1URX

Crystallographic structure of beta-agarase A in complex with oligoagarose

Summary for 1URX

• Entry DOI: 10.2210/pdb1urx/pdb
• Descriptor: BETA-AGARASE A, 3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose-(1-3)-alpha-D-galactopyranose, 3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose, ... (5 entities in total)
• Functional Keywords: hydrolase, beta-agarase, agarose, glycoside hydrolase, family 16, double helix, two binding-sites
• Biological source: ZOBELLIA GALACTANIVORANS (ZOBELLIA GALACTANIVORA, S)
• Total number of polymer chains: 1
• Total formula weight: 33886.96

Authors

Allouch, J.,Helbert, W.,Henrissat, B.,Czjzek, M. (deposition date: 2003-11-12, release date: 2004-03-04, Last modification date: 2023-12-13)

Primary citation

Allouch, J.,Helbert, W.,Henrissat, B.,Czjzek, M.
Parallel Substrate Binding Sites in a Beta-Agarase Suggest a Novel Mode of Action on Double-Helical Agarose
Structure, 12:623-, 2004

PubMed Abstract: 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.

PubMed: 15062085
DOI: 10.1016/J.STR.2004.02.020

Experimental method

X-RAY DIFFRACTION (1.7 Å)