Bacterial polysaccharide lyase family 33: Specificity from an evolutionarily conserved binding tunnel

• 成果类型: Article
• 署名作者: Loiodice, Melanie; Drula, Elodie; Mciver, Zak; Antonyuk, Svetlana; Basle, Arnaud; Lima, Marcelo; Yates, Edwin A.; Byrne, Dominic P.; Coughlan, Jamie; Leech, Andrew; Mesdaghi, Shahram; Rigden, Daniel J.; Drouillard, Sophie; Helbert, William; Henrissat, Bernard; Terrapon, Nicolas; Wright, Gareth S. A.; Couturier, Marie; Cartmell, Alan
• 署名单位: Communaute Universite Grenoble Alpes; Universite Grenoble Alpes (UGA); Centre National de la Recherche Scientifique (CNRS); Aix-Marseille Universite; INRAE; Centre National de la Recherche Scientifique (CNRS); INRAE; University of York - UK; University of Liverpool; Newcastle University - UK; Keele University; University of York - UK; University of Liverpool; King Abdulaziz University; Technical University of Denmark; University of Essex; University of York - UK; University of York - UK
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-12734
• DOI: 10.1073/pnas.2421623122
• 发表日期: 2025-02-18
• 关键词: crystal-structure; pedobacter-heparinus; mechanism; site

摘要

Acidic glycans are essential for the biology of multicellular eukaryotes. To utilize them, microbial life including symbionts and pathogens has evolved polysaccharide lyases (PL) that cleave their 1,4 glycosidic linkages via a beta- elimination mechanism. PL family 33 (PL33) enzymes have the unusual ability to target a diverse range of glycosamino-glycans (GAGs), as well as the bacterial polymer, gellan gum. In order to gain more detailed insight into PL33 activities we recombinantly expressed 10 PL33 members derived from all major environments and further elucidated the detailed biochemical and biophysical properties of five, showing that their substrate specificity is conferred by variations in tunnel length and topography. The key amino acids involved in catalysis and substrate interactions were identified, and employing a combination of comple-mentary biochemical, structural, and modeling approaches, we show that the tunnel topography is induced by substrate binding to the glycan. Structural and bioinformatic analyses revealed that these features are conserved across several lyase families as well as in mammalian GAG epimerases.