Information on EC 1.1.1.282 - quinate/shikimate dehydrogenase

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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria

EC NUMBER
COMMENTARY hide
1.1.1.282
-
RECOMMENDED NAME
GeneOntology No.
quinate/shikimate dehydrogenase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
L-quinate + NAD(P)+ = 3-dehydroquinate + NAD(P)H + H+
show the reaction diagram
shikimate + NAD(P)+ = 3-dehydroshikimate + NAD(P)H + H
show the reaction diagram
shikimate + NAD(P)+ = 3-dehydroshikimate + NAD(P)H + H+
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oxidation
-
-
-
-
redox reaction
-
-
-
-
reduction
-
-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
chorismate metabolism
-
-
Phenylalanine, tyrosine and tryptophan biosynthesis
-
-
Metabolic pathways
-
-
Biosynthesis of secondary metabolites
-
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Biosynthesis of antibiotics
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chorismate biosynthesis from 3-dehydroquinate
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-
SYSTEMATIC NAME
IUBMB Comments
L-quinate:NAD(P)+ 3-oxidoreductase
This is the second shikimate dehydrogenase enzyme found in Escherichia coli and differs from EC 1.1.1.25, shikimate dehydrogenase, in that it can use both quinate and shikimate as substrate and either NAD+ or NADP+ as acceptor.
CAS REGISTRY NUMBER
COMMENTARY hide
9026-87-3
cf. EC 1.1.1.25
9028-28-8
cf. EC 1.1.1.24
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
12 years old
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
20 days old saplings
-
-
Manually annotated by BRENDA team
20 years old
-
-
Manually annotated by BRENDA team
trees grown in a field at the University of Victoria
-
-
Manually annotated by BRENDA team
trees grown in a field at the University of Victoria
-
-
Manually annotated by BRENDA team
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UniProt
Manually annotated by BRENDA team
strain N75
-
-
Manually annotated by BRENDA team
strain N75
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
malfunction
metabolism
physiological function
additional information
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
3-dehydroquinate + NADPH + H+
L-quinate + NADP+
show the reaction diagram
3-dehydroshikimate + NAD(P)H + H+
shikimate + NAD(P)+
show the reaction diagram
-
YdiB catalyzes the reduction of 3-dehydroshikimate to shikimate as part of the shikimate pathway
-
-
?
3-dehydroshikimate + NADH + H+
shikimate + NAD+
show the reaction diagram
-
-
-
-
r
dihydroshikimate + NAD+
(1S,3R,4S)-3,4-dihydroxy-5-oxocyclohexanecarboxylic acid + NADH + H+
show the reaction diagram
L-quinate + 3-acetylpyridine adenine dinucleotide
3-dehydroquinate + ?
show the reaction diagram
L-quinate + beta-NAD+
3-dehydroquinate + beta-NADH + H+
show the reaction diagram
L-quinate + NAD(P)+
3-dehydroquinate + NAD(P)H + H+
show the reaction diagram
L-quinate + NAD+
3-dehydroquinate + NADH + H+
show the reaction diagram
L-quinate + NADP+
3-dehydroquinate + NADPH + H+
show the reaction diagram
L-quinate + nicotinamide 1,N6-ethenoadenine dinucleotide
3-dehydroquinate + ?
show the reaction diagram
-
69% of the activity with NAD+
-
-
?
