Literature summary for 4.2.1.46 extracted from

Ma, G.; Dong, L.; Liu, Y.
Insights into the catalytic mechanism of dTDP-glucose 4,6-dehydratase from quantum mechanics/molecular mechanics simulations (2014), RSC Adv., 4, 35449-35458 .

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Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
dTDP-alpha-D-glucose	Streptomyces venezuelae	-	dTDP-4-dehydro-6-deoxy-alpha-D-glucose + H2O	-	?

Organism

Organism	UniProt	Comment	Textmining
Streptomyces venezuelae	Q9ZGH3	-	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
dTDP-alpha-D-glucose	-	Streptomyces venezuelae	dTDP-4-dehydro-6-deoxy-alpha-D-glucose + H2O	-	?
dTDP-alpha-D-glucose	QM/MM investigation of the detailed mechanism of dTDP-glucose 4,6-dehydratase. The computational results demonstrate that the whole catalytic reaction contains four enzymatic elementary steps and one nonenzymatic enol-keto tautomerisation step. In the oxidation step, the NAD+ abstracts the hydride from glycosyl C4 and a conserved tyrosine residue removes a proton from the glycosyl C4-hydroxyl group. This oxidation step proceeds through a concerted asynchronous mechanism with a calculated free energy barrier of 21.1 kcal/mol, in which the hydride transfer lags behind the proton transfer. Different from the proposal based on experiments that the dehydration follows a concerted mechanism. The QM/MM calculation results show that the elimination of water is stepwise, in which two highly conserved residues are involved. Glu129 firstly deprotonates the glycosyl C5 and subsequently Asp128 protonates the leaving C6-hydroxyl group to give a water molecule and dTDP-4-dehydroglucose-5,6-ene intermediate. In the reduction step, NADH returns the hydride back to glycosyl C6 and the phenolic hydroxyl of Tyr151 spontaneously denotes its proton to C4-keto group, forming an enol	Streptomyces venezuelae	dTDP-4-dehydro-6-deoxy-alpha-D-glucose + H2O	-	?

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Release 2023.1 (January 2023)