7D88 image
Deposition Date 2020-10-07
Release Date 2021-08-18
Last Version Date 2023-11-29
Entry Detail
PDB ID:
7D88
Keywords:
Title:
Crystal structure of a novel thermostable GH10 xylanase XynA
Biological Source:
Source Organism:
Bacillus sp. (Taxon ID: 1409)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.34 Å
R-Value Free:
0.24
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 41 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Beta-xylanase
Gene (Uniprot):xyn10A
Chain IDs:A
Chain Length:428
Number of Molecules:1
Biological Source:Bacillus sp.
Ligand Molecules
Primary Citation
Insights into the Catalytic Mechanism of a Novel XynA and Structure-Based Engineering for Improving Bifunctional Activities.
Biochemistry 60 2071 2083 (2021)
PMID: 34156819 DOI: 10.1021/acs.biochem.1c00134

Abstact

Xylan and cellulose are the two major constituents of numerous types of lignocellulose. The bifunctional enzyme that exhibits xylanase/cellulase activity has attracted a great deal of attention in biofuel production. Previously, a thermostable GH10 family enzyme (XynA) from Bacillus sp. KW1 was found to degrade both xylan and cellulose. To improve bifunctional activity on the basis of structure, we first determined the crystal structure of XynA at 2.3 Å. Via molecular docking and activity assays, we revealed that Gln250 and His252 were indispensable to bifunctionality, because they could interact with two conserved catalytic residues, Glu182 and Glu280, while bringing the substrate close to the activity pocket. Then we used a structure-based engineering strategy to improve xylanase/cellulase activity. Although no mutants with increased bifunctional activity were obtained after much screening, we found the answer in the N-terminal 36-amino acid truncation of XynA. The activities of XynA_ΔN36 toward beechwood xylan, wheat arabinoxylan, filter paper, and barley β-glucan were significantly increased by 0.47-, 0.53-, 2.46-, and 1.04-fold, respectively. Furthermore, upon application, this truncation released more reducing sugars than the wild type in the degradation of pretreated corn stover and sugar cane bagasse. These results showed the detailed molecular mechanism of the GH10 family bifunctional endoxylanase/cellulase. The basis of these catalytic performances and the screened XynA_ΔN36 provide clues for the further use of XynA in industrial applications.

Legend

Protein

Chemical

Disease

Primary Citation of related structures