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Enzyme Nomenclature
Information on EC 1.1.1.282 - quinate/shikimate dehydrogenase
for references in articles please use BRENDA:EC1.1.1.282
Word Map on EC 1.1.1.282
- 1.1.1.282
- 3-dehydroquinate
- nad+
- glutamicum
-
corynebacterium
-
nad+-dependent
-
herbicides
-
cosubstrate
- dehydroshikimate
-
lignin
-
hydroaromatic
- drug development
-
dehydratase
- protocatechuate
- medicine
- agriculture
- pharmacology
- synthesis
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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria
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EC NUMBER 
COMMENTARY 
1.1.1.282
-
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RECOMMENDED NAME
GeneOntology No.
quinate/shikimate dehydrogenase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
L-quinate + NAD(P)+ = 3-dehydroquinate + NAD(P)H + H+
This is the second shikimate dehydrogenase enzyme found in Escherichia coli and differs from EC 1.1.1.25, shikimate 3-dehydrogenase, in that it can use both quinate and shikimate as substrate and either NAD+ or NADP+ as acceptor
-
-
-
L-quinate + NAD(P)+ = 3-dehydroquinate + NAD(P)H + H+
reaction mechanism, in which an aspartate acts as the general acid/base catalyst during the hydride transfer
-
L-quinate + NAD(P)+ = 3-dehydroquinate + NAD(P)H + H+
stereospecificity
-
L-quinate + NAD(P)+ = 3-dehydroquinate + NAD(P)H + H+
catalytic reaction mechanism; catalytic reaction mechanism
-
L-quinate + NAD(P)+ = 3-dehydroquinate + NAD(P)H + H+
catalytic reaction mechanism
-
-
L-quinate + NAD(P)+ = 3-dehydroquinate + NAD(P)H + H+
stereospecificity
-
-
shikimate + NAD(P)+ = 3-dehydroshikimate + NAD(P)H + H
catalytic reaction mechanism
-
shikimate + NAD(P)+ = 3-dehydroshikimate + NAD(P)H + H
-
-
-
-
shikimate + NAD(P)+ = 3-dehydroshikimate + NAD(P)H + H+
This is the second shikimate dehydrogenase enzyme found in Escherichia coli and differs from EC 1.1.1.25, shikimate 3-dehydrogenase, in that it can use both quinate and shikimate as substrate and either NAD+ or NADP+ as acceptor
-
-
-
shikimate + NAD(P)+ = 3-dehydroshikimate + NAD(P)H + H+
reaction mechanism
-
shikimate + NAD(P)+ = 3-dehydroshikimate + NAD(P)H + H+
reaction mechanism, in which an aspartate acts as the general acid/base catalyst during the hydride transfer
-
shikimate + NAD(P)+ = 3-dehydroshikimate + NAD(P)H + H+
stereospecificity
-
shikimate + NAD(P)+ = 3-dehydroshikimate + NAD(P)H + H+
catalytic reaction mechanism
-
shikimate + NAD(P)+ = 3-dehydroshikimate + NAD(P)H + H+
catalytic reaction mechanism
-
-
shikimate + NAD(P)+ = 3-dehydroshikimate + NAD(P)H + H+
stereospecificity
-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
oxidation
-
-
-
-
redox reaction
-
-
-
-
reduction
-
-
-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
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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.
