PDBsum entry: 1w9t

Sugar-binding protein

PDB id: 1w9t

Contents

Protein chains

134 a.a. *

Ligands

XYP-XYP ×2

XYS-XYP-XYP ×2

Metals

_NA ×6

Waters ×372

* Residue conservation analysis

PDB id:

1w9t

Name:

Sugar-binding protein

Title:

Structure of a beta-1,3-glucan binding cbm6 from bacillus halodurans in complex with xylobiose

Structure:

Bh0236 protein. Chain: a, b. Fragment: cbm, residues 790-925. Synonym: bhcbm6. Engineered: yes

Source:

Bacillus halodurans. Organism_taxid: 86665. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

1.62Å R-factor: 0.121 R-free: 0.179

Authors:

A.B.Boraston,A.L.Van Bueren

Key ref:

A.L.van Bueren et al. (2005). Family 6 carbohydrate binding modules recognize the non-reducing end of beta-1,3-linked glucans by presenting a unique ligand binding surface. J Biol Chem, 280, 530-537. PubMed id: 15501830 DOI: 10.1074/jbc.M410113200

Date:

18-Oct-04 Release date: 03-Nov-04

Protein chains

Q9KG76  (Q9KG76_BACHD) -  BH0236 protein

Seq: 1020 a.a.

Struc: 134 a.a.

 Gene Ontology (GO) functional annotation 

• Biochemical function: carbohydrate binding (1 term)

DOI no: 10.1074/jbc.M410113200

J Biol Chem 280:530-537 (2005)

PubMed id: 15501830

Family 6 carbohydrate binding modules recognize the non-reducing end of beta-1,3-linked glucans by presenting a unique ligand binding surface.

A.L.van Bueren, C.Morland, H.J.Gilbert, A.B.Boraston.

ABSTRACT

Enzymes that hydrolyze insoluble complex polysaccharide structures contain non-catalytic carbohydrate binding modules (CBMS) that play a pivotal role in the action of these enzymes against recalcitrant substrates. Family 6 CBMs (CBM6s) are distinct from other CBM families in that these protein modules contain multiple distinct ligand binding sites, a feature that makes CBM6s particularly appropriate receptors for the beta-1,3-glucan laminarin, which displays an extended U-shaped conformation. To investigate the mechanism by which family 6 CBMs recognize laminarin, we report the biochemical and structural properties of a CBM6 (designated BhCBM6) that is located in an enzyme, which is shown, in this work, to display beta-1,3-glucanase activity. BhCBM6 binds beta-1,3-glucooligosaccharides with affinities of approximately 1 x 10(5) m(-1). The x-ray crystal structure of this CBM in complex with laminarihexaose reveals similarity with the structures of other CBM6s but a unique binding mode. The binding cleft in this protein is sealed at one end, which prevents binding of linear polysaccharides such as cellulose, and the orientation of the sugar at this site prevents glycone extension of the ligand and thus conferring specificity for the non-reducing ends of glycans. The high affinity for extended beta-1,3-glucooligosaccharides is conferred by interactions with the surface of the protein located between the two binding sites common to CBM6s and thus reveals a third ligand binding site in family 6 CBMs. This study therefore demonstrates how the multiple binding clefts and highly unusual protein surface of family 6 CBMs confers the extensive range of specificities displayed by this protein family. This is in sharp contrast to other families of CBMs where variation in specificity between different members reflects differences in the topology of a single binding site.

Selected figure(s)

Figure 4.
FIG. 4. Observed electron density for xylobiose (A) and laminarihexaose (B) bound to BhCBM6. All maps are maximum-likelihood (25)/ [A] (38) weighted 2F[obs] - F[calc] electron density maps contoured at 1 (0.40 and 0.13 electrons/Å3 for xylobiose and laminarihexaose, respectively). Asn132, Trp42, and Trp99 are shown in a licorice representation. The red sphere and its electron density indicate the water molecule at the base of the binding cleft that is conserved among CBM6s.

Figure 5.
FIG. 5. A schematic showing the interactions of BhCBM6 with xylobiose (A) and laminarihexaose (B). Binding subsites referred to in the text are shown above the schematics with brackets and are numbered in accordance with IUPAC nomenclature. The water molecule conserved in the cleft A binding site of CBM6s is indicated with an arrow.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 530-537) copyright 2005.

Figures were selected by an automated process.