Structure-function analyses of a PL24 family ulvan lyase reveal key features and suggest its catalytic mechanism

J Biol Chem. 2018 Mar 16;293(11):4026-4036. doi: 10.1074/jbc.RA117.001642. Epub 2018 Jan 30.

Abstract

Ulvan is a major cell wall component of green algae of the genus Ulva, and some marine bacteria encode enzymes that can degrade this polysaccharide. The first ulvan-degrading lyases have been recently characterized, and several putative ulvan lyases have been recombinantly expressed, confirmed as ulvan lyases, and partially characterized. Two families of ulvan-degrading lyases, PL24 and PL25, have recently been established. The PL24 lyase LOR_107 from the bacterial Alteromonadales sp. strain LOR degrades ulvan endolytically, cleaving the bond at the C4 of a glucuronic acid. However, the mechanism and LOR_107 structural features involved are unknown. We present here the crystal structure of LOR_107, representing the first PL24 family structure. We found that LOR_107 adopts a seven-bladed β-propeller fold with a deep canyon on one side of the protein. Comparative sequence analysis revealed a cluster of conserved residues within this canyon, and site-directed mutagenesis disclosed several residues essential for catalysis. We also found that LOR_107 uses the His/Tyr catalytic mechanism, common to several PL families. We captured a tetrasaccharide substrate in the structures of two inactive mutants, which indicated a two-step binding event, with the first substrate interaction near the top of the canyon coordinated by Arg320, followed by sliding of the substrate into the canyon toward the active-site residues. Surprisingly, the LOR_107 structure was very similar to that of the PL25 family PLSV_3936, despite only ∼14% sequence identity between the two enzymes. On the basis of our structural and mutational analyses, we propose a catalytic mechanism for LOR_107 that differs from the typical His/Tyr mechanism.

Keywords: His/Tyr mechansim; Polysaccharide lyase; Ulvan lyase; carbohydrate processing; catalysis; crystallography; mutagenesis; polysaccharide; structural biology; substrate specificity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alteromonadaceae / enzymology*
  • Catalysis
  • Catalytic Domain
  • Crystallography, X-Ray
  • Models, Molecular
  • Mutagenesis, Site-Directed
  • Mutation*
  • Polysaccharide-Lyases / chemistry*
  • Polysaccharide-Lyases / genetics
  • Polysaccharide-Lyases / metabolism*
  • Polysaccharides / metabolism*
  • Protein Conformation
  • Structure-Activity Relationship
  • Substrate Specificity

Substances

  • Polysaccharides
  • ulvan
  • Polysaccharide-Lyases
  • ulvan-lyase

Associated data

  • PDB/3PE7
  • PDB/6BYP
  • PDB/6BYX
  • PDB/6BYT

Grant support