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CAS REGISTRY NUMBER
COMMENTARY
9026-87-3
cf. EC 1.1.1.25
9028-28-8
cf. EC 1.1.1.24
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
metabolism
physiological function
additional information
evolution
-
SDH is the archetypal member of a large protein family, which contains at least four additional functional classes with diverse metabolic roles. The different members of the SDH family share a highly similar three-dimensional structure and utilize a conserved catalytic mechanism, but exhibit distinct substrate preferences; SDH is the archetypal member of a large protein family, which contains at least four additional functional classes with diverse metabolic roles. The different members of the SDH family share a highly similar three-dimensional structure and utilize a conserved catalytic mechanism, but exhibit distinct substrate preferences
evolution
-
members of the same gene family encode enzymes with either shikimate or quinate dehydrogenase activity. Plant SDHs are generally more similar to bacterial SDH/QDH YdiB (25-30% similarity) than to bacterial SDH AroE (21-28%)
evolution
-
SDH is the archetypal member of a large protein family, which contains at least four additional functional classes with diverse metabolic roles. The different members of the SDH family share a highly similar three-dimensional structure and utilize a conserved catalytic mechanism, but exhibit distinct substrate preferences
-
malfunction
-
disruption of the qdh gene in prevents growth on both compounds, demonstrating the important role of the enzyme in hydroaromatic catabolism; disruption of the qdh gene in prevents growth on both compounds, demonstrating the important role of the enzyme in hydroaromatic catabolism
malfunction
-
disruption of the qdh gene in prevents growth on both compounds, demonstrating the important role of the enzyme in hydroaromatic catabolism
-
metabolism
-
the enzyme catalyzes the fourth step of the shikimate pathway, a conserved biosynthetic route in plants, fungi, bacteria, and apicomplexan parasites; the enzyme catalyzes the fourth step of the shikimate pathway, a conserved biosynthetic route in plants, fungi, bacteria, and apicomplexan parasites
metabolism
-
the enzyme catalyzes the fourth step of the shikimate pathway, a conserved biosynthetic route in plants, fungi, bacteria, and apicomplexan parasites
-
physiological function
-
QsuD is essential for growth on shikimate and quinate as sole carbon sources, suggesting that it is the key enzyme for shikimate/quinate utilization
physiological function
-
shikimate dehydrogenase catalyzes the NADPH-dependent reduction of 3-deydroshikimate to shikimate, an essential reaction in the biosynthesis of the aromatic amino acids and a large number of other secondary metabolites in plants and microbes. The reduced efficiency of Corynebacterium glutamicum enzyme with shikimate as a substrate may also result in part from the flexibility of the catalytic group, Lys73, which adopts multiple conformations in the shikimate-liganded enzyme structure; shikimate dehydrogenase catalyzes the NADPH-dependent reduction of 3-deydroshikimate to shikimate, an essential reaction in the biosynthesis of the aromatic amino acids and a large number of other secondary metabolites in plants and microbes. The reduced efficiency of Corynebacterium glutamicum enzyme with shikimate as a substrate may also result in part from the flexibility of the catalytic group, Lys73, which adopts multiple conformations in the shikimate-liganded enzyme structure
physiological function
-
quinate and its derivatives are protective secondary metabolites, quinate is an astringent feeding deterrent that can be formed in a single step reaction from 3-dehydroquinate catalyzed by quinate dehydrogenase
physiological function
-
shikimate dehydrogenase catalyzes the NADPH-dependent reduction of 3-deydroshikimate to shikimate, an essential reaction in the biosynthesis of the aromatic amino acids and a large number of other secondary metabolites in plants and microbes. The reduced efficiency of Corynebacterium glutamicum enzyme with shikimate as a substrate may also result in part from the flexibility of the catalytic group, Lys73, which adopts multiple conformations in the shikimate-liganded enzyme structure
-
physiological function
-
QsuD is essential for growth on shikimate and quinate as sole carbon sources, suggesting that it is the key enzyme for shikimate/quinate utilization
-
physiological function
-
quinate and its derivatives are protective secondary metabolites, quinate is an astringent feeding deterrent that can be formed in a single step reaction from 3-dehydroquinate catalyzed by quinate dehydrogenase
-
additional information
-
substrate binding site structure, overview. Quinate binding causes a slight closure of the N- and C-terminal domain of CglQSDH. Shikimate binding causes a alternative side-chain conformation of Lys73
additional information
-
enzyme RifI2 lacks a conserved C-terminal alpha-helix
additional information
enzyme RifI2 lacks a conserved C-terminal alpha-helix
additional information
-
the enzymes have Gly residues instead of Ser residues in the active sites. The Ser-to-Gly conversion ompared to SDHs may generate extra space in the inferred Poptr isozymes active sites that can accommodate the hydroxyl group at the C1 position of quinate
additional information
-
substrate binding site structure, overview. Quinate binding causes a slight closure of the N- and C-terminal domain of CglQSDH. Shikimate binding causes a alternative side-chain conformation of Lys73
-
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
3-dehydroshikimate + NAD(P)H + H+
shikimate + NAD(P)+
-
YdiB catalyzes the reduction of 3-dehydroshikimate to shikimate as part of the shikimate pathway
-
-
?
dihydroshikimate + NAD+
(1S,3R,4S)-3,4-dihydroxy-5-oxocyclohexanecarboxylic acid + NADH + H+
L-quinate + nicotinamide 1,N6-ethenoadenine dinucleotide
3-dehydroquinate + ?
-
69% of the activity with NAD+
-
-
?
L-quinate + nicotinamide hypoxanthine dinucleotide
3-dehydroquinate + ?
