PDBsum entry: 2cdp

Hydrolase

PDB id: 2cdp

Contents

Protein chains

138 a.a. *

128 a.a. *

Ligands

GAL-AAL-GAL-AAL-GAL-AAL ×4

EDO ×6

Metals

_CL ×9

_CA ×8

Waters ×572

* Residue conservation analysis

PDB id:

2cdp

Name:

Hydrolase

Title:

Structure of a cbm6 in complex with neoagarohexaose

Structure:

Beta-agarase 1. Chain: a, b, c, d. Fragment: carbohydrate-binding module, residues 456-593. Engineered: yes

Source:

Saccharophagus degradans. Organism_taxid: 203122. Strain: 2-40. Atcc: 43691. Expressed in: escherichia coli. Expression_system_taxid: 469008. Other_details: from the laboratory of ron weiner

Resolution:

1.59Å R-factor: 0.212 R-free: 0.253

Authors:

J.Henshaw,A.Horne,A.L.Van Bueren,V.A.Money,D.N.Bolam, M.Czjzek,R.M.Weiner,S.W.Hutcheson,G.J.Davies,A.B.Boraston, H.J.Gilbert

Key ref:

J.Henshaw et al. (2006). Family 6 carbohydrate binding modules in beta-agarases display exquisite selectivity for the non-reducing termini of agarose chains. J Biol Chem, 281, 17099-17107. PubMed id: 16601125 DOI: 10.1074/jbc.M600702200

Date:

26-Jan-06 Release date: 08-Feb-06

Protein chain

Q6DN99  (Q6DN99_9ALTE) -  Beta-agarase I

Seq: 593 a.a.

Struc: 138 a.a.

Protein chains

Q6DN99  (Q6DN99_9ALTE) -  Beta-agarase I

Seq: 593 a.a.

Struc: 128 a.a.

 Gene Ontology (GO) functional annotation 

• Biochemical function: carbohydrate binding (1 term)

DOI no: 10.1074/jbc.M600702200

J Biol Chem 281:17099-17107 (2006)

PubMed id: 16601125

Family 6 carbohydrate binding modules in beta-agarases display exquisite selectivity for the non-reducing termini of agarose chains.

J.Henshaw, A.Horne-Bitschy, A.L.van Bueren, V.A.Money, D.N.Bolam, M.Czjzek, N.A.Ekborg, R.M.Weiner, S.W.Hutcheson, G.J.Davies, A.B.Boraston, H.J.Gilbert.

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.

Selected figure(s)

Figure 1.
FIGURE 1. The structure of agarobiose, the repeating unit of agarose.

Figure 2.
FIGURE 2. Schematic of the molecular architecture of Aga16B and Aga86E. Catalytic modules CBMs and signal peptides are depicted in light gray, white, and black boxes, respectively, while the black lines represent linker sequences.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 17099-17107) copyright 2006.

Figures were selected by an automated process.