
-
4
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
741418
Kuivanen
A novel pathway for fungal D-g ...
Aspergillus niger
Sci. Rep.
6
26329
2016
-
-
1
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
2
-
-
-
-
-
1
2
-
-
-
-
-
-
-
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-
-
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
1
1
-
-
-
739910
Kataoka
Efficient production of 2,5-di ...
Gluconobacter japonicus, Gluconobacter japonicus NBRC3271
Appl. Environ. Microbiol.
81
3552-3560
2015
-
-
1
-
1
-
-
-
1
-
-
2
-
2
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
1
-
-
-
-
-
1
1
-
1
-
-
-
-
-
1
-
-
2
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
1
1
-
-
-
742168
Han
Crystallization and structura ...
Ketogulonicigenium vulgare, Ketogulonicigenium vulgare Y25
Biotechnol. Lett.
36
295-300
2014
-
-
1
1
-
-
-
3
-
-
-
2
-
6
-
-
1
-
-
-
-
-
4
1
-
-
-
-
-
-
-
3
-
-
-
-
-
1
3
1
-
-
-
-
-
3
-
-
-
2
-
-
-
1
-
-
-
-
4
1
-
-
-
-
-
-
-
-
-
2
2
-
-
-
721369
Rauch
Characterization of enzymes in ...
Gluconobacter oxydans, Gluconobacter oxydans 621H
Appl. Microbiol. Biotechnol.
88
711-718
2010
-
-
1
-
-
-
-
3
-
-
2
4
-
7
-
-
-
-
-
-
-
-
8
1
-
-
-
1
-
-
-
2
-
-
-
-
-
1
2
-
-
-
-
-
-
3
-
-
2
4
-
-
-
-
-
-
-
-
8
1
-
-
-
1
-
-
-
-
-
-
-
-
1
1
695779
De Werra
Role of gluconic acid producti ...
Pseudomonas fluorescens, Pseudomonas fluorescens CHA0
Appl. Environ. Microbiol.
75
4162-4174
2009
-
-
1
-
1
-
-
-
1
-
-
-
-
11
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
1
-
-
-
-
-
1
1
-
1
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
700265
Pajaniappan
A temperature-regulated Campyl ...
Campylobacter jejuni, Campylobacter jejuni 81-176
Mol. Microbiol.
68
474-491
2008
1
1
1
-
1
-
-
-
1
-
2
-
-
13
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
1
-
2
-
1
1
1
1
-
1
-
-
-
-
-
1
-
2
-
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
684567
Toyama
Membrane-bound, 2-keto-D-gluco ...
Gluconobacter frateurii, Gluconobacter frateurii IFO 3271
Appl. Environ. Microbiol.
73
6551-6556
2007
-
-
1
-
-
-
-
-
1
1
3
2
-
3
-
-
1
-
-
-
1
-
4
1
1
-
-
-
1
-
-
3
-
-
-
-
-
1
3
-
-
-
-
-
-
-
1
1
3
2
-
-
-
1
-
-
1
-
4
1
1
-
-
-
1
-
-
-
-
-
-
-
-
-
685666
Saichana
Preparation of enzymes require ...
Gluconobacter oxydans, Gluconobacter oxydans 621H
Biosci. Biotechnol. Biochem.
71
2478-2486
2007
-
-
1
-
-
-
-
-
1
1
-
2
-
6
-
-
-
-
-
-
-
-
2
-
1
-
-
-
1
-
-
3
-
-
-
-
-
1
3
-
-
-
-
-
-
-
1
1
-
2
-
-
-
-
-
-
-
-
2
-
1
-
-
-
1
-
-
-
-
-
-
-
-
-
286278
Yum
Purification and characterizat ...
Brevibacterium ketosoreductum
Biosci. Biotechnol. Biochem.
62
154-156
1998
-
-
-
-
-
-
-
2
-
-
2
4
-
3
-
-
1
-
-
-
1
-
8
1
-
-
-
-
1
-
1
2
-
-
-
-
-
-
2
-
-
-
-
-
-
2
-
-
2
4
-
-
-
1
-
-
1
-
8
1
-
-
-
-
1
-
1
-
-
-
-
-
-
-
286279
Yum
The yiaE gene, located at 80.1 ...
Escherichia coli
J. Bacteriol.
180
5984-5988
1998
-
-
1
-
-
-
-
-
1
-
2
2
-
4
-
-
1
-
-
-
-
-
5
1
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
1
-
2
2
-
-
-
1
-
-
-
-
5
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
5693
Pitt
Enzymes of gluconate metabolis ...
Penicillium chrysogenum, Penicillium chrysogenum Westling
Antonie van Leeuwenhoek
51
353-364
1985
-
-
-
-
-
1
-
-
-
-
-
-
-
3
-
-
-
-
-
-
-
1
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
286275
Ameyama
-
2-keto-D-Gluconate reductase f ...
Acetobacter ascendens, Acetobacter pasteurianus, Gluconacetobacter liquefaciens, Gluconobacter oxydans
Methods Enzymol.
89
203-210
1982
-
-
-
3
-
-
8
-
4
4
5
3
-
4
-
-
3
-
-
-
3
4
31
2
-
-
4
-
8
-
4
12
-
-
-
-
-
-
12
3
-
-
-
8
-
-
4
4
5
3
-
-
-
3
-
-
3
4
31
2
-
-
4
-
8
-
4
-
-
-
-
-
-
-
286274
Adachi
-
Crystalline 2-ketogluconate re ...
Acetobacter ascendens
Agric. Biol. Chem.
42
2057-2062
1978
-
-
-
1
-
3
1
4
1
1
2
-
-
1
-
-
1
-
-
-
1
1
7
1
1
1
3
-
2
2
-
2
-
-
-
-
-
-
2
1
-
3
-
1
-
4
1
1
2
-
-
-
-
1
-
-
1
1
7
1
1
1
3
-
2
2
-
-
-
-
-
-
-
-
286276
Shinagawa
-
Distribution of gluconate dehy ...
acetic acid bacteria, no activity in a number of oxidative or aerobic bacteria
Agric. Biol. Chem.
42
1055-1057
1978
-
-
-
-
-
-
-
-
-
-
-
1
-
2
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
286273
Chiyonobu
-
Purification, crystallization ...
Acetobacter pasteurianus
Agric. Biol. Chem.
40
175-184
1976
-
-
-
1
-
2
9
12
1
1
2
1
-
1
-
-
1
-
-
-
1
2
10
1
1
1
2
-
2
2
1
2
-
-
-
-
-
-
2
1
-
2
-
9
-
12
1
1
2
1
-
-
-
1
-
-
1
2
10
1
1
1
2
-
2
2
1
-
-
-
-
-
-
-