-
1.3fold higher activity than with NAD+
-
-
?
quinate + NAD(P)+
3-dehydroquinate + NAD(P)H + H+
-
-
-
?
t-3,t-4-dihydroxycyclohexane-c-1-carboxylate + NAD+
4-hydroxy-3-oxocyclohexane-c-1-carboxylate + NADH + H+
-
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+
?
-
6% of the activity with (-)-quinate
-
-
?
3-dehydroquinate + NADPH + H+
L-quinate + NADP+
-
may be responsible for the synthesis of quinic acid from the intermediate compound of the shikimate pathway, dehydroquinic acid
-
-
?
dihydroshikimate + NAD+
(1S,3R,4S)-3,4-dihydroxy-5-oxocyclohexanecarboxylic acid + NADH + H+
-
highly stereospecific with regard to hydroaromatic substrates, oxidizes only the axial hydroxyl group at C-3 of the (-)-enantiomer, 38% of the activity with (-)-quinate
(-)-enantiomer, reverse reaction: 3.3fold higher activity than with (-)-3-dehydroquinate
-
r
dihydroshikimate + NAD+
(1S,3R,4S)-3,4-dihydroxy-5-oxocyclohexanecarboxylic acid + NADH + H+
-
highly stereospecific with regard to hydroaromatic substrates, oxidizes only the axial hydroxyl group at C-3 of the (-)-enantiomer, 38% of the activity with (-)-quinate
(-)-enantiomer, reverse reaction: 3.3fold higher activity than with (-)-3-dehydroquinate
-
r
L-quinate + 3-acetylpyridine adenine dinucleotide
3-dehydroquinate + ?
-
67% of the activity with NAD+
-
-
?
L-quinate + 3-acetylpyridine adenine dinucleotide
3-dehydroquinate + ?
-
67% of the activity with NAD+
-
-
?
L-quinate + beta-NAD+
3-dehydroquinate + beta-NADH + H+
-
highly stereospecific with regard to hydroaromatic substrates, oxidizes only the axial hydroxyl group at C-3 of the (-)-enantiomer, a single enzyme with both quinate and shikimate dehydrogenase activity
(-)-enantiomer, reverse reaction: lower activity than with t-4,c-5-dihydroxy-3-oxocyclohexane-c-1-carboxylate or 4-hydroxy-3-oxocyclohexane-c-1-carboxylate
-
r
L-quinate + beta-NAD+
3-dehydroquinate + beta-NADH + H+
-
highly stereospecific with regard to hydroaromatic substrates, oxidizes only the axial hydroxyl group at C-3 of the (-)-enantiomer, a single enzyme with both quinate and shikimate dehydrogenase activity
(-)-enantiomer, reverse reaction: lower activity than with t-4,c-5-dihydroxy-3-oxocyclohexane-c-1-carboxylate or 4-hydroxy-3-oxocyclohexane-c-1-carboxylate
-
r
L-quinate + NAD(P)+
3-dehydroquinate + NAD(P)H + H+
-
detailed strucure of YdiB, specificity for binding NAD+/NADH over NADP+/NADPH
-
-
r
L-quinate + NAD(P)+
3-dehydroquinate + NAD(P)H + H+
YdiB is a dual specific quinate/shikimate dehydrogenase that utilizes either NAD+ or NADP+ as cofactor, YdiB is equally active with shikimate or quinate, but has a tendency to be more efficient with NAD+ than with NADP+, detailed structure of YdiB, mechanism
-
-
?
L-quinate + NAD(P)+
3-dehydroquinate + NAD(P)H + H+
-
bifunctional enzyme with a single binding site for both substrates quinate and shikimate, the velocity is approximately 3fold lower with quinate than with shikimate
-
-
?
L-quinate + NAD+
3-dehydroquinate + NADH + H+
-
-
-
-
r
L-quinate + NADP+
3-dehydroquinate + NADPH + H+
-
both quinate and shikimate dehydrogenase activities are catalyzed by a single broad-specificity quinate (shikimate) dehydrogenase with a common substrate binding site, the velocity is 2fold greater with quinate than with shikimate
-
-
r
L-quinate + NADP+
3-dehydroquinate + NADPH + H+
-
0.3% of the activity with NAD+
-
-
?
