Deciphering the structural insights and concentration‐dependent dimerisation of endo‐β‐1,4‐xylanase ( Ac Xyn30B_12) from Acetivibrio clariflavus using SAXS and computational methods
Year: 2026
Type: article
Abstract: Structure of full‐length thermophilic multi‐modular endo‐ β ‐1,4‐xylanase, Ac Xyn30B_12 from Acetivibrio clariflavus DSM 19732 was determined by computational analysis and SAXS studies. Ac Xyn30B_12 comprised N‐terminal glycoside hydrolase family 30 catalytic module, followed by family 6 carbohydrate‐binding module and dockerin typeI. The experiments involved Ac Xyn30B_12 cloned into pET‐28a(+) vector including an N‐terminal His6‐tag encoding 653 amino. The catalytic residues—Glu151 and Glu259—were conserved based on multiple sequence alignment and superposition with homologous protein sequence analysis. Circular dichroism analysis of Ac Xyn30B_12 showed 26.2% α ‐helices and 28.1% β ‐strands, corroborating with PSIPRED and SOPMA servers. Molecular docking revealed highest affinity of Ac Xyn30B_12 with xylotriose (−11.2 kcal mol −1 ) followed by xylobiose (−9.6 kcal mol −1 ). Molecular dynamics simulation showed that the docked Ac Xyn30B_12‐xylotriose complex is more stable and compact than unbound Ac Xyn30B_12. SAXS analysis of Ac Xyn30B_12 confirmed the polydisperse and elongated structure of Ac Xyn30B_12 at 3 mg mL −1 and 5 mg mL −1 . Dummy atom model analysis of Ac Xyn30B_12 revealed monomeric and dimeric form at 3 and 5 mg mL −1 , respectively. Dynamic light scattering analysis of Ac Xyn30B_12 confirmed the polydisperse nature at 1, 3 and 5 mg mL −1 . DLS study showed R h , 4.2 nm, 4.5 nm and 5.3 nm at 1, 3 and 5 mg mL −1 , respectively, matching the R g results from SAXS analysis. A lower zeta potential of −4.0 mV at 5 mg mL −1 than −10.5 mV at 3 mg mL −1 indicated protein aggregation and dimerisation at higher concentration. A stable‐dimeric structure conserved the catalytic machinery of Ac Xyn30B_12, making it a promising biocatalyst for efficient hydrolysis of xylan into value‐added products.
Source: FEBS Journal
DOI: 10.1111/febs.70432
Authors: Bipasha Choudhury, Arun Goyal
Institution: Indian Institute of Technology Guwahati
Language: English
Subfield: Materials Chemistry
Field: Materials Science
Domain: Physical Sciences
Open Access status: bronze
OpenAlex ID: W7128785134