Crystal structure of alginate lyase A1-III from Sphingomonas species A1 at 1.78 A resolution

J Mol Biol. 1999 Jul 9;290(2):505-14. doi: 10.1006/jmbi.1999.2883.


The three-dimensional structure of alginate lyase A1-III (ALYIII) from a Sphingomonas species A1 was determined by X-ray crystallography. The enzyme was crystallized by the hanging-drop vapour-diffusion method in the presence of 49% ammonium sulfate at 20 degrees C. The crystals are monoclinic and belong to the space group C2 with unit cell dimensions of a=49.18 A, b=93.08 A, c=82.10 A and beta=104.12 degrees. There was one molecule of alginate lyase in the asymmetric unit of the crystal. The diffraction data up to 1. 71 A were collected with Rsymof 5.0%. The crystal structure of ALYIII was solved by the multiple isomorphous replacement method and refined at 1.78 A resolution using X-PLOR with a final R -factor of 18.0% for 10.0 to 1.78 A resolution data. The refined model of ALYIII contained 351 amino acid residues, 299 water molecules and two sulfate ions. The three-dimensional structure of ALYIII was abundant in helices and had a deep tunnel-like cleft in a novel (alpha6/alpha5)-barrel structure, which was similar to the (alpha6/alpha6)-barrel found in glucoamylase and cellulase. This structure presented the possibility that alginate molecules might penetrate into the cleft to interact with the catalytic site of ALYIII.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alginates / metabolism
  • Amino Acid Sequence
  • Binding Sites
  • Cellulase / chemistry
  • Conserved Sequence / genetics
  • Crystallization
  • Crystallography, X-Ray
  • Disulfides / chemistry
  • Glucan 1,4-alpha-Glucosidase / chemistry
  • Hydrogen Bonding
  • Models, Molecular
  • Molecular Sequence Data
  • Polysaccharide-Lyases / chemistry*
  • Protein Structure, Secondary
  • Sensitivity and Specificity
  • Solvents
  • Sulfates / chemistry
  • Sulfates / metabolism
  • Temperature
  • Water / chemistry
  • Water / metabolism
  • Zymomonas / enzymology*


  • Alginates
  • Disulfides
  • Solvents
  • Sulfates
  • Water
  • Glucan 1,4-alpha-Glucosidase
  • Cellulase
  • Polysaccharide-Lyases
  • poly(beta-D-mannuronate) lyase

Associated data

  • PDB/1QAZ