PDBsum entry: 1uxx

Carbohydrate binding module

PDB-id: 1uxx

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Description

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References

PROCHECK

Protein chain

125 a.a. *

Ligands

XYP-XYP-XYP-XYP-XYP

Metal ions

_CA

Waters ×108

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

1uxx

Name:

Carbohydrate binding module

Title:

Cbm6ct from clostridium thermocellum in complex with xylopentaose

Structure:

Xylanase u. Chain: x. Fragment: carbohydrate binding module, residues 248-380. Synonym: endo-1,4-beta-xylanase. Engineered: yes

Source:

Clostridium thermocellum. Organism_taxid: 1515. Expressed in: escherichia coli. Expression_system_taxid: 562

UniProt:

O52780 (O52780_CLOTM)

Seq:

Struc:

Seq:

Struc:

Seq:

683 a.a.

Struc:

125 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Resolution:

1.6Å

R-factor:

0.182

R-free:

0.222

Authors:

M.Czjzek,V.M.R.Pires,J.Henshaw,J.A.M.Prates,D.B.B.Henrissat, H.J.Gilbert

Key ref:

V.M.Pires et al. (2004). The crystal structure of the family 6 carbohydrate binding module from Cellvibrio mixtus endoglucanase 5a in complex with oligosaccharides reveals two distinct binding sites with different ligand specificities.. J Biol Chem, 279, 21560-21568. [PubMed id: 15010454] [DOI: 10.1074/jbc.M401599200]

Date:

01-Mar-04

Release date:

11-Mar-04

Related entries:

1gmm carbohydrate binding module cbm6 from xylanase u clostridium thermocellum

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Clefts

Surface

Key reference

DOI no: 10.1074/jbc.M401599200

J Biol Chem 279:21560-21568 (2004)

PubMed id: 15010454

The crystal structure of the family 6 carbohydrate binding module from Cellvibrio mixtus endoglucanase 5a in complex with oligosaccharides reveals two distinct binding sites with different ligand specificities.

V.M.Pires, J.L.Henshaw, J.A.Prates, D.N.Bolam, L.M.Ferreira, C.M.Fontes, B.Henrissat, A.Planas, H.J.Gilbert, M.Czjzek.

ABSTRACT

Glycoside hydrolases that release fixed carbon from the plant cell wall are of considerable biological and industrial importance. These hydrolases contain non-catalytic carbohydrate binding modules (CBMs) that, by bringing the appended catalytic domain into intimate association with its insoluble substrate, greatly potentiate catalysis. Family 6 CBMs (CBM6) are highly unusual because they contain two distinct clefts (cleft A and cleft B) that potentially can function as binding sites. Henshaw et al. (Henshaw, J., Bolam, D. N., Pires, V. M. R., Czjzek, M., Henrissat, B., Ferreira, L. M. A., Fontes, C. M. G. A., and Gilbert, H. J. (2003) J. Biol. Chem. 279, 21552-21559) show that CmCBM6 contains two binding sites that display both similarities and differences in their ligand specificity. Here we report the crystal structure of CmCBM6 in complex with a variety of ligands that reveals the structural basis for the ligand specificity displayed by this protein. In cleft A the two faces of the terminal sugars of beta-linked oligosaccharides stack against Trp-92 and Tyr-33, whereas the rest of the binding cleft is blocked by Glu-20 and Thr-23, residues that are not present in CBM6 proteins that bind to the internal regions of polysaccharides in cleft A. Cleft B is solvent-exposed and, therefore, able to bind ligands because the loop, which occludes this region in other CBM6 proteins, is much shorter and flexible (lacks a conserved proline) in CmCBM6. Subsites 2 and 3 of cleft B accommodate cellobiose (Glc-beta-1,4-Glc), subsite 4 will bind only to a beta-1,3-linked glucose, whereas subsite 1 can interact with either a beta-1,3- or beta-1,4-linked glucose. These different specificities of the subsites explain how cleft B can accommodate beta-1,4-beta-1,3- or beta-1,3-beta-1,4-linked gluco-configured ligands.

Selected figure(s)

Figure 3.
FIG. 3. A, observed electron density map for xylopentaose bound in cleft A of CtCBM6. The map is a maximum-likelihood/ [A]-weighted 2 F[obs]-F[calc] electron density map contoured at a 1 level, corresponding to 1.6 e Å-3. B, the xylopentaose bound to CtCBM6, represented as sticks. The residues interacting with the ligand are highlighted. C, schematic representation of the protein/ligand hydrogen bonds and stacking interactions within the five binding subsites.

Figure 7.
FIG. 7. Ribbon representation of mixed -1,3-1,4-linked glucan tetrasaccharides bound to CmCBM6-2. A, the tetrasaccharide Glc-4Glc-3Glc-4Glc-OMe is bound to two neighboring CmCBM6-2 molecules. The glucose unit at the reducing end is bound to cleft A of one molecule (Mol A), whereas the following glucose units are bound to a second CmCBM6-2 molecule (Mol B). B, the tetrasaccharide Glc-3Glc-4Glc-3Glc is bound to subsites 4, 3, 2, and 1 of binding cleft B. Residues important for binding are highlighted.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 21560-21568) copyright 2004.

Figures were selected by the author.