6KWC

Crystal Structure Analysis of Endo-beta-1,4-xylanase II

Summary for 6KWC

• Entry DOI: 10.2210/pdb6kwc/pdb
• Descriptor: Endo-1,4-beta-xylanase 2, GLYCEROL, IODIDE ION, ... (4 entities in total)
• Functional Keywords: xylanase ii, xylotriose, hydrolase
• Biological source: Trichoderma reesei RUT C-30 (Hypocrea jecorina RUT C-30)
• Total number of polymer chains: 1
• Total formula weight: 21485.20

Authors

Li, C.,Wan, Q. (deposition date: 2019-09-06, release date: 2021-01-27, Last modification date: 2023-11-22)

Primary citation

Li, Z.,Zhang, X.,Li, C.,Kovalevsky, A.,Wan, Q.
Studying the Role of a Single Mutation of a Family 11 Glycoside Hydrolase Using High-Resolution X-ray Crystallography.
Protein J., 39:671-680, 2020

PubMed Abstract: XynII is a family 11 glycoside hydrolase that uses the retaining mechanism for catalysis. In the active site, E177 works as the acid/base and E86 works as the nucleophile. Mutating an uncharged residue (N44) to an acidic residue (D) near E177 decreases the enzyme's optimal pH by ~ 1.0 unit. D44 was previously suggested to be a second proton carrier for catalysis. To test this hypothesis, we abolished the activity of E177 by mutating it to be Q, and mutated N44 to be D or E. These double mutants have dramatically decreased activities. Our high-resolution crystallographic structures and the microscopic pK calculations show that D44 has similar position and pK value during catalysis, indicating that D44 changes electrostatics around E177, which makes it prone to rotate as the acid/base in acidic conditions, thus decreases the pH optimum. Our results could be helpful to design enzymes with different pH optimum.

PubMed: 33128114
DOI: 10.1007/s10930-020-09938-5

Experimental method

X-RAY DIFFRACTION (1.3 Å)