3b' carbohydrate-binding module from the Cel9V glycoside hydrolase from Clostridium thermocellum. Orthorhombic structure

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.163 

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Structure of a Family 3B' Carbohydrate-Binding Module from the Cel9V Glycoside Hydrolase from Clostridium Thermocellum: Structural Diversity and Implications for Carbohydrate Binding

Petkun, S.Jindou, S.Shimon, L.J.W.Bayer, E.A.Lamed, R.Frolow, F.

(2010) Acta Crystallogr D Biol Crystallogr 66: 33

  • DOI: https://doi.org/10.1107/S0907444909043030
  • Primary Citation of Related Structures:  
    2WNX, 2WO4, 2WOB

  • PubMed Abstract: 

    Family 3 carbohydrate-binding modules (CBM3s) are associated with both cellulosomal scaffoldins and family 9 glycoside hydrolases (GH9s), which are multi-modular enzymes that act on cellulosic substrates. CBM3s bind cellulose. X-ray crystal structures of these modules have established an accepted cellulose-binding mechanism based on stacking interactions between the sugar rings of cellulose and a planar array of aromatic residues located on the CBM3 surface. These planar-strip residues are generally highly conserved, although some CBM3 sequences lack one or more of these residues. In particular, CBM3b' from Clostridium thermocellum Cel9V exhibits such sequence changes and fails to bind cellulosic substrates. A crystallographic investigation of CBM3b' has been initiated in order to understand the structural reason(s) for this inability. CBM3b' crystallized in space group C222(1) (diffraction was obtained to 2.0 A resolution in-house) with three independent molecules in the asymmetric unit and in space group P4(1)2(1)2 (diffraction was obtained to 1.79 A resolution in-house and to 1.30 A resolution at a synchrotron) with one molecule in the asymmetric unit. The molecular structure of Cel9V CBM3b' revealed that in addition to the loss of several cellulose-binding residues in the planar strip, changes in the backbone create a surface 'hump' which could interfere with the formation of cellulose-protein surface interactions and thus prevent binding to crystalline cellulose.

  • Organizational Affiliation

    Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
B [auth C],
C [auth E]
170Acetivibrio thermocellusMutation(s): 0 
Find proteins for A3DJ30 (Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372))
Explore A3DJ30 
Go to UniProtKB:  A3DJ30
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3DJ30
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.163 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.029α = 90
b = 86.611β = 90
c = 242.37γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2013-01-30
    Changes: Database references
  • Version 1.3: 2017-07-05
    Changes: Data collection
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description