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1.6 A structure of an NAD(+)-dependent quinate dehydrogenase from Corynebacterium glutamicum

Schoepe, J.; Niefind, K.; Schomburg, D.; Acta Crystallogr. Sect. D 64, 803-809 (2008)

Data extracted from this reference:

Crystallization (Commentary)
Crystallization
Organism
NAD+-dependent enzyme, X-ray diffraction structure determination and anaylsis at 1.64-8.0 A resolution, molecular replacement method, modelling of the ternary complexes, overview
Corynebacterium glutamicum
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
10.2
-
L-quinate
pH 9.0, 30C
Corynebacterium glutamicum
46.6
-
shikimate
pH 10.0, 30C
Corynebacterium glutamicum
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
L-quinate + NAD+
Corynebacterium glutamicum
QDH plays a key role in the quinate-degradation pathway
3-dehydroquinate + NADH + H+
-
-
r
shikimate + NAD+
Corynebacterium glutamicum
-
3-dehydroshikimate + NADH + H+
-
-
r
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Corynebacterium glutamicum
-
ORF Cgl0424
-
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
L-quinate + NAD+
QDH plays a key role in the quinate-degradation pathway
684153
Corynebacterium glutamicum
3-dehydroquinate + NADH + H+
-
-
-
r
L-quinate + NAD+
Thr88 and Thr221 are involved in quinate binding
684153
Corynebacterium glutamicum
3-dehydroquinate + NADH + H+
-
-
-
r
additional information
structure of the potential binding site of quinate and shikimate includign the the completely conserved residues Lys92 and Asp102, overview. The crystal structure reveals that in contrast to shikimate, quinate forms a hydrogen bond to the NAD+. In addition, the hydroxyl group of a conserved active-site threonine hydrogen binds to quinate more effectively than to shikimate. Also, the hydroxyl group of a conserved tyrosine approaches the carboxylate group of quinate more closely than it does the carboxylate group of shikimate, active site structure, overview
684153
Corynebacterium glutamicum
?
-
-
-
-
shikimate + NAD+
-
684153
Corynebacterium glutamicum
3-dehydroshikimate + NADH + H+
-
-
-
r
Subunits
Subunits
Commentary
Organism
More
seconfdary and tertiary enzyme structures, the enzyme is composed of two alphabetaalpha domains containing two discontinuous segments, Asp22-Asn127 and Gly287-Leu302, overview
Corynebacterium glutamicum
Temperature Optimum [C]
Temperature Optimum [C]
Temperature Optimum Maximum [C]
Commentary
Organism
30
-
assay at
Corynebacterium glutamicum
Turnover Number [1/s]
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
61.9
-
L-quinate
pH 9.0, 30C
Corynebacterium glutamicum
85.2
-
shikimate
pH 10.0, 30C
Corynebacterium glutamicum
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
9
-
quinate dehydrogenase activity
Corynebacterium glutamicum
10
-
shikimate dehydrogenase activity
Corynebacterium glutamicum
Cofactor
Cofactor
Commentary
Organism
Structure
NAD+
dependent on, 300fold higher activity compared to NADP+
Corynebacterium glutamicum
NADH
binding site structure, overview
Corynebacterium glutamicum
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
NAD+
dependent on, 300fold higher activity compared to NADP+
Corynebacterium glutamicum
NADH
binding site structure, overview
Corynebacterium glutamicum
Crystallization (Commentary) (protein specific)
Crystallization
Organism
NAD+-dependent enzyme, X-ray diffraction structure determination and anaylsis at 1.64-8.0 A resolution, molecular replacement method, modelling of the ternary complexes, overview
Corynebacterium glutamicum
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
10.2
-
L-quinate
pH 9.0, 30C
Corynebacterium glutamicum
46.6
-
shikimate
pH 10.0, 30C
Corynebacterium glutamicum
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
L-quinate + NAD+
Corynebacterium glutamicum
QDH plays a key role in the quinate-degradation pathway
3-dehydroquinate + NADH + H+
-
-
r
shikimate + NAD+
Corynebacterium glutamicum
-
3-dehydroshikimate + NADH + H+
-
-
r
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
L-quinate + NAD+
QDH plays a key role in the quinate-degradation pathway
684153
Corynebacterium glutamicum
3-dehydroquinate + NADH + H+
-
-
-
r
L-quinate + NAD+
Thr88 and Thr221 are involved in quinate binding
684153
Corynebacterium glutamicum
3-dehydroquinate + NADH + H+
-
-
-
r
additional information
structure of the potential binding site of quinate and shikimate includign the the completely conserved residues Lys92 and Asp102, overview. The crystal structure reveals that in contrast to shikimate, quinate forms a hydrogen bond to the NAD+. In addition, the hydroxyl group of a conserved active-site threonine hydrogen binds to quinate more effectively than to shikimate. Also, the hydroxyl group of a conserved tyrosine approaches the carboxylate group of quinate more closely than it does the carboxylate group of shikimate, active site structure, overview
684153
Corynebacterium glutamicum
?
-
-
-
-
shikimate + NAD+
