6K6V

Crystal structure of barley exohydrolaseI W434A mutant in complex with methyl 6-thio-beta-gentiobioside

Summary for 6K6V

• Entry DOI: 10.2210/pdb6k6v/pdb
• Related PRD ID: PRD_900098
• Descriptor: BETA-D-GLUCAN GLUCOHYDROLASE ISOENZYME EXO1, beta-D-glucopyranose-(1-6)-methyl 6-thio-beta-D-glucopyranoside, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... (7 entities in total)
• Functional Keywords: barley exohydrolasei, hydrolase, enzyme function
• Biological source: Hordeum vulgare subsp. vulgare (Domesticated barley)
• Total number of polymer chains: 1
• Total formula weight: 67626.60

Authors

Luang, S.,Streltsov, V.A.,Hrmova, M. (deposition date: 2019-06-05, release date: 2020-08-19, Last modification date: 2024-10-09)

Primary citation

Luang, S.,Fernandez-Luengo, X.,Nin-Hill, A.,Streltsov, V.A.,Schwerdt, J.G.,Alonso-Gil, S.,Ketudat Cairns, J.R.,Pradeau, S.,Fort, S.,Marechal, J.D.,Masgrau, L.,Rovira, C.,Hrmova, M.
The evolutionary advantage of an aromatic clamp in plant family 3 glycoside exo-hydrolases.
Nat Commun, 13:5577-5577, 2022

PubMed Abstract: 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.

PubMed: 36151080
DOI: 10.1038/s41467-022-33180-5

Experimental method

X-RAY DIFFRACTION (1.98 Å)