The evolutionary advantage of an aromatic clamp in plant family 3 glycoside exo-hydrolases

• Published in: Nature communications 2022-09, Vol.13 (1), p.5577-5577, Article 5577
• Main Authors: Luang, Sukanya, Fernández-Luengo, Xavier, Nin-Hill, Alba, Streltsov, Victor A., Schwerdt, Julian G., Alonso-Gil, Santiago, Ketudat Cairns, James R., Pradeau, Stéphanie, Fort, Sébastien, Maréchal, Jean-Didier, Masgrau, Laura, Rovira, Carme, Hrmova, Maria
• Format: Article
• Language: English
• Subjects: 101/58; 119/118; 631/181/735; 631/45/173; 631/535/1266; 631/57/2272; 631/92/72/1203; 64; 82/16; 82/29; 82/80; 82/83; Barley; Binding; Catalysis; Cellobiase; Chemical Sciences; Crystallography; Dynamic structural analysis; Enzyme kinetics; Glucan; Glucosidase; Glucosides; Glycosidases; Glycoside hydrolase; Glycosides; Humanities and Social Sciences; Hydrolase; Lateral displacement; Life Sciences; Molecular dynamics; Molecular modelling; multidisciplinary; Mutagenesis; Mutation; Organic chemistry; Plant growth; Science; Science (multidisciplinary); Substrates; Tryptophan; X-ray crystallography
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-022-33180-5

In the barley β- d -glucan glucohydrolase, a glycoside hydrolase family 3 (GH3) enzyme, the Trp286/Trp434 clamp ensures β- d -glucosides binding, which is fundamental for substrate hydrolysis during plant growth and development. We employ mutagenesis, high-resolution X-ray crystallography, and multi-scale molecular modelling methods to examine the binding and conformational behaviour of isomeric β- d -glucosides during substrate-product assisted processive catalysis that operates in GH3 hydrolases. Enzyme kinetics reveals that the W434H mutant retains broad specificity, while W434A behaves as a strict (1,3)-β- d -glucosidase. Investigations of reactant movements on the nanoscale reveal that processivity is sensitive to mutation-specific alterations of the tryptophan clamp. While wild-type and W434H utilise a lateral cavity for glucose displacement and sliding of (1,3)-linked hydrolytic products through the catalytic site without dissociation, consistent with their high hydrolytic rates, W434A does not adopt processive catalysis. Phylogenomic analyses of GH3 hydrolases disclose the evolutionary advantage of the tryptophan clamp that confers broad specificity, high catalytic efficiency, and processivity. Barley β- d -glucan glucohydrolase is a glycoside hydrolase family 3 (GH3) enzyme critical for growth and development. Here the authors carryout mutagenesis, structural analyses and multi-scale molecular dynamics to examine the binding and conformational behaviour of several β- d -glucosides during the substrate-product assisted catalysis that operates in GH3 hydrolases.