-
684153
Corynebacterium glutamicum
3-dehydroshikimate + NADH + H+
-
-
-
r
Subunits (protein specific)
Subunits
Commentary
Organism
More
seconfdary and tertiary enzyme structures, the enzyme is composed of two alphabetaalpha domains containing two discontinuous segments, Asp22-Asn127 and Gly287-Leu302, overview
Corynebacterium glutamicum
Temperature Optimum [C] (protein specific)
Temperature Optimum [C]
Temperature Optimum Maximum [C]
Commentary
Organism
30
-
assay at
Corynebacterium glutamicum
Turnover Number [1/s] (protein specific)
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
61.9
-
L-quinate
pH 9.0, 30C
Corynebacterium glutamicum
85.2
-
shikimate
pH 10.0, 30C
Corynebacterium glutamicum
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
9
-
quinate dehydrogenase activity
Corynebacterium glutamicum
10
-
shikimate dehydrogenase activity
Corynebacterium glutamicum
Other publictions for EC 1.1.1.24
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)
727115
Hppner
Enzyme-substrate complexes of ...
Corynebacterium glutamicum, Corynebacterium glutamicum ATCC 13032
Biol. Chem.
394
1505-1516
2013
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1
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8
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1
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8
2
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8
8
698068
Marsh
Changes in quinic acid metabol ...
Actinidia arguta, Actinidia arguta var. arguta, Actinidia chinensis, Actinidia deliciosa, Actinidia deliciosa var. deliciosa
Funct. Plant Biol.
36
463-470
2009
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5
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3
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5
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1
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3
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3
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3
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3
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684153
Schoepe
1.6 A structure of an NAD(+)-d ...
Corynebacterium glutamicum
Acta Crystallogr. Sect. D
64
803-809
2008
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4
1
1
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2
2
-
-
-
-
-
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657345
Shein
-
The content of phenolic compou ...
Pinus sylvestris
Russ. J. Plant Physiol.
50
516-521
2003
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1
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286364
Ossipov
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Broad-specificity quinate (shi ...
Daucus carota, Pinus taeda
Plant Physiol.
38
923-928
2000
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-
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4
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1
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2
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1
1
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3
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286363
Grund
Utilization of quinate and p-h ...
Pseudonocardia sp., Rhodococcus rhodochrous, Streptomyces sp.
J. Basic Microbiol.
38
241-255
1998
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286362
Kang
-
Subcellular localization of qu ...
Vigna radiata var. radiata
Z. Naturforsch. C
49
415-420
1994
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5487
Hawkins
Characterization of the 3-dehy ...
Aspergillus nidulans
Biochem. J.
296
451-457
1993
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286365
Kang
-
Purification and characterizat ...
Vigna radiata var. radiata
Phytochemistry
33
769-773
1993
3
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2
8
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3
1
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286359
Graziana
-
The reversible association of ...
Daucus carota
FEBS Lett.
163
306-311
1983
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286356
Barea
Purification and characterizat ...
Neurospora crassa
Biochim. Biophys. Acta
524
1-14
1978
1
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286357
Cain
The identity of shikimate dehy ...
Aspergillus niger
Biochem. J.
127
15P
1972
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684945
Cain
Metabolism of shikimate and qu ...
Aspergillus niger
Biochem. J.
127
15P-16P
1972
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286358
Gamborg
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Aromatic metabolism in plants ...
Vigna radiata var. radiata
Biochim. Biophys. Acta
128
483-491
1966
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286360
Davies
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Enzymes of aromatic biosynthes ...
Enterobacter aerogenes
Methods Enzymol.
2
307-311
1955
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