shikimate + NAD(P)+
3-dehydroshikimate + NAD(P)H + H+
-
detailed strucure of YdiB, catalytic mechanism, specificity for binding NAD+/NADH over NADP+/NADPH
-
-
r
shikimate + NAD(P)+
3-dehydroshikimate + NAD(P)H + H+
YdiB is a dual specific quinate/shikimate dehydrogenase that utilizes either NAD+ or NADP+ as cofactor, YdiB is equally active with shikimate or quinate, but has a tendency to be more efficient with NAD+ than with NADP+, detailed structure of YdiB, mechanism
model for 3-dehydroshikimate recognition
-
?
shikimate + NAD(P)+
3-dehydroshikimate + NAD(P)H + H+
-
bifunctional enzyme with a single binding site for both substrates quinate and shikimate, the velocity is approximately 3fold higher with shikimate than with quinate
-
-
?
shikimate + NAD(P)+
3-dehydroshikimate + NAD(P)H + H+
-
-
-
?
shikimate + NAD+
3-dehydroshikimate + NADH + H+
-
-
-
?
shikimate + NAD+
3-dehydroshikimate + NADH + H+
-
-
-
-
r
shikimate + NAD+
3-dehydroshikimate + NADH + H+
-
-
-
-
?
shikimate + NAD+
3-dehydroshikimate + NADH + H+
-
highly stereospecific with regard to hydroaromatic substrates, oxidizes only the axial hydroxyl group at C-3 of the (-)-enantiomer, a single enzyme with both quinate and shikimate dehydrogenase activity, 72% of the activity with (-)-quinate
(-)-enantiomer, reverse reaction: 15% of the activity with (-)-3-dehydroquinate
-
r
shikimate + NAD+
3-dehydroshikimate + NADH + H+
-
-
-
-
r
shikimate + NADP+
3-dehydroshikimate + NADPH + H+
-
both quinate and shikimate dehydrogenase activities are catalyzed by a single broad-specificity quinate (shikimate) dehydrogenase with a common substrate binding site, the velocity is 2fold lower with shikimate than with quinate
-
-
r
shikimate + NADP+
3-dehydroshikimate + NADPH + H+
very low activity with NADP+
-
-
?
additional information
?
-
-
the enzyme CglQSDH shows a substrate preference for quinate compared with shikimate both at the pH optimum and in a physiological pH range, which is a remarkable contrast to closely related SDH/QDH enzymes
-
-
-
additional information
?
-
the enzyme CglQSDH shows a substrate preference for quinate compared with shikimate both at the pH optimum and in a physiological pH range, which is a remarkable contrast to closely related SDH/QDH enzymes
-
-
-
additional information
?
-
QsuD reduces 3-dehydroquinate using NADH and oxidizes quinate using NAD+ as cofactor
-
-
-
additional information
?
-
-
the enzyme is capable of recognizing both quinate and shikimate, it is usually considered to have dual substrate specificity
-
-
-
additional information
?
-
the enzyme CglQSDH shows a substrate preference for quinate compared with shikimate both at the pH optimum and in a physiological pH range, which is a remarkable contrast to closely related SDH/QDH enzymes
-
-
-
additional information
?
-
-
the enzyme is capable of recognizing both quinate and shikimate, it is usually considered to have dual substrate specificity
-
-
-
additional information
?
-
-
QsuD reduces 3-dehydroquinate using NADH and oxidizes quinate using NAD+ as cofactor
-
-
-
additional information
?
-
-
YdiB may be involved in shikimate pathway or may be essential for growth of the organism with quinate as a sole carbon source
-
-
-
additional information
?
-
YdiB may be involved in shikimate pathway or may be essential for growth of the organism with quinate as a sole carbon source
-
-
-
additional information
?
-
-
the synthesis of quinate results from the reduction of 3-dehydroquinate by YdiB before its conversion to 3-dehydroshikimate. In Escherichia coli strain W3110.shik, YdiB, rather than AroE, catalyzes the oxidation of shikimate to 3-dehydroshikimate and the reduction of 3-dehydroquinate to quinate
-
-
-
additional information
?
-
-
the synthesis of quinate results from the reduction of 3-dehydroquinate by YdiB before its conversion to 3-dehydroshikimate. In Escherichia coli strain W3110.shik, YdiB, rather than AroE, catalyzes the oxidation of shikimate to 3-dehydroshikimate and the reduction of 3-dehydroquinate to quinate
-
-
-
additional information
?
-
-
catalyzes the first reaction in the inducible quinic acid catabolic pathway
-
-
-
additional information
?
-
-
the enzyme preferentially uses quinate as a substrate in vitro like a quinate dehydrogenase, EC 1.1.1.24, with only residual shikimate dehydrogenase, SDH, activity, cf. EC 1.1.1.25
-
-
-
additional information
?
