2CDP

Structure of a CBM6 in complex with neoagarohexaose

Summary for 2CDP

• Entry DOI: 10.2210/pdb2cdp/pdb
• Related: 2CDO
• Descriptor: BETA-AGARASE 1, 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, CALCIUM ION, ... (6 entities in total)
• Functional Keywords: carbohydrate-binding module, hydrolase
• Biological source: SACCHAROPHAGUS DEGRADANS
• Total number of polymer chains: 4
• Total formula weight: 72287.81

Authors

Henshaw, J.,Horne, A.,Van Bueren, A.L.,Money, V.A.,Bolam, D.N.,Czjzek, M.,Weiner, R.M.,Hutcheson, S.W.,Davies, G.J.,Boraston, A.B.,Gilbert, H.J. (deposition date: 2006-01-26, release date: 2006-02-08, Last modification date: 2023-12-13)

Primary citation

Henshaw, J.,Horne, A.,Van Bueren, A.L.,Money, V.A.,Bolam, D.N.,Czjzek, M.,Ekborg, N.A.,Weiner, R.M.,Hutcheson, S.W.,Davies, G.J.,Boraston, A.B.,Gilbert, H.J.
Family 6 Carbohydrate Binding Modules in Beta-Agarases Display Exquisite Selectivity for the Non- Reducing Termini of Agarose Chains.
J.Biol.Chem., 281:17099-, 2006

PubMed Abstract: Carbohydrate recognition is central to the biological and industrial exploitation of plant structural polysaccharides. These insoluble polymers are recalcitrant to microbial degradation, and enzymes that catalyze this process generally contain non-catalytic carbohydrate binding modules (CBMs) that potentiate activity by increasing substrate binding. Agarose, a repeat of the disaccharide 3,6-anhydro-alpha-L-galactose-(1,3)-beta-D-galactopyranose-(1,4), is the dominant matrix polysaccharide in marine algae, yet the role of CBMs in the hydrolysis of this important polymer has not previously been explored. Here we show that family 6 CBMs, present in two different beta-agarases, bind specifically to the non-reducing end of agarose chains, recognizing only the first repeat of the disaccharide. The crystal structure of one of these modules Aga16B-CBM6-2, in complex with neoagarohexaose, reveals the mechanism by which the protein displays exquisite specificity, targeting the equatorial O4 and the axial O3 of the anhydro-L-galactose. Targeting of the CBM6 to the non-reducing end of agarose chains may direct the appended catalytic modules to areas of the plant cell wall attacked by beta-agarases where the matrix polysaccharide is likely to be more amenable to further enzymic hydrolysis.

PubMed: 16601125
DOI: 10.1074/JBC.M600702200

Experimental method

X-RAY DIFFRACTION (1.59 Å)