L-quinate + nicotinamide hypoxanthine dinucleotide
3-dehydroquinate + ?
show the reaction diagram
-
1.3fold higher activity than with NAD+
-
-
?
quinate + NAD(P)+
3-dehydroquinate + NAD(P)H + H+
show the reaction diagram
-
-
-
?
shikimate + NAD(P)+
3-dehydroshikimate + NAD(P)H + H+
show the reaction diagram
shikimate + NAD+
3-dehydroshikimate + NADH + H+
show the reaction diagram
shikimate + NADP+
3-dehydroshikimate + NADPH + H+
show the reaction diagram
t-3,t-4-dihydroxycyclohexane-c-1-carboxylate + NAD+
4-hydroxy-3-oxocyclohexane-c-1-carboxylate + NADH + H+
show the reaction diagram
-
highly stereospecific with regard to hydroaromatic substrates, oxidizes only the axial hydroxyl group at C-3 of the (-)-enantiomer, 44% of the activity with (-)-quinate
(-)-isomer, reverse reaction: 2.2fold higher activity than with (-)-3-dehydroquinate
-
r
t-3-hydroxy-4-oxocyclohexane-c-1-carboxylate + NAD+
?
show the reaction diagram
-
6% of the activity with (-)-quinate
-
-
?
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
3-dehydroquinate + NADPH + H+
L-quinate + NADP+
show the reaction diagram
-
may be responsible for the synthesis of quinic acid from the intermediate compound of the shikimate pathway, dehydroquinic acid
-
-
?
3-dehydroshikimate + NAD(P)H + H+
shikimate + NAD(P)+
show the reaction diagram
-
YdiB catalyzes the reduction of 3-dehydroshikimate to shikimate as part of the shikimate pathway
-
-
?
L-quinate + NAD+
3-dehydroquinate + NADH + H+
show the reaction diagram
L-quinate + NADP+
3-dehydroquinate + NADPH + H+
show the reaction diagram
-
-
-
-
r
shikimate + NAD+
3-dehydroshikimate + NADH + H+
show the reaction diagram
shikimate + NADP+
3-dehydroshikimate + NADPH + H+
show the reaction diagram
-
-
-
-
r
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3-acetylpyridine adenine dinucleotide
-
67% of the activity with NAD+
NADP+
NADPH
nicotinamide 1,N6-ethenoadenine dinucleotide
-
69% of the activity with NAD+
nicotinamide hypoxanthine dinucleotide
-
1.3fold higher activity than with NAD+
additional information
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
L-quinate
-
competitive inhibitor with respect to shikimate
shikimate
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competitive inhibitor with respect to L-quinate
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.65
3-acetylpyridine adenine dinucleotide
-
pH 10, cosubstrate (-)-quinate
0.42 - 1.141
3-dehydroquinate
0.2 - 5.933
3-dehydroshikimate
0.15
beta-NAD+
-
pH 10, cosubstrate (-)-quinate
1 - 5.3
dehydroquinate
2.56
dihydroshikimate
-
pH 10, (-)-enantiomer, cosubstrate NAD+
0.0054 - 32.68
L-quinate
0.0004 - 1.083
NAD+
0.001 - 2.65
NADP+
0.005 - 0.012
NADPH
-
pH 10, 20°C, cosubstrate dehydroquinate, both forms of quinate (shikimate) dehydrogenase
0.51
nicotinamide 1,N6-ethanoadenine dinucleotide
-
pH 10, cosubstrate (-)-quinate
0.48
nicotinamide hypoxanthine dinucleotide
-
pH 10, cosubstrate (-)-quinate
0.783
quinate
in the presence of 2 mM NAD+
0.0017 - 55.88
shikimate
2.47
t-3,t-4-dihydroxycyclohexane-c-1-carboxylate
-
pH 10, (-)-enantiomer, cosubstrate NAD+
additional information
additional information
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
9.31 - 114
3-dehydroquinate
5.67 - 329
3-dehydroshikimate
0.0063 - 104.9
L-quinate
0.004 - 223.1
NAD+
0.022 - 0.117
NADP+
37.7
quinate
in the presence of 2 mM NAD+
0.011 - 214.1
shikimate
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
8.16 - 271.4
3-dehydroquinate
0.96
3-dehydroshikimate
-
pH 7.0, temperature not specified in the publication, recombinant enzyme, with NADH
0.0034 - 44.05
L-quinate
0.013 - 826.6
NAD+
0.0083
NADP+
pH 8.8, 25°C, with shikimate
0.012 - 4.24
shikimate
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.00383
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needles of 20 days old saplings, quinate and NADP+ as substrates
0.00391
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hypocotyls of 20 days old saplings, quinate and NADP+ as substrates
0.0664
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needles, in June, the period of maximal quinate dehydrogenase content, quinate and NADP+ as substrates
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6
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reduction of 3-dehydroquinate with NADH
7.5
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reduction reaction, assay at
7.7
