New Ulvan-Degrading Polysaccharide Lyase Family: Structure and Catalytic Mechanism Suggests Convergent Evolution of Active Site Architecture

Thirumalaiselvi Ulaganathan, Michal T. Boniecki, Elizabeth Foran, Vitaliy Buravenkov, Naama Mizrachi, Ehud Banin, William Helbert, Miroslaw Cygler

Research output: Contribution to journalArticlepeer-review

48 Scopus citations

Abstract

Ulvan is a complex sulfated polysaccharide biosynthesized by green seaweed and contains predominantly rhamnose, xylose, and uronic acid sugars. Ulvan-degrading enzymes have only recently been identified and added to the CAZy (www.cazy.org) database as family PL24, but neither their structure nor catalytic mechanism(s) are yet known. Several homologous, new ulvan lyases, have been discovered in Pseudoalteromonas sp. strain PLSV, Alteromonas LOR, and Nonlabens ulvanivorans, defining a new family PL25, with the lyase encoded by the gene PLSV-3936 being one of them. This enzyme cleaves the glycosidic bond between 3-sulfated rhamnose (R3S) and glucuronic acid (GlcA) or iduronic acid (IdoA) via a β-elimination mechanism. We report the crystal structure of PLSV-3936 and its complex with a tetrasaccharide substrate. PLSV-3936 folds into a seven-bladed β-propeller, with each blade consisting of four antiparallel β-strands. Sequence conservation analysis identified a highly conserved region lining at one end of a deep crevice on the protein surface. The putative active site was identified by mutagenesis and activity measurements. Crystal structure of the enzyme with a bound tetrasaccharide substrate confirmed the identity of base and acid residues and allowed determination of the catalytic mechanism and also the identification of residues neutralizing the uronic acid carboxylic group. The PLSV-3936 structure provides an example of a convergent evolution among polysaccharide lyases toward a common active site architecture embedded in distinct folds.

Original languageEnglish
Pages (from-to)1269-1280
Number of pages12
JournalACS Chemical Biology
Volume12
Issue number5
DOIs
StatePublished - 19 May 2017

Bibliographical note

Publisher Copyright:
© 2017 American Chemical Society.

Fingerprint

Dive into the research topics of 'New Ulvan-Degrading Polysaccharide Lyase Family: Structure and Catalytic Mechanism Suggests Convergent Evolution of Active Site Architecture'. Together they form a unique fingerprint.

Cite this