title: Crystal structure of alginate lyase A1-III from Sphingomonas species A1 at 1.78 A resolution.
abstract: 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.
authors.affiliation: Kyoto University, Uji Kyoto, 611-0011, Japan.
authors.forename: H J
authors.initials: HJ
authors.lastname: Yoon
authors.forename: B
authors.initials: B
authors.lastname: Mikami
authors.forename: W
authors.initials: W
authors.lastname: Hashimoto
authors.forename: K
authors.initials: K
authors.lastname: Murata
mesh_terms: D000464:Alginates / Q000378:metabolism; D000595:Amino Acid Sequence; D001665:Binding Sites; D002480:Cellulase / Q000737:chemistry; D017124:Conserved Sequence / Q000235:genetics; D003460:Crystallization; D018360:Crystallography, X-Ray; D004220:Disulfides / Q000737:chemistry; D005087:Glucan 1,4-alpha-Glucosidase / Q000737:chemistry; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011133:Polysaccharide-Lyases / Q000737:chemistry*; D017433:Protein Structure, Secondary; D012680:Sensitivity and Specificity; D012997:Solvents; D013431:Sulfates / Q000737:chemistry / Q000378:metabolism; D013696:Temperature; D014867:Water / Q000737:chemistry / Q000378:metabolism; D017355:Zymomonas / Q000201:enzymology*
chemical_list: D000464:Alginates; D004220:Disulfides; D012997:Solvents; D013431:Sulfates; D014867:Water; D005087:Glucan 1,4-alpha-Glucosidase; D002480:Cellulase; D011133:Polysaccharide-Lyases; C016158:poly(beta-D-mannuronate) lyase