9KU5

Crystal structure of substrate bound GH5_22 exo-beta-xylosidase from the seaweed-derived thermophile Geobacillus thermodenitrificans OS27

Summary for 9KU5

• Entry DOI: 10.2210/pdb9ku5/pdb
• Related PRD ID: PRD_900117
• Descriptor: Glycoside hydrolase, beta-D-xylopyranose-(1-4)-beta-D-xylopyranose, GLYCEROL, ... (5 entities in total)
• Functional Keywords: glycoside hydrolase, hydrolase
• Biological source: Geobacillus thermodenitrificans
• Total number of polymer chains: 2
• Total formula weight: 119559.35

Authors

Hino, T.,Lee, W.,Okamoto, T.,Ohshiro, T.,Nagano, S.,Suzuki, H. (deposition date: 2024-12-03, release date: 2026-02-04, Last modification date: 2026-02-18)

Primary citation

Lee, W.,Hino, T.,Fujii, K.,Tanimoto, S.,Naka, R.,Hara, K.,Okamoto, T.,Okazaki, F.,Nagano, S.,Ohshiro, T.,Suzuki, H.
Structural and biochemical characterization of a GH5_22 enzyme from the seaweed-derived thermophile Geobacillus thermodenitrificans OS27.
Arch.Biochem.Biophys., 778:110736-110736, 2026

PubMed Abstract: Geobacillus thermodenitrificans OS27 is a seaweed-derived thermophile that harbors a GH5_22 gene (bxlA) that encodes for a glycoside hydrolase fused with the cyclin box domain. In this study, we characterized the catalytic activity, enzymatic properties, three-dimensional structure, and physiological role of the gene product, GtBxlA. The enzyme was produced as a thermostable dimer, acting on p-nitrophenyl-β-d-xylopyranoside among 23 substrates. β-1,4-Linked xylooligosaccharides were also hydrolyzed from the nonreducing end. The activity indicated that GtBxlA functions as an exo-β-1,4-xylosidase. We determined the crystal structure of the Glu188Ala variant complexed with β-1,4-xylotriose at 1.52 Å resolution. GtBxlA exhibited an atypical (β/α)-barrel architecture. The cyclin box constituted a single α-helix within the core barrel and a lid-like domain that contributes to dimer formation. Structural analysis revealed that Glu188 and Glu318 are positioned to serve as the acid/base and nucleophile catalysts, respectively. Alanine mutagenesis confirmed the essential role of Glu188 and Glu318 in catalysis. We also determined the ligand-free structure of the Glu188Ala variant. Both structures were almost identical; however, a loop at the substrate entry site was fixed in the ligand-free structure, suggesting a conformational change upon substrate binding. Although bxlA deletion did not affect β-1,4-xylan utilization, its expression was induced by β-1,4-xylan. These observations suggest that G. thermodenitrificans OS27 employed GtBxlA in utilizing β-1,4-xylan. Notably, GtBxlA could hydrolyze β-1,3-linked xylooligosaccharides. This highlights the possibility that GtBxlA also assists the host in utilizing β-1,3-xylan, which is abundant in certain seaweeds.

PubMed: 41548701
DOI: 10.1016/j.abb.2026.110736

Experimental method

X-RAY DIFFRACTION (1.52 Å)