4B4H

Thermobifida fusca cellobiohydrolase Cel6B(E3) catalytic domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Structure of a Bacterial Cellobiohydrolase: The Catalytic Core of the Thermobifida Fusca Family Gh6 Cellobiohydrolase Cel6B.

Sandgren, M.Wu, M.Karkehabadi, S.Mitchinson, C.Kelemen, B.R.Larenas, E.A.Stahlberg, J.Hansson, H.

(2013) J Mol Biol 425: 622

  • DOI: 10.1016/j.jmb.2012.11.039
  • Primary Citation of Related Structures:  
    4B4F, 4B4H

  • PubMed Abstract: 
  • Cellulases, glycoside hydrolases that catalyze the degradation of cellulose, are classified as either endoglucanases or cellobiohydrolases (CBHs) based on their architecture and mode of action on the cellulose. CBHs bind the cellulose chain in a more or less closed tunnel and cleave off cellobiose units processively from one end of the cellulosic polymer, while endoglucanases have their active sites in a more or less open cleft and show a higher tendency to cut bonds internally in the polymer ...

    Cellulases, glycoside hydrolases that catalyze the degradation of cellulose, are classified as either endoglucanases or cellobiohydrolases (CBHs) based on their architecture and mode of action on the cellulose. CBHs bind the cellulose chain in a more or less closed tunnel and cleave off cellobiose units processively from one end of the cellulosic polymer, while endoglucanases have their active sites in a more or less open cleft and show a higher tendency to cut bonds internally in the polymer. The CBH Cel6A (also called CBH2) from the ascomycete Hypocrea jecorina has a much shorter substrate-binding tunnel and seems less processive than the CBH Cel7A (CBH1), from the same fungus. Here, we present the X-ray crystal structure of the catalytic domain of the CBH Cel6B, also called E3, from the soil bacterium Thermobifida fusca, both in its apo form and co-crystallized with cellobiose. The enzyme structure reveals that the Cel6B enzyme has a much longer substrate-binding site than its fungal GH6 counterparts. The tunnel is comparable in length to that of GH7 CBHs. In the ligand structure with cellobiose, the tunnel exit is completely closed by a 13-residue loop not present in fungal GH6 enzymes. The loop needs to be displaced to allow cellobiose product release for a processive action by the enzyme. When ligand is absent, seven of these residues are not visible in the electron density and the tunnel exit is open.


    Organizational Affiliation

    Department of Molecular Biology, Swedish University of Agricultural Sciences, Biomedical Centre, PO Box 590, S-751 24 Uppsala, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BETA-1,4-EXOCELLULASEA, B420Thermobifida fuscaMutation(s): 0 
Gene Names: E3
EC: 3.2.1.91 (PDB Primary Data), 3.2.1 (UniProt)
UniProt
Find proteins for Q60029 (Thermobifida fusca)
Explore Q60029 
Go to UniProtKB:  Q60029
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ60029
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.75α = 90
b = 93.35β = 90.02
c = 96.59γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-19
    Type: Initial release
  • Version 1.1: 2013-01-30
    Changes: Database references
  • Version 1.2: 2013-02-27
    Changes: Database references