6WN6

Crystal structure of 3-keto-D-glucoside 4-epimerase, YcjR, from E. coli, apo form

Summary for 6WN6

• Entry DOI: 10.2210/pdb6wn6/pdb
• Descriptor: 3-keto-D-glucoside 4-epimerase, MANGANESE (II) ION, 1,2-ETHANEDIOL, ... (4 entities in total)
• Functional Keywords: microbiome, prebiotic, isomerase, epimerase
• Biological source: Escherichia coli
• Total number of polymer chains: 4
• Total formula weight: 146476.51

Authors

Mabanglo, M.F.,Raushel, F.M.,Mukherjee, K. (deposition date: 2020-04-22, release date: 2020-06-10, Last modification date: 2024-03-06)

Primary citation

Mabanglo, M.F.,Huddleston, J.P.,Mukherjee, K.,Taylor, Z.W.,Raushel, F.M.
Structure and Reaction Mechanism of YcjR, an Epimerase That Facilitates the Interconversion of d-Gulosides to d-Glucosides inEscherichia coli.
Biochemistry, 59:2069-2077, 2020

PubMed Abstract: YcjR from K-12 MG1655 catalyzes the manganese-dependent reversible epimerization of 3-keto-α-d-gulosides to the corresponding 3-keto-α-d-glucosides as a part of a proposed catabolic pathway for the transformation of d-gulosides to d-glucosides. The three-dimensional structure of the manganese-bound enzyme was determined by X-ray crystallography. The divalent manganese ion is coordinated to the enzyme by ligation to Glu-146, Asp-179, His-205, and Glu-240. When either of the two active site glutamate residues is mutated to glutamine, the enzyme loses all catalytic activity for the epimerization of α-methyl-3-keto-d-glucoside at C4. However, the E240Q mutant can catalyze hydrogen-deuterium exchange of the proton at C4 of α-methyl-3-keto-d-glucoside in solvent DO. The E146Q mutant does not catalyze this exchange reaction. These results indicate that YcjR catalyzes the isomerization of 3-keto-d-glucosides via proton abstraction at C4 by Glu-146 to form a -enediolate intermediate that is subsequently protonated on the opposite face by Glu-240 to generate the corresponding 3-keto-d-guloside. This conclusion is supported by docking of the -enediolate intermediate into the active site of YcjR based on the known binding orientation of d-fructose and d-psicose in the active site of d-psicose-3-epimerase.

PubMed: 32437133
DOI: 10.1021/acs.biochem.0c00334

Experimental method

X-RAY DIFFRACTION (1.86 Å)