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back reaction, dehydroquinate or dehydroshikimate and NADPH as substrates
8.5
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oxidation of quinate with NAD+
8.5 - 9.5
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-
9 - 9.5
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quinate oxidation
9
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assay at
10 - 10.5
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shikimate oxidation
10
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oxidation reaction, quinate or shikimate as substrates, 50 mM glycine-KOH
10.3
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quinate or shikimate and NADP+ as substrates
10.6
-
assay at
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7 - 8.5
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the rate of activity decreases more rapidly, maximal 25% at pH 7.5, at pH values from 8.5 to 7 when shikimate rather than quinate is used as substrate
additional information
-
the catalytic reaction of QsuD is highly susceptible to pH
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
22
-
assay at room temperature
25
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assay at
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
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Poptr3 and Poptr4
Manually annotated by BRENDA team
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of 20 days old saplings
Manually annotated by BRENDA team
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Poptr4
Manually annotated by BRENDA team
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Poptr2 and Poptr3 are highly expressed in roots and root tips, respectively
Manually annotated by BRENDA team
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Poptr3 is highly expressed in bark and some vascular tissues
Manually annotated by BRENDA team
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Poptr4
Manually annotated by BRENDA team
additional information
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Poptr4 shows a distinct expression pattern with predominant expression in leaves, seedlings, and stomata and some expression in bark and differentiating tissues. Isozyme expression profiles, overview
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
UNIPROT
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
31350
-
2 * 31350, wild type enzyme, gel filtration
31500
-
1 * 31500, SDS-PAGE
33000
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SDS-PAGE, mutant N92A
35000
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two forms of the bifunctional quinate (shikimate) dehydrogenase, gel filtration
41000
-
1 * 41000
44000
-
gel filtration
53000
-
two forms of the bifunctional quinate (shikimate) dehydrogenase, gel filtration
57000
-
SDS-PAGE, wild type enzyme
60000
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about, gel filtration
64000
-
apoprotein, gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
monomer
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystal structure analysis of binary and ternary complexes of enzyme and substrates, PDB IDs 3JYP, 2NLO, 3JYO, and 3JYQ; crystal structure determination as enzyme in binary complex with NAD+ (PDB ID 3JYO), or in ternary complex with shikimate and NADH (PDB ID 3JYQ), or in ternary complex with quinate and NADH (PDB ID 3JYP)
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purified enzyme with bound NAD+ in a binary complex, and as ternary complexes with NADH plus either shikimate or quinate, sitting drop vapour diffusion method, for the ternary complexes: mixing of 0.002 ml of 10 mg/ml protein in 50 mM Tris-HCl, pH 7.5, 500 mM NaCl, 20% v/v glycerol, with 1 mM NAD+/NADH or additonally with 35 mM of either quinate or shikimate, with 0.002 ml of crystallization solution containing for the QSDH-NAD+ crystals 1.6 M trisodium citrate, pH 6.5-6.9, 25-62 mM CoCl2, or for crystals of the QSDH-quinate-NADH and QSDH-shikimate-NADH 24% w/v polyethylene glycol 6000, 360-400 mM CaCl2, 100 mM Tris-HCl, pH 8.0-9.5. Crystals are soaked in a cryoprotectant containing 30% w/v polyethylene glycol 6000, 25% v/v glycerol, 100 mM Tris-HCl, pH 8.5, for 1 h, X-ray diffraction structure determination and analysis at 1.0-1.6 A resolution, structure modelling
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YdiB, with bound cofactors NAD+ or NADP+
