Crystal structure of alginate lyase A1-III complexed with trisaccharide product at 2.0 A resolution.
The structure of A1-III from a Sphingomonas species A1 complexed with a trisaccharide product (4-deoxy-l-erythro-hex-4-enepyranosyluronate-mannuronate-mannuronic acid) was determined by X-ray crystallography at 2.0 A with an R-factor of 0.16. The final model of the complex form comprising 351 amino acid residues, 245 water molecules, one sulfate ion and one trisaccharide product exhibited a C(alpha) r.m.s.d. value of 0.154 A with the reported apo form of the enzyme. The trisaccharide was bound in the active cleft at subsites -3 approximately -1 from the non-reducing end by forming several hydrogen bonds and van der Waals interactions with protein atoms. The catalytic residue was estimated to be Tyr246, which existed between subsites -1 and +1 based on a mannuronic acid model oriented at subsite +1.
Yoon
H J
HJ
Research Institute for Food Science, Kyoto University, Uji Kyoto 611-0011, Japan.
Hashimoto
W
W
Miyake
O
O
Murata
K
K
Mikami
B
B
D001665:Binding Sites; D002240:Carbohydrate Sequence; D002384:Catalysis; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011133:Polysaccharide-Lyases / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D020578:Sphingomonas / Q000737:chemistry / Q000201:enzymology*; D014312:Trisaccharides / Q000737:chemistry* / Q000378:metabolism
D014312:Trisaccharides; D011133:Polysaccharide-Lyases; C016158:poly(beta-D-mannuronate) lyase