1GMM

Carbohydrate binding module CBM6 from xylanase U Clostridium thermocellum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The Location of the Ligand-Binding Site of Carbohydrate-Binding Modules that Have Evolved from a Common Sequence is not Conserved.

Czjzek, M.Bolam, D.Mosbah, A.Allouch, J.Fontes, C.M.Ferreira, L.M.Bornet, O.Zamboni, V.Darbon, H.Smith, N.L.Black, G.W.Henrissat, B.Gilbert, H.J.

(2001) J Biol Chem 276: 48580

  • DOI: https://doi.org/10.1074/jbc.M109142200
  • Primary Citation of Related Structures:  
    1GMM

  • PubMed Abstract: 

    Polysaccharide-degrading enzymes are generally modular proteins that contain non-catalytic carbohydrate-binding modules (CBMs), which potentiate the activity of the catalytic module. CBMs have been grouped into sequence-based families, and three-dimensional structural data are available for half of these families. Clostridium thermocellum xylanase 11A is a modular enzyme that contains a CBM from family 6 (CBM6), for which no structural data are available. We have determined the crystal structure of this module to a resolution of 2.1 A. The protein is a beta-sandwich that contains two potential ligand-binding clefts designated cleft A and B. The CBM interacts primarily with xylan, and NMR spectroscopy coupled with site-directed mutagenesis identified cleft A, containing Trp-92, Tyr-34, and Asn-120, as the ligand-binding site. The overall fold of CBM6 is similar to proteins in CBM families 4 and 22, although surprisingly the ligand-binding site in CBM4 and CBM22 is equivalent to cleft B in CBM6. These structural data define a superfamily of CBMs, comprising CBM4, CBM6, and CBM22, and demonstrate that, although CBMs have evolved from a relatively small number of ancestors, the structural elements involved in ligand recognition have been assembled at different locations on the ancestral scaffold.


  • Organizational Affiliation

    Laboratoire d'Architecture et de Fonction des Macromolécules Biologiques, IBSM, CNRS Marseille and University Aix-Marseille I & II, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France. czjzek@afmb.cnrs-mrs.fr


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CBM6133Acetivibrio thermocellusMutation(s): 0 
EC: 3.2.1.8
UniProt
Find proteins for O52780 (Acetivibrio thermocellus)
Explore O52780 
Go to UniProtKB:  O52780
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO52780
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.65α = 90
b = 59.65β = 90
c = 157.45γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
SHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-11-28
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other