8P67

Crystal structure of Thermothelomyces thermophila (double mutant EE) in complex with aldotetrauronic acid

Summary for 8P67

• Entry DOI: 10.2210/pdb8p67/pdb
• Related: 6KRN 7NCX 8C48 8CBC
• Descriptor: GH30 family xylanase, beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose, ... (6 entities in total)
• Functional Keywords: glucuronoxylanase, glucuronic acid, aldotetrauronic acid, gh30_7, hydrolase
• Biological source: Thermothelomyces thermophilus
• Total number of polymer chains: 2
• Total formula weight: 106312.47

Authors

Dimarogona, M.,Pentari, C.,Kosinas, C.,Topakas, E. (deposition date: 2023-05-25, release date: 2024-05-22, Last modification date: 2024-10-16)

Primary citation

Pentari, C.,Kosinas, C.,Nikolaivits, E.,Dimarogona, M.,Topakas, E.
Structural and molecular insights into a bifunctional glycoside hydrolase 30 xylanase specific to glucuronoxylan.
Biotechnol.Bioeng., 121:2067-2078, 2024

PubMed Abstract: Glycoside hydrolase (GH) 30 family xylanases are enzymes of biotechnological interest due to their capacity to degrade recalcitrant hemicelluloses, such as glucuronoxylan (GX). This study focuses on a subfamily 7 GH30, TtXyn30A from Thermothelomyces thermophilus, which acts on GX in an "endo" and "exo" mode, releasing methyl-glucuronic acid branched xylooligosaccharides (XOs) and xylobiose, respectively. The crystal structure of inactive TtXyn30A in complex with 2-(4-O-methyl-α-D-glucuronosyl)-xylotriose (UXX), along with biochemical analyses, corroborate the implication of E233, previously identified as alternative catalytic residue, in the hydrolysis of decorated xylan. At the -1 subsite, the xylose adopts a distorted conformation, indicative of the Michaelis complex of TtXyn30AEE with UXX trapped in the semi-functional active site. The most significant structural rearrangements upon substrate binding are observed at residues W127 and E233. The structures with neutral XOs, representing the "exo" function, clearly show the nonspecific binding at aglycon subsites, contrary to glycon sites, where the xylose molecules are accommodated via multiple interactions. Last, an unproductive ligand binding site is found at the interface between the catalytic and the secondary β-domain which is present in all GH30 enzymes. These findings improve current understanding of the mechanism of bifunctional GH30s, with potential applications in the field of enzyme engineering.

PubMed: 38678481
DOI: 10.1002/bit.28731

Experimental method

X-RAY DIFFRACTION (1.37 Å)