Literature summary for 1.1.1.25 extracted from

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 (2017), J. Mol. Microbiol. Biotechnol., 27, 11-21 .

Cloned(Commentary)

Cloned (Comment)	Organism
gene ydiB, the ydiB gene is 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	Escherichia coli

Cloned (Comment)

Organism

gene ydiB, the ydiB gene is 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

Escherichia coli

Protein Variants

Protein Variants	Comment	Organism
additional information	ydiB-encoded enzyme knockout in Escherichia coli strain PB12	Escherichia coli

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.
L-quinate + NAD+	Escherichia coli	-	3-dehydroquinate + NADH + H+	-	r
L-quinate + NAD+	Escherichia coli PB12	-	3-dehydroquinate + NADH + H+	-	r
shikimate + NAD+	Escherichia coli	-	3-dehydroshikimate + NADH + H+	-	r
shikimate + NAD+	Escherichia coli PB12	-	3-dehydroshikimate + NADH + H+	-	r

Organism

Organism	UniProt	Comment	Textmining
Escherichia coli	P0A6D5	-	-
Escherichia coli PB12	P0A6D5	-	-

Source Tissue

Source Tissue	Comment	Organism	Textmining
additional information	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	Escherichia coli	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
L-quinate + NAD+	-	Escherichia coli	3-dehydroquinate + NADH + H+	-	r
L-quinate + NAD+	-	Escherichia coli PB12	3-dehydroquinate + NADH + H+	-	r
shikimate + NAD+	-	Escherichia coli	3-dehydroshikimate + NADH + H+	-	r
shikimate + NAD+	-	Escherichia coli PB12	3-dehydroshikimate + NADH + H+	-	r

Synonyms

Synonyms	Comment	Organism
NAD+-dependent enzyme quinate/shikimate dehydrogenase	-	Escherichia coli
quinate/shikimate dehydrogenase	-	Escherichia coli
YdiB	-	Escherichia coli

Cofactor

Cofactor	Comment	Organism	Structure
NAD+	-	Escherichia coli
NADH	-	Escherichia coli

General Information

General Information	Comment	Organism
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	Escherichia coli
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	Escherichia coli