Insight into the binding of the wild type and mutated alginate lyase (AlyVI) with its substrate: a computational and experimental study

Biochim Biophys Acta. 2011 Dec;1814(12):1739-47. doi: 10.1016/j.bbapap.2011.08.018. Epub 2011 Sep 14.

Abstract

The homology model of the wild type alginate lyase (AlyVI) marine bacterium Vibrio sp. protein, was built using the crystal structure of the Family 7 alginate lyase from Sphingomonas sp. A1. To rationalize the observed structure-affinity relationships of aliginate lyase alyVI with its (GGG) substrate, molecular docking, MD imulations and binding free energy calculations followed by site-directed mutagenesis and alyVI activity assays were carried out. Per-residue decomposition of the (GGG) binding energy revealed that the most important contributions were from polar and charged residues, such as Asn138, Arg143, Asn217, and Lys308, while van der Waals interactions were responsible for binding with the catalytic His200 and Tyr312 residues. The mutants H200A, K308A, Y312A, Y312F, and W165A were found to be inactive or almost inactive. However, the catalytic efficiency (k(cat)/K(m)) of the double mutant L224V/D226G increased by two-fold compared to the wild type enzyme. This first structural model with its substrate binding mode and the agreement with experimental results provide a suitable base for the future rational design of new mutated alyVI structures with improved catalytic activity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Chemistry Techniques, Analytical
  • Computational Biology
  • Hexuronic Acids / metabolism
  • Models, Molecular
  • Molecular Sequence Data
  • Mutagenesis, Site-Directed
  • Mutant Proteins / metabolism
  • Polysaccharide-Lyases / chemistry*
  • Polysaccharide-Lyases / genetics*
  • Polysaccharide-Lyases / metabolism*
  • Protein Binding / genetics
  • Protein Interaction Mapping / methods
  • Sequence Homology
  • Substrate Specificity
  • Validation Studies as Topic
  • Vibrio alginolyticus / enzymology
  • Vibrio alginolyticus / genetics

Substances

  • Hexuronic Acids
  • Mutant Proteins
  • guluronic acid
  • Polysaccharide-Lyases
  • poly(beta-D-mannuronate) lyase