Any feedback?
Information on EC 1.1.1.282 - quinate/shikimate dehydrogenase [NAD(P)+] and Organism(s) Escherichia coli and UniProt Accession P0A6D5
for references in articles please use BRENDA:EC1.1.1.282Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
EC Tree
1.1.1.282 quinate/shikimate dehydrogenase [NAD(P)+]IUBMB Comments
This is the second shikimate dehydrogenase enzyme found in Escherichia coli. It can use both quinate and shikimate as substrates and either NAD+ or NADP+ as acceptor. The low catalytic efficiency with both quinate and shikimate suggests that neither may be the physiological substrate. cf. EC 1.1.1.24, quinate/shikimate dehydrogenase (NAD+), EC 1.1.5.8, quinate/shikimate dehydrogenase (quinone), and EC 1.1.1.25, shikimate dehydrogenase (NADP+).
Specify your search results
Word Map
- 1.1.1.282
- 3-dehydroquinate
- lignin
-
corynebacterium
-
nad+-dependent
- glutamicum
-
cosubstrate
- drug development
- dehydrogenases
- agriculture
- synthesis
- medicine
- pharmacology
The taxonomic range for the selected organisms is: Escherichia coli
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Reaction Schemes
Synonyms
rifi2, sdh/qdh, poptr2, quinate/shikimate 5-dehydrogenase, shikimate/quinate dehydrogenase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
YdiB
additional information
YdiB is a class A NAD(P)+-dependent oxidoreductase
YdiB
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
L-quinate + NAD(P)+ = 3-dehydroquinate + NAD(P)H + H+
reaction mechanism
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
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
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
redox reaction
-
-
-
-
oxidation
-
-
-
-
reduction
-
-
-
-
PATHWAY SOURCE
PATHWAYS
BRENDA
-
-
SYSTEMATIC NAME
IUBMB Comments
L-quinate:NAD(P)+ 3-oxidoreductase
This is the second shikimate dehydrogenase enzyme found in Escherichia coli. It can use both quinate and shikimate as substrates and either NAD+ or NADP+ as acceptor. The low catalytic efficiency with both quinate and shikimate suggests that neither may be the physiological substrate. cf. EC 1.1.1.24, quinate/shikimate dehydrogenase (NAD+), EC 1.1.5.8, quinate/shikimate dehydrogenase (quinone), and EC 1.1.1.25, shikimate dehydrogenase (NADP+).
CAS REGISTRY NUMBER
COMMENTARY
9026-87-3
cf. EC 1.1.1.25
9028-28-8
cf. EC 1.1.1.24
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
-
-
?
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
-
-
?
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
-
?
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
-
-
?
NATURAL SUBSTRATE
NATURAL 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
-
-
?
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
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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+
utilizes either NAD+ or NADP+ as a cofactor, tendency to be more efficient with NAD+ than with NADP+, mode of binding
NADP+
utilizes either NAD+ or NADP+ as a cofactor, tendency to be more efficient with NAD+ than with NADP+, mode of binding
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0122
NAD+
wild type enzyme, in the presence of shikimate, 20°C, pH 9.0
0.0158
NAD+
mutant T106A, in the presence of shihikimat, 20°C, pH 9.0
0.0184
NAD+
wild type enzyme, in the presence of L-quinate, 20°C, pH 9.0
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.105
NAD+
wild type enzyme, in the presence of shikimate, 20°C, pH 9.0
0.142
NAD+
wild type enzyme, in the presence of L-quinate, 20°C, pH 9.0
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
-
Escherichia coli constitutively expresses two shikimate dehydrogenase paralogues, AroE and the NAD+-dependent enzyme quinate/shikimate dehydrogenase (YdiB), sharing 25% sequence identity. While AroE is NADP+-dependent, YdiB uses NADP+ or NAD+. Contrary to AroE, YdiB displays a clear activity on quinate, with either NADP+ or NAD+ as a cofactor in addition to shikimate
malfunction
-
in the ydiB knockout mutant, QA production is 6.17% relative to SA (mol/mol), indicating that the inactivation of ydiB is a suitable strategy to reduce QA production below 10% (mol/mol) relative to SA in culture fermentations for SA production. The inactivation of ydiB in Escherichia coli strain PB12.SA22 and the reduction in QA production support the role of YdiB in the synthesis of this compound from DHQ. In the absence of YdiB, the DHS concentration detected in supernatant cultures is maintained relatively constant during the stationary phase
physiological function
physiological function
-
