PDBsum entry 1uy1

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Carbohydrate-binding module PDB id
Protein chain
132 a.a. *
GOL ×2
Waters ×154
* Residue conservation analysis
PDB id:
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.
1.8Å     R-factor:   0.140     R-free:   0.178
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
01-Mar-04     Release date:   18-Jun-04    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q8GJ44  (XYNA1_CLOSR) -  Endo-1,4-beta-xylanase A
651 a.a.
132 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     carbohydrate binding     1 term  


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.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20594934 E.Fadda, and R.J.Woods (2010).
Molecular simulations of carbohydrates and protein-carbohydrate interactions: motivation, issues and prospects.
  Drug Discov Today, 15, 596-609.  
18292090 K.J.Gregg, R.Finn, D.W.Abbott, and A.B.Boraston (2008).
Divergent modes of glycan recognition by a new family of carbohydrate-binding modules.
  J Biol Chem, 283, 12604-12613.
PDB codes: 2vmg 2vmh 2vmi 2vng 2vno 2vnr
16230347 A.B.Boraston, M.Healey, J.Klassen, E.Ficko-Blean, A.Lammerts van Bueren, and V.Law (2006).
A structural and functional analysis of alpha-glucan recognition by family 25 and 26 carbohydrate-binding modules reveals a conserved mode of starch recognition.
  J Biol Chem, 281, 587-598.
PDB codes: 2c3g 2c3h 2c3v 2c3w 2c3x
16990278 E.Ficko-Blean, and A.B.Boraston (2006).
The interaction of a carbohydrate-binding module from a Clostridium perfringens N-acetyl-beta-hexosaminidase with its carbohydrate receptor.
  J Biol Chem, 281, 37748-37757.
PDB codes: 2j1a 2j1e 2j1f 2j7m
15501830 A.L.van Bueren, C.Morland, H.J.Gilbert, and A.B.Boraston (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.
PDB codes: 1w9s 1w9t 1w9w
15866877 H.Ichinose, M.Yoshida, T.Kotake, A.Kuno, K.Igarashi, Y.Tsumuraya, M.Samejima, J.Hirabayashi, H.Kobayashi, and S.Kaneko (2005).
An exo-beta-1,3-galactanase having a novel beta-1,3-galactan-binding module from Phanerochaete chrysosporium.
  J Biol Chem, 280, 25820-25829.  
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