4YTS

Crystal structure of D-tagatose 3-epimerase C66S from Pseudomonas cichorii in complex with 1-deoxy 3-keto D-galactitol

Summary for 4YTS

• Entry DOI: 10.2210/pdb4yts/pdb
• Related: 4XSL 4XSM 4YTQ 4YTR 4YTT 4YTU 4YVL
• Descriptor: D-tagatose 3-epimerase, MANGANESE (II) ION, 1-deoxy-D-xylo-hex-3-ulose, ... (5 entities in total)
• Functional Keywords: epimerase, isomerase
• Biological source: Pseudomonas cichorii
• Total number of polymer chains: 4
• Total formula weight: 137624.08

Authors

Yoshida, H.,Yoshihara, A.,Ishii, T.,Izumori, K.,Kamitori, S. (deposition date: 2015-03-18, release date: 2016-03-23, Last modification date: 2023-11-08)

Primary citation

Yoshida, H.,Yoshihara, A.,Ishii, T.,Izumori, K.,Kamitori, S.
X-ray structures of the Pseudomonas cichorii D-tagatose 3-epimerase mutant form C66S recognizing deoxy sugars as substrates
Appl. Microbiol. Biotechnol., 100:10403-10415, 2016

PubMed Abstract: Pseudomonas cichorii D-tagatose 3-epimerase (PcDTE), which has a broad substrate specificity, efficiently catalyzes the epimerization of not only D-tagatose to D-sorbose but also D-fructose to D-psicose (D-allulose) and also recognizes the deoxy sugars as substrates. In an attempt to elucidate the substrate recognition and catalytic reaction mechanisms of PcDTE for deoxy sugars, the X-ray structures of the PcDTE mutant form with the replacement of Cys66 by Ser (PcDTE_C66S) in complexes with deoxy sugars were determined. These X-ray structures showed that substrate recognition by the enzyme at the 1-, 2-, and 3-positions is responsible for enzymatic activity and that substrate-enzyme interactions at the 4-, 5-, and 6-positions are not essential for the catalytic reaction of the enzyme leading to the broad substrate specificity of PcDTE. They also showed that the epimerization site of 1-deoxy 3-keto D-galactitol is shifted from C3 to C4 and that 1-deoxy sugars may bind to the catalytic site in the inhibitor-binding mode. The hydrophobic groove that acts as an accessible surface for substrate binding is formed through the dimerization of PcDTE. In PcDTE_C66S/deoxy sugar complex structures, bound ligand molecules in both the linear and ring forms were detected in the hydrophobic groove, while bound ligand molecules in the catalytic site were in the linear form. This result suggests that the sugar-ring opening of a substrate may occur in the hydrophobic groove and also that the narrow channel of the passageway to the catalytic site allows a substrate in the linear form to pass through.

PubMed: 27368739
DOI: 10.1007/s00253-016-7673-7

Experimental method

X-RAY DIFFRACTION (2.14 Å)