2WOB

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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.,Sect.D 66: 33

  • DOI: 10.1107/S0907444909043030
  • Primary Citation of Related Structures:  

  • 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 structure ...

    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.


    Related Citations: 
    • Novel Architecture of Family-9 Glycoside Hydrolases Identified in Cellulosomal Enzymes of Acetivibrio Cellulolyticus and Clostridium Thermocellum.
      Jindou, S.,Xu, Q.,Kenig, R.,Shulman, M.,Shoham, Y.,Bayer, E.A.,Lamed, R.
      (2006) Fems Microbiol.Lett. 254: 308


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLYCOSIDE HYDROLASE, FAMILY 9
A, C, E
170Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)Mutation(s): 0 
Find proteins for A3DJ30 (Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372))
Go to UniProtKB:  A3DJ30
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, C, E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.160 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 57.029α = 90.00
b = 86.611β = 90.00
c = 242.370γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2013-01-30
    Type: Database references
  • Version 1.3: 2017-07-05
    Type: Data collection