-
broad extent to which the SDH enzyme superfamily has diversified. 5 evolutionarily distinct SDH homologs in the genome of the common soil-inhabiting bacterium, Pseudomonas putida KT2440
-
-
-
additional information
?
-
broad extent to which the SDH enzyme superfamily has diversified. 5 evolutionarily distinct SDH homologs in the genome of the common soil-inhabiting bacterium, Pseudomonas putida KT2440
-
-
-
additional information
?
-
broad extent to which the SDH enzyme superfamily has diversified. 5 evolutionarily distinct SDH homologs in the genome of the common soil-inhabiting bacterium, Pseudomonas putida KT2440
-
-
-
additional information
?
-
-
initial enzyme of the hydroaromatic pathway
-
-
-
additional information
?
-
-
substrate specificity, enzyme is highly stereospecific with regard to hydroaromatic substrates, oxidizing only the axial hydroxyl group at C-3 of (-)-enantiomer of quinate, shikimate, dihydroshikimate and t-3,t-4-dihydroxycyclohexane-c-1-carboxylate, enzyme shows activity with several NAD+ analogues, reverse reaction: not 4-hydroxy-3-oxocyclohex-4-ene-c-1-carboxylate, not: alpha-NAD+, beta-NMN or nicotinic acid dinucleotide
-
-
-
additional information
?
-
-
initial enzyme of the hydroaromatic pathway
-
-
-
additional information
?
-
-
substrate specificity, enzyme is highly stereospecific with regard to hydroaromatic substrates, oxidizing only the axial hydroxyl group at C-3 of (-)-enantiomer of quinate, shikimate, dihydroshikimate and t-3,t-4-dihydroxycyclohexane-c-1-carboxylate, enzyme shows activity with several NAD+ analogues, reverse reaction: not 4-hydroxy-3-oxocyclohex-4-ene-c-1-carboxylate, not: alpha-NAD+, beta-NMN or nicotinic acid dinucleotide
-
-
-
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
3-dehydroquinate + NADPH + H+
L-quinate + NADP+
-
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)+
-
YdiB catalyzes the reduction of 3-dehydroshikimate to shikimate as part of the shikimate pathway
-
-
?
L-quinate + NAD+
3-dehydroquinate + NADH + H+
-
-
-
-
r
shikimate + NAD+
3-dehydroshikimate + NADH + H+
Q9X5C9
-
-
-
?
shikimate + NAD+
3-dehydroshikimate + NADH + H+
-
-
-
-
r
shikimate + NAD+
3-dehydroshikimate + NADH + H+
-
-
-
-
?
additional information
?
-
-
the enzyme CglQSDH shows a substrate preference for quinate compared with shikimate both at the pH optimum and in a physiological pH range, which is a remarkable contrast to closely related SDH/QDH enzymes
-
-
-
additional information
?
-
Q9X5C9
the enzyme CglQSDH shows a substrate preference for quinate compared with shikimate both at the pH optimum and in a physiological pH range, which is a remarkable contrast to closely related SDH/QDH enzymes
-
-
-
additional information
?
-
Q9X5C9
the enzyme CglQSDH shows a substrate preference for quinate compared with shikimate both at the pH optimum and in a physiological pH range, which is a remarkable contrast to closely related SDH/QDH enzymes
-
-
-
additional information
?
-
-
YdiB may be involved in shikimate pathway or may be essential for growth of the organism with quinate as a sole carbon source
-
-
-
additional information
?
-
P0A6D5
YdiB may be involved in shikimate pathway or may be essential for growth of the organism with quinate as a sole carbon source
-
-
-
additional information
?
-
-
the synthesis of quinate results from the reduction of 3-dehydroquinate by YdiB before its conversion to 3-dehydroshikimate. In Escherichia coli strain W3110.shik, YdiB, rather than AroE, catalyzes the oxidation of shikimate to 3-dehydroshikimate and the reduction of 3-dehydroquinate to quinate
-
-
-
additional information
?
-
-
the synthesis of quinate results from the reduction of 3-dehydroquinate by YdiB before its conversion to 3-dehydroshikimate. In Escherichia coli strain W3110.shik, YdiB, rather than AroE, catalyzes the oxidation of shikimate to 3-dehydroshikimate and the reduction of 3-dehydroquinate to quinate
-
-
-
additional information
?
-
-
catalyzes the first reaction in the inducible quinic acid catabolic pathway
-
-
-
additional information
?