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RifI2 X-ray diffraction structure determination and analysis at 2.15 A resolution, modelling
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
45
-
t1/2: 1.85 min
additional information
-
the thermal stability of enzyme is greatly enhanced by low concentrations of quinate, shikimate, NADH or high ionic strength
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
4°C, 10 mM Tris-HCl buffer, pH 7.5, 500 mM NaCl, 5% glycerol
-
4°C, 10 mM Tris–HCl buffer, pH 7.5, 500 mM NaCl, 5% glycerol
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
3000fold, two forms of the bifunctional quinate (shikimate) dehydrogenase: P1 and P2
-
by nickel-nitrilotriacetic acid affinity chromatography; by nickel-nitrilotriacetic acid affinity chromatography; by nickel-nitrilotriacetic acid affinity chromatography
recombinant enzyme from Escherichia coli
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recombinant His6-tagged isozymes from Escherichia coli strain M15 by nickel affinity chromatography
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recombinant His6-tagged wild-type and mutant enzymes from Escherichia coli strain BL21 gold by nickel affinity chromatography, dialysis, tag cleavage through TEV protease and removal by nickel affinity chromatography, followed by gel filtration
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
five putative SDH-encoding genes amplified and cloned into either a modified pET28a vector or the p15TVLIC vector, a ligation-independent vector due to incompatible cloning sites between the insert and pET28.3. Expressed in either the Escherichia coli strain BL21 gold (p15TV-LIC constructs) or the Escherichia coli BL21CodonPlus (pET28.3constructs); five putative SDH-encoding genes amplified and cloned into either a modified pET28a vector or the p15TVLIC vector, a ligation-independent vector due to incompatible cloning sites between the insert and pET28.3. Expressed in either the Escherichia coli strain BL21 gold (p15TV-LIC constructs) or the Escherichia coli BL21CodonPlus (pET28.3constructs); five putative SDH-encoding genes amplified and cloned into either a modified pET28a vector or the p15TVLIC vector, a ligation-independent vector due to incompatible cloning sites between the insert and pET28.3. Expressed in either the Escherichia coli strain BL21 gold (p15TV-LIC constructs) or the Escherichia coli BL21CodonPlus (pET28.3constructs)
gene cgR_0495, recombinant expression; gene qsuD, recombinant expression
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gene qsuD, recombinant expression in Escherichia coli
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gene ydiB, recombinant overexpression in Escherichia coli strain PB12 causing a 500% increase in the molar yield of quinate and results in a 152% increase in quinate (mol/mol) relative to shikimate, with a sharp decrease in shikimate production. Transcriptomic analysis of PB12.SA22 and ydiB derivative strains
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recombinant expression of His6-tagged isozymes in Escherichia coli strain M15
-
recombinant expression of His6-tagged wild-type and mutant enzymes in Escherichia coli strain BL21 gold
ydiB gene, expression in Escherichia coli BL21(DE3)
-
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
qsuD mRNA expression is upregulated in shikimate-grown cells relative to that in the glucose-grown cells
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D107A
-
site-directed mutagenesis
K71G
-
site-directed mutagenesis
N92A
-
site-directed mutagenesis
Q262A
-
site-directed mutagenesis
S22A
-
site-directed mutagenesis
S67A
-
site-directed mutagenesis, increased activity compared to wild type enzyme
T106A
-
site-directed mutagenesis
Y39F
-
site-directed mutagenesis
N193D
site-directed mutagenesis, inactive mutant
N193L
site-directed mutagenesis, inactive mutant
N193Q
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
N193S
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
agriculture
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development of novel herbicides
drug development
medicine
-
development of novel antimicrobial agents
pharmacology
-
enzymes of the shikimate pathway has been promoted as a target for the development of antimicrobial agents
synthesis
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