Atomic (0.94 Å) resolution structure of an inverting glycosidase in complex with substrate

• DOI: 10.1006/jmbi.2001.5404
• Publication Date: 2002-10-06T18:37:32Z
• Authors: Diego M.A Guérin; Marie-Bernard Las...; Marcelo Costabel; Hélène Souchon; Victor Lamzin; Pierre Béguin; Pedro M Alzari
• Keywords: Models, Molecular; Protein Conformation; [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph]; atomic resolution; Oligosaccharides; PROTEIN-CARBOHYDRATE INTERACTIONS; [SDV.BC]Life Sciences [q-bio]/Cellular Biology; Crystallography, X-Ray; Ligands; ATOMIC RESOLUTION; 03 medical and health sciences; MESH: Protein Conformation; Cellulase; https://purl.org/becyt/ford/1.6; INVERTING GLYCOSIDASE; MESH: Water; MESH: Ligands; [CHIM.CRIS]Chemical Sciences/Cristallography; MESH: Protein Binding; [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology; MESH: Hydrogen Bonding; https://purl.org/becyt/ford/1; X-ray crystallography; Clostridium; 0303 health sciences; Binding Sites; [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM]; inverting glycosidase; MESH: Clostridium; REACTION MECHANISM; MESH: Cellulase; Water; Hydrogen Bonding; MESH: Crystallography, X-Ray; X-RAY CRYSTALLOGRAPHY; MESH: Binding Sites; protein-carbohydrate interactions; reaction mechanism; [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]; MESH: Oligosaccharides; MESH: Models, Molecular; Protein Binding

The crystal structure of Clostridium thermocellum endoglucanase CelA in complex with cellopentaose has been determined at 0.94 A resolution. The oligosaccharide occupies six D-glucosyl-binding subsites, three on either side of the scissile glycosidic linkage. The substrate and product of the reaction occupy different positions at the reducing end of the cleft, where an extended array of hydrogen-bonding interactions with water molecules fosters the departure of the leaving group. Severe torsional strain upon the bound substrate forces a distorted boat(2,5) B conformation for the glucosyl residue bound at subsite -1, which facilitates the formation of an oxocarbenium ion intermediate and might favor the breakage of the sugar ring concomitant with catalysis.