-
-
the enzyme preferentially uses quinate as a substrate in vitro like a quinate dehydrogenase, EC 1.1.1.24, with only residual shikimate dehydrogenase, SDH, activity, cf. EC 1.1.1.25
-
-
-
additional information
?
-
-
initial enzyme of the hydroaromatic pathway
-
-
-
additional information
?
-
-
initial enzyme of the hydroaromatic pathway
-
-
-
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
3-acetylpyridine adenine dinucleotide
-
67% of the activity with NAD+
nicotinamide 1,N6-ethenoadenine dinucleotide
-
69% of the activity with NAD+
nicotinamide hypoxanthine dinucleotide
-
1.3fold higher activity than with NAD+
NAD+
-
utilizes either NAD+ or NADP+ as a cofactor, tendency to be more efficient with NAD+ than with NADP+, mode of binding
NAD+
-
NAD+ binding site, bound very tightly, NAD+ is bound to the Rossmann domain in an elongated fashion with the nicotinamide ring in the pro-R conformation, specificity for binding NAD+ over NADP+
NAD+
the C-terminal domain of each protomer in the RifI2 asymmetric unit contains a bound molecule of NAD+, Cofactor binding structure and mechanism, detailed overview
NADP+
-
utilizes either NAD+ or NADP+ as a cofactor, tendency to be more efficient with NAD+ than with NADP+, mode of binding
additional information
-
absolute requirement for a nicotinamide nucleotide cofactor for the oxidation of quinate or shikimate, cofactor specificity, not: alpha-NAD+, beta-NMN or nicotinic acid dinucleotide
-
additional information
-
the turnover number is lower with NADP+ instead of NAD+ as cofactor. NADP(H) is just only for 3-dehydroquinate reduction by the enzyme
-
additional information
-
CglQSDH is strictly NAD(H)-dependent due to structural features
-
additional information
-
in the RifI2 structure, the NADP+-specifying motif is replaced with Asp-Pro-Ser-Thr-Ala-Arg (residues 156-161). The side chain of Asp156 binds to the adenine ribose of NAD+, while its negative charge is predicted to repel the additional phosphate of NADP+. RifI2 possesses low apparent binding affinity for NADP+. Analysis of the cofactor-binding sites of the RifI2–NAD+ complex and structure comparison, inportance of the invariant residue Asn193 in the cofactor-binding site, overview
-
additional information
in the RifI2 structure, the NADP+-specifying motif is replaced with Asp-Pro-Ser-Thr-Ala-Arg (residues 156-161). The side chain of Asp156 binds to the adenine ribose of NAD+, while its negative charge is predicted to repel the additional phosphate of NADP+. RifI2 possesses low apparent binding affinity for NADP+. Analysis of the cofactor-binding sites of the RifI2–NAD+ complex and structure comparison, inportance of the invariant residue Asn193 in the cofactor-binding site, overview
-
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
-
divalent cations are not required for the activity of RifI2, as the reaction rate is not altered in the presence of 5 mM Ca2+, Mg2+, Mn2+, or Zn2+. Similarly, the reaction is not affected by the addition of 10 mM EDTA to chelate any endogenous divalent cations associated with the enzyme
additional information
divalent cations are not required for the activity of RifI2, as the reaction rate is not altered in the presence of 5 mM Ca2+, Mg2+, Mn2+, or Zn2+. Similarly, the reaction is not affected by the addition of 10 mM EDTA to chelate any endogenous divalent cations associated with the enzyme
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.65
3-acetylpyridine adenine dinucleotide
-
pH 10, cosubstrate (-)-quinate
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
2.47
t-3,t-4-dihydroxycyclohexane-c-1-carboxylate
-
pH 10, (-)-enantiomer, cosubstrate NAD+
0.42
3-dehydroquinate
-
pH 7.0, temperature not specified in the publication, recombinant enzyme, with NADH
1.141
3-dehydroquinate
-
pH 7.0, temperature not specified in the publication, recombinant enzyme, with NADPH
5.933
3-dehydroshikimate
-
pH 7.0, temperature not specified in the publication, recombinant enzyme, with NADH
1
dehydroquinate
-
pH 10, 20°C, cosubstrate NADPH, form P1 of quinate (shikimate) dehydrogenase
5.3
dehydroquinate
-
pH 10, 20°C, cosubstrate NADPH, form P2 of quinate (shikimate) dehydrogenase
0.444
L-quinate
-
pH 7.0, temperature not specified in the publication, recombinant enzyme, with NAD+
3.4 - 3.6
L-quinate
-
pH 10, 20°C, cosubstrate NADP+, both forms of quinate (shikimate) dehydrogenase
0.0158
NAD+
-
mutant T106A, in the presence of shihikimat, 20°C, pH 9.0; mutant Y39F, in the presence of shikimate, 20°C, pH 9.0
0.001
NADP+
-
pH 10, 20°C, cosubstrate shikimate, both forms of quinate (shikimate) dehydrogenase
0.007
NADP+
-
pH 10, 20°C, cosubstrate L-quinate, both forms of quinate (shikimate) dehydrogenase
0.7 - 0.8
shikimate
-
pH 10, 20°C, cosubstrate NADP+, both forms of quinate (shikimate) dehydrogenase
1.299
shikimate
-
pH 7.0, temperature not specified in the publication, recombinant enzyme, with NAD+
additional information