Escherichia coli strain PB12.SA22 and the derivatives ydiB- and ydiB+ are evaluated for their ability to produce shikimate (SA), quinate (QA), 3-dehydroshikimate (DHS), and 3-dehydroquinate (DHQ) in batch culture fermentations growing in 1-l fermentors using 500 ml of a mineral broth supplemented with 25 g/l glucose and 15 g/l YE. Biomass and glucose consumption and the production of aromatic intermediates of the SA pathway, SA, QA, DHQ, and DHS are determined for all derivatives, overview. The highest production of DHQ and DHS is 0.07 and 0.074 g/l, respectively. SA and QA are produced during the early exponential stage, as these compounds are detected during the first 5 h of cultivation (SA = 0.49 g/l and QA = 0.38 g/l, respectively). In the stationary stage and until 20 h of cultivation, this strain consumes the remaining residual glucose. From this time until the end of fermentation, the supernatant concentration of detected SA shows no significant changes, reaching 8.2 g/l by the end of fermentation (50 h), whereas the final QA concentration is 1.52 g/l
physiological function
-
inactivation of ydiB results in a 75% decrease in the molar yield of quinic acid and a 6.17% reduction in the yield of quinic acid (mol/mol) relative to shikimic acid with respect to the parental strain. The overexpression of ydiB causes a 500% increase in the molar yield of quinic acid and results in a 152% increase in quinic acid (mol/mol) relative to shikimic acid, with a sharp decrease in shikimic acid production
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
S67A
site-directed mutagenesis, increased activity compared to wild type enzyme
additional information
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
-
ydiB-encoded enzyme knockout in Escherichia coli strain PB12
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
-
gene ydiB, the ydiB gene s cloned into plasmid pTOPO aroB aroE , resulting in the pTOPO ydiB aroB aroE derivative, enzyme overexpression in Escherichia coli strain PB12, quantitative RT-PCR analysis, coexpression of plasmid pTOPO aroB aroE and pJLB aroG fbr tktA and the cultivation of this derivative in Escherichia coli strain PB12.SA2 resulting in very high level expression of gene ydiB during exponential and stationary growth stages
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pharmacology
enzymes of the shikimate pathway has been promoted as a target for the development of antimicrobial agents
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
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Michel, G.; Roszak, A.W.; Sauv, V.; Maclean, J.; Matte, A.; Coggins, J.R.; Cygler, M.; Lapthorn, A.J.
Structures of shikimate dehydrogenase AroE and its paralog YdiB. A common structural framework for different activitie
J. Biol. Chem.
278
19463-19472
2003
Escherichia coli, Escherichia coli (P0A6D5)
Benach, J.; Lee, I.; Edstrom, W.; Kuzin, A.P.; Chiang, Y.; Acton, T.B.; Montelione, G.T.; Hunt, J.F.
The 2.3- crystal structure of the shikimate 5-dehydrogenase orthologue YdiB from Escherichia coli suggests a novel catalytic environment for an NAD-dependent dehydrogenase
J. Biol. Chem.
278
19176-19182
2003
Escherichia coli (P0A6D5)
Lindner, H.A.; Nadeau, G.; Matte, A.; Michel, G.; Menard, R.; Cygler, M.
Site-directed mutagenesis of the active site region in the quinate/shikimate 5-dehydrogenase YdiB of Escherichia coli
J. Biol. Chem.
280
7162-7169
2005
Escherichia coli (P0A6D5), Escherichia coli
Singh, S.; Korolev, S.; Koroleva, O.; Zarembinski, T.; Collart, F.; Joachimiak, A.; Christendat, D.
Crystal structure of a novel shikimate dehydrogenase from Haemophilus influenzae
J. Biol. Chem.
280
17101-17108
2005
Enterococcus faecalis, Enterococcus faecium, Escherichia coli (P0A6D5), Haemophilus influenzae (P44774), Lactiplantibacillus plantarum, Listeria monocytogenes, Salmonella enterica subsp. enterica serovar Typhimurium, Shigella flexneri, Streptococcus pyogenes
Garcia, S.; Flores, N.; De Anda, R.; Hernandez, G.; Gosset, G.; Bolivar, F.; Escalante, A.
The role of the ydiB gene, which encodes quinate/shikimate dehydrogenase, in the production of quinic, dehydroshikimic and shikimic acids in a PTS- strain of Escherichia coli
J. Mol. Microbiol. Biotechnol.
27
11-21
2016
Escherichia coli, Escherichia coli JM101
Garcia, S.; Flores, N.; De Anda, R.; Hernandez, G.; Gosset, G.; Bolivar, F.; Escalante, A.
The role of the ydiB gene, which encodes quinate/shikimate dehydrogenase, in the production of quinic, dehydroshikimic and shikimic acids in a PTS-strain of Escherichia coli
J. Mol. Microbiol. Biotechnol.
27
11-21
2017
Escherichia coli, Escherichia coli PB12
EXTERNAL LINKS (specific for EC-Number 1.1.1.282)
Use of this online version of BRENDA is free under the CC BY 4.0 license. See terms of use for full details.
Release 2023.1 (January 2023)
Legal
Curated at
Member of
