PDBsum entry: 1uy2

Carbohydrate-binding module

PDB-id: 1uy2

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Description

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References

PROCHECK

Protein chain

131 a.a. *

Ligands

XYP-XYP

GOL

Metal ions

_NA

_CA

Waters ×159

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

1uy2

Name:

Carbohydrate-binding module

Title:

Binding sub-site dissection of a family 6 carbohydrate-binding module by x-ray crystallography and isothermal titration calorimetry

Structure:

Endo-1,4-beta-xylanase a. Chain: a. Fragment: carbohydrate-binding module, residues 1-139. Synonym: cscbm6-1,1,4-beta-d-xylan xylanohydrolase a. Engineered: yes

Source:

Clostridium stercorarium. Organism_taxid: 1510. Strain: ncib 11745. Expressed in: escherichia coli. Expression_system_taxid: 469008.

UniProt:

Q8GJ44 (XYNA1_CLOSR)

Seq:

Struc:

Seq:

Struc:

Seq:

651 a.a.

Struc:

131 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme class:

E.C.3.2.1.8   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Endohydrolysis of 1,4-beta-D-xylosidic linkages in xylans.

Resolution:

1.7Å

R-factor:

0.149

R-free:

0.189

Authors:

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

Key ref:

A.Lammerts van Bueren and A.B.Boraston (2004). Binding sub-site dissection of a carbohydrate-binding module reveals the contribution of entropy to oligosaccharide recognition at "non-primary" binding subsites.. J Mol Biol, 340, 869-879. [PubMed id: 15223327] [DOI: 10.1016/j.jmb.2004.05.038]

Date:

01-Mar-04

Release date:

18-Jun-04

Related entries:

1nae structure of cscbm6-3 from clostridium stercorarium incomplex with xylotriose
1od3 structure of cbm6-3 in complex with laminaribiose
1uy1 structure of carbohydrate-binding module laminaribiose
1uy3 structure of carbohydrate-binding module laminaribiose
1uy4 structure of carbohydrate-binding module laminaribiose

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Key reference

DOI no: 10.1016/j.jmb.2004.05.038

J Mol Biol 340:869-879 (2004)

PubMed id: 15223327

Binding sub-site dissection of a carbohydrate-binding module reveals the contribution of entropy to oligosaccharide recognition at "non-primary" binding subsites.

A.Lammerts van Bueren, A.B.Boraston.

ABSTRACT

The optimal ligands for many carbohydrate-binding proteins are often oligosaccharides comprising two, three, or more monosaccharide units. The binding affinity for these sugars is increased incrementally by contributions from binding subsites on the protein that accommodate the individual monosaccharide residues of the oligosaccharide. Here, we use CsCBM6-1, a xylan-specific type B carbohydrate-binding module (CBM) from Clostridium stercorarium falling into amino acid sequence family CBM6, as a model system to investigate the structural and thermodynamic contributions of binding subsites in this protein to carbohydrate recognition. The three-dimensional structures of uncomplexed CsCBM6-1 (at 1.8 A resolution) and bound to the oligosaccharides xylobiose, xylotriose, and xylotetraose (at 1.70 A, 1.89 A, and 1.69 A resolution, respectively) revealed the sequential occupation of four subsites within the binding site in the order of subsites 2, 3, 4 then 1. Overall, binding to all of the xylooligosaccharides tested was enthalpically favourable and entropically unfavourable, like most protein-carbohydrate interactions, with the primary subsites 2 and 3 providing the bulk of the free energy and enthalpy of binding. In contrast, the contributions to the changes in entropy of the non-primary subsites 1 and 4 to xylotriose and xylotetraose binding, respectively, were positive. This observation is remarkable, in that it shows that the 10-20-fold improvement in association constants for oligosaccharides longer than a disaccharide is facilitated by favourable entropic contributions from the non-primary binding subsites.