Parallel substrate binding sites in a beta-agarase suggest a novel mode of action on double-helical agarose.
Agarose is a gel-forming polysaccharide with an alpha-L(1,4)-3,6-anhydro-galactose, beta-D(1,3)-galactose repeat unit, from the cell walls of marine red algae. beta-agarase A, from the Gram-negative bacterium Zobellia galactanivorans, is secreted to the external medium and degrades agarose with an endo-mechanism. The structure of the inactive mutant beta-agarase A-E147S in complex with agaro-octaose has been solved at 1.7 A resolution. Two oligosaccharide chains are bound to the protein. The first one resides in the active site channel, spanning subsites -4 to -1. A second oligosaccharide binding site, on the opposite side of the protein, was filled with eight sugar units, parallel to the active site. The crystal structure of the beta-agarase A with agaro-octaose provides detailed information on agarose recognition in the catalytic site. The presence of the second, parallel, binding site suggests that the enzyme might be able to unwind the double-helical structure of agarose prior to the catalytic cleavage.
Allouch
Julie
J
Architecture et Fonction de la Macromolécules Biologiques, UMR 6098, Centre National de la Recherche Scientifique and Universités Aix-Marseille I and II, 31 chemin Joseph Aiguier, F-13402 Marseille Cedex 20, France [corrected]
Helbert
William
W
Henrissat
Bernard
B
Czjzek
Mirjam
M
D001665:Binding Sites; D020134:Catalytic Domain; D003460:Crystallization; D006026:Glycoside Hydrolases / Q000737:chemistry* / Q000378:metabolism; D006090:Gram-Negative Bacteria / Q000201:enzymology / Q000378:metabolism; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D012685:Sepharose / Q000378:metabolism*
D012685:Sepharose; D006026:Glycoside Hydrolases; C019624:agarase