1E5C

Internal xylan binding domain from C. fimi Xyn10A, R262G mutant


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 
  • Selection Criteria: 5 REPRESENTATIVE STRUCTURES CHOSEN FROM 33 LOW ENERGY STRUCTURES 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

The Structural Basis for the Ligand Specificity of Family 2 Carbohydrate Binding Nodules

Simpson, P.J.Hefang, X.Bolam, D.N.Gilbert, H.J.Williamson, M.P.

(2000) J.Biol.Chem. 275: 41137

  • DOI: 10.1074/jbc.M006948200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The interactions of proteins with polysaccharides play a key role in the microbial hydrolysis of cellulose and xylan, the most abundant organic molecules in the biosphere, and are thus pivotal to the recycling of photosynthetically fixed carbon. Enzy ...

    The interactions of proteins with polysaccharides play a key role in the microbial hydrolysis of cellulose and xylan, the most abundant organic molecules in the biosphere, and are thus pivotal to the recycling of photosynthetically fixed carbon. Enzymes that attack these recalcitrant polymers have a modular structure comprising catalytic modules and non-catalytic carbohydrate-binding modules (CBMs). The largest prokaryotic CBM family, CBM2, contains members that bind cellulose (CBM2a) and xylan (CBM2b), respectively. A possible explanation for the different ligand specificity of CBM2b is that one of the surface tryptophans involved in the protein-carbohydrate interaction is rotated by 90 degrees compared with its position in CBM2a (thus matching the structure of the binding site to the helical secondary structure of xylan), which may be promoted by a single amino acid difference between the two families. Here we show that by mutation of this single residue (Arg-262-->Gly), a CBM2b xylan-binding module completely loses its affinity for xylan and becomes a cellulose-binding module. The structural effect of the mutation has been revealed using NMR spectroscopy, which confirms that Trp-259 rotates 90 degrees to lie flat against the protein surface. Except for this one residue, the mutation only results in minor changes to the structure. The mutated protein interacts with cellulose using the same residues that the wild-type CBM2b uses to interact with xylan, suggesting that the recognition is of the secondary structure of the polysaccharide rather than any specific recognition of the absence or presence of functional groups.


    Organizational Affiliation

    Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Sheffield S10 2TN, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
XYLANASE D
A
87Cellulomonas fimiMutation(s): 1 
Gene Names: xynD
Find proteins for P54865 (Cellulomonas fimi)
Go to UniProtKB:  P54865
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 
  • Selection Criteria: 5 REPRESENTATIVE STRUCTURES CHOSEN FROM 33 LOW ENERGY STRUCTURES 
  • Olderado: 1E5C Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-05-25
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-06-14
    Type: Structure summary
  • Version 1.4: 2018-10-24
    Type: Data collection, Source and taxonomy