8H1K

Crystal structure of glucose-2-epimerase from Runella slithyformis Runsl_4512

Summary for 8H1K

• Entry DOI: 10.2210/pdb8h1k/pdb
• Descriptor: N-acylglucosamine 2-epimerase, FORMIC ACID, GLYCEROL, ... (4 entities in total)
• Functional Keywords: apo form, isomerase, runsl
• Biological source: Runella slithyformis
• Total number of polymer chains: 1
• Total formula weight: 49405.38

Authors

Wang, H.,Sun, X.M.,Saburi, W.,Yu, J.,Yao, M. (deposition date: 2022-10-03, release date: 2023-07-12, Last modification date: 2023-11-29)

Primary citation

Wang, H.,Sun, X.,Saburi, W.,Hashiguchi, S.,Yu, J.,Ose, T.,Mori, H.,Yao, M.
Structural insights into the substrate specificity and activity of a novel mannose 2-epimerase from Runella slithyformis.
Acta Crystallogr D Struct Biol, 79:585-595, 2023

PubMed Abstract: Mannose 2-epimerase (ME), a member of the acylglucosamine 2-epimerase (AGE) superfamily that catalyzes epimerization of D-mannose and D-glucose, has recently been characterized to have potential for D-mannose production. However, the substrate-recognition and catalytic mechanism of ME remains unknown. In this study, structures of Runella slithyformis ME (RsME) and its D254A mutant [RsME(D254A)] were determined in their apo forms and as intermediate-analog complexes [RsME-D-glucitol and RsME(D254A)-D-glucitol]. RsME possesses the (α/α)-barrel of the AGE superfamily members but has a unique pocket-covering long loop (loop). The RsME-D-glucitol structure showed that loop moves towards D-glucitol and closes the active pocket. Trp251 and Asp254 in loop are only conserved in MEs and interact with D-glucitol. Kinetic analyses of the mutants confirmed the importance of these residues for RsME activity. Moreover, the structures of RsME(D254A) and RsME(D254A)-D-glucitol revealed that Asp254 is vital for binding the ligand in a correct conformation and for active-pocket closure. Docking calculations and structural comparison with other 2-epimerases show that the longer loop in RsME causes steric hindrance upon binding to disaccharides. A detailed substrate-recognition and catalytic mechanism for monosaccharide-specific epimerization in RsME has been proposed.

PubMed: 37314406
DOI: 10.1107/S205979832300390X

Experimental method

X-RAY DIFFRACTION (1.6 Å)