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Literature summary 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 .
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
1.1.1.25 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
1.1.1.282 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 Escherichia coli

Protein Variants

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

Natural Substrates/ Products (Substrates)

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

Organism

EC Number Organism UniProt Comment Textmining
1.1.1.25 Escherichia coli P0A6D5
-
-
1.1.1.25 Escherichia coli PB12 P0A6D5
-
-
1.1.1.282 Escherichia coli
-
-
-
1.1.1.282 Escherichia coli PB12
-
-
-

Source Tissue

EC Number Source Tissue Comment Organism Textmining
1.1.1.25 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)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.1.1.25 L-quinate + NAD+
-
 Escherichia coli 3-dehydroquinate + NADH + H+
-
 r
1.1.1.25 L-quinate + NAD+
-
 Escherichia coli PB12 3-dehydroquinate + NADH + H+
-
 r
1.1.1.25 shikimate + NAD+
-
 Escherichia coli 3-dehydroshikimate + NADH + H+
-
 r
1.1.1.25 shikimate + NAD+
-
 Escherichia coli PB12 3-dehydroshikimate + NADH + H+
-
 r
1.1.1.282 L-quinate + NAD(P)+
-
 Escherichia coli 3-dehydroquinate + NAD(P)H + H+
-
 ?
1.1.1.282 L-quinate + NAD(P)+
-
 Escherichia coli PB12 3-dehydroquinate + NAD(P)H + H+
-
 ?
1.1.1.282 L-quinate + NAD+
-
 Escherichia coli 3-dehydroquinate + NADH + H+
-
 r
1.1.1.282 L-quinate + NAD+
-
 Escherichia coli PB12 3-dehydroquinate + NADH + H+
-
 r
1.1.1.282 shikimate + NAD(P)+
-
 Escherichia coli 3-dehydroshikimate + NAD(P)H + H+
-
 ?
1.1.1.282 shikimate + NAD(P)+
-
 Escherichia coli PB12 3-dehydroshikimate + NAD(P)H + H+
-
 ?
1.1.1.282 shikimate + NAD+
-
 Escherichia coli 3-dehydroshikimate + NADH + H+
-
 r
1.1.1.282 shikimate + NAD+
-
 Escherichia coli PB12 3-dehydroshikimate + NADH + H+
-
 r

Synonyms

EC Number Synonyms Comment Organism
1.1.1.25 NAD+-dependent enzyme quinate/shikimate dehydrogenase
-
 Escherichia coli
1.1.1.25 quinate/shikimate dehydrogenase
-
 Escherichia coli
1.1.1.25 YdiB
-
 Escherichia coli
1.1.1.282 NAD+-dependent enzyme quinate/shikimate dehydrogenase
-
 Escherichia coli
1.1.1.282 quinate/shikimate dehydrogenase
-
 Escherichia coli
1.1.1.282 YdiB
-
 Escherichia coli

Cofactor

EC Number Cofactor Comment Organism Structure
1.1.1.25 NAD+
-
 Escherichia coli
1.1.1.25 NADH
-
 Escherichia coli
1.1.1.282 NAD+
-
 Escherichia coli
1.1.1.282 NADH
-
 Escherichia coli

General Information

EC Number General Information Comment Organism
1.1.1.25 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
1.1.1.25 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
1.1.1.282 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
1.1.1.282 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
1.1.1.282 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 Escherichia coli
1.1.1.282 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 Escherichia coli