additional information
-
Michaelis constant with quinate as substrate is lower than that with shikimate under optimal conditions
-
additional information
additional information
-
Michaelis-Menten kinetics
-
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
9.31
3-dehydroquinate
-
pH 7.0, temperature not specified in the publication, recombinant enzyme, with NADPH
114
3-dehydroquinate
-
pH 7.0, temperature not specified in the publication, recombinant enzyme, with NADH
5.67
3-dehydroshikimate
-
pH 7.0, temperature not specified in the publication, recombinant enzyme, with NADH
14.6
L-quinate
-
pH 7.0, temperature not specified in the publication, recombinant enzyme, with NAD+
0.022
NAD+
-
mutant D107A, in the presence of shikimate, 20°C, pH 9.0; mutant Q262A, in the presence of shikimate, 20°C, pH 9.0
1.75
shikimate
-
pH 7.0, temperature not specified in the publication, recombinant enzyme, with NAD+
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.96
3-dehydroshikimate
-
pH 7.0, temperature not specified in the publication, recombinant enzyme, with NADH
8.16
3-dehydroquinate
-
pH 7.0, temperature not specified in the publication, recombinant enzyme, with NADPH
271.4
3-dehydroquinate
-
pH 7.0, temperature not specified in the publication, recombinant enzyme, with NADH
32.88
L-quinate
-
pH 7.0, temperature not specified in the publication, recombinant enzyme, with NAD+
1.35
shikimate
-
pH 7.0, temperature not specified in the publication, recombinant enzyme, with NAD+
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
0.00391
-
hypocotyls of 20 days old saplings, quinate and NADP+ as substrates
0.0664
-
needles, in June, the period of maximal quinate dehydrogenase content, quinate and NADP+ as substrates
additional information
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
10
-
oxidation reaction, quinate or shikimate as substrates, 50 mM glycine-KOH
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7 - 8.5
-
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
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
20
30
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
-
Poptr2 and Poptr3 are highly expressed in roots and root tips, respectively
additional information
-
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
-
from current-year shoots of 20 years old trees, the youngest basal parts of needles
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PDB
SCOP
CATH
ORGANISM
UNIPROT
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
35000
-
two forms of the bifunctional quinate (shikimate) dehydrogenase, gel filtration
53000
-
two forms of the bifunctional quinate (shikimate) dehydrogenase, gel filtration
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SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
homodimer
monomer
additional information
dimer
distinct mode of dimerization in which the individual molecules interact in a back-to-front manner, overview. The molecules of the RifI2 dimer associate via hydrophobic interactions between residues on alpha-helix alpha8 of the first molecule and alpha10' of the second molecule. In addition, the side chain of Gln167 on apha-helix alpha8 forms a hydrogen bond with the guanidinium group of Arg243' on beta-strand beta10'. A second hydrogen bond to Arg243' may be made by Asn171. Asp53 and Arg56 on alpha-helix alpha2 bind the imidazole ring of His31' on alpha-helix alpha1'
additional information
-
enzyme three-dimensional structure determination, analysis, and comparisons, overview. The N-terminal or catalytic domain comprises residues 1 to 113 and 256 to 283, whereas the C-terminal or nucleotide-binding domain is build up of residues 114 to 255. The catalytic domain forms an open alpha/beta sandwich, which is characteristic for enzymes of the SDH/QDH family. The substrate-binding site is located in the N-terminal domain, close to the nicotinamide ring of the cofactor
additional information
-
enzyme three-dimensional structure determination, analysis, and comparisons, overview. The N-terminal or catalytic domain comprises residues 1 to 113 and 256 to 283, whereas the C-terminal or nucleotide-binding domain is build up of residues 114 to 255. The catalytic domain forms an open alpha/beta sandwich, which is characteristic for enzymes of the SDH/QDH family. The substrate-binding site is located in the N-terminal domain, close to the nicotinamide ring of the cofactor
-
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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)
-
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
-
RifI2 X-ray diffraction structure determination and analysis at 2.15 A resolution, modelling
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
the thermal stability of enzyme is greatly enhanced by low concentrations of quinate, shikimate, NADH or high ionic strength
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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
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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 His6-tagged isozymes from Escherichia coli strain M15 by nickel affinity chromatography
-
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
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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
-
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
-
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
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
qsuD mRNA expression is upregulated in shikimate-grown cells relative to that in the glucose-grown cells
qsuD mRNA expression is upregulated in shikimate-grown cells relative to that in the glucose-grown cells
-
qsuD mRNA expression is upregulated in shikimate-grown cells relative to that in the glucose-grown cells
-
-
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
S67A
-
site-directed mutagenesis, increased activity compared to wild type enzyme
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
additional information
-
construction of a gene qsuD deletion mutant. Cell cultures of the qsuD-deficient strain in glucose-containing medium are light yellow, whereas those of the wild-type in shikimate or quinate-containing medium are brown
additional information
-
construction of a gene qsuD deletion mutant. Cell cultures of the qsuD-deficient strain in glucose-containing medium are light yellow, whereas those of the wild-type in shikimate or quinate-containing medium are brown
-
additional information
-
construction of an enzyme ydiB- knockout mutant JM101 strain. Fermentation processes for the production of shikimate in overproducing strains of Escherichia coli result in the simultaneous synthesis of quinic acid and 3-dehydroshikimic acid. The production of high amounts of these byproducts significantly reduces the yield of shikimate, and more importantly, the presence of quinate impairs the efficiency of shikimate extraction from supernatant cultures, reducing its purity and increasing downstream processing costs. The inactivation of the ydiB gene increases the molar proportion of shikimate and 3-dehydroshikimate with respect to quinate, showing a molar ratio of 0.81/0.05/0.14 (mol/mol/mol) of shikimate/quinate/3-dehydroshikimate. In this derivative strain, quinate production is 6.17% relative to shikimate (mol/mol), indicating that the inactivation of ydiB is a suitable strategy to reduce quinate production below 10% (mol/mol) relative to ahkimate in culture fermentations for shikimate production
additional information
-
construction of an enzyme ydiB- knockout mutant JM101 strain. Fermentation processes for the production of shikimate in overproducing strains of Escherichia coli result in the simultaneous synthesis of quinic acid and 3-dehydroshikimic acid. The production of high amounts of these byproducts significantly reduces the yield of shikimate, and more importantly, the presence of quinate impairs the efficiency of shikimate extraction from supernatant cultures, reducing its purity and increasing downstream processing costs. The inactivation of the ydiB gene increases the molar proportion of shikimate and 3-dehydroshikimate with respect to quinate, showing a molar ratio of 0.81/0.05/0.14 (mol/mol/mol) of shikimate/quinate/3-dehydroshikimate. In this derivative strain, quinate production is 6.17% relative to shikimate (mol/mol), indicating that the inactivation of ydiB is a suitable strategy to reduce quinate production below 10% (mol/mol) relative to ahkimate in culture fermentations for shikimate production
-
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
drug development
pharmacology
-
enzymes of the shikimate pathway has been promoted as a target for the development of antimicrobial agents
synthesis
drug development
-
the essential enzyme is a potential target for herbicides and antimicrobials; the essential enzyme is a potential target for herbicides and antimicrobials
drug development
-
the essential enzyme is a potential target for herbicides and antimicrobials
-
synthesis
-
enzyme YdiB displays a clear activity on quinate, with either NADP+ or NAD+ as a cofactor in addition to shikimate, making this enzyme an important candidate for quinate production. Production of shikimate, quinate, 3-dehydroshikimate and other aromatic derivatives in strain PB12.SA22 during batch culture fermentation
synthesis
-
enzyme YdiB displays a clear activity on quinate, with either NADP+ or NAD+ as a cofactor in addition to shikimate, making this enzyme an important candidate for quinate production. Production of shikimate, quinate, 3-dehydroshikimate and other aromatic derivatives in strain PB12.SA22 during batch culture fermentation
-
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LINKS TO OTHER DATABASES (specific for EC-Number 1.1.1.282)
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