2RFZ

Crystal structure of cellobiohydrolase from Melanocarpus albomyces complexed with cellotriose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of Melanocarpus albomyces cellobiohydrolase Cel7B in complex with cello-oligomers show high flexibility in the substrate binding

Parkkinen, T.Koivula, A.Rouvinen, J.

(2008) Protein Sci. 17: 1383-1394

  • DOI: 10.1110/ps.034488.108
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cellobiohydrolase from Melanocarpus albomyces (Cel7B) is a thermostable, single-module, cellulose-degrading enzyme. It has relatively low catalytic activity under normal temperatures, which allows structural studies of the binding of unmodified subst ...

    Cellobiohydrolase from Melanocarpus albomyces (Cel7B) is a thermostable, single-module, cellulose-degrading enzyme. It has relatively low catalytic activity under normal temperatures, which allows structural studies of the binding of unmodified substrates to the native enzyme. In this study, we have determined the crystal structure of native Ma Cel7B free and in complex with three different cello-oligomers: cellobiose (Glc(2)), cellotriose (Glc(3)), and cellotetraose (Glc(4)), at high resolution (1.6-2.1 A). In each case, four molecules were found in the asymmetric unit, which provided 12 different complex structures. The overall fold of the enzyme is characteristic of a glycoside hydrolase family 7 cellobiohydrolase, where the loops extending from the core beta-sandwich structure form a long tunnel composed of multiple subsites for the binding of the glycosyl units of a cellulose chain. The catalytic residues at the reducing end of the tunnel are conserved, and the mechanism is expected to be retaining similarly to the other family 7 members. The oligosaccharides in different complex structures occupied different subsite sets, which partly overlapped and ranged from -5 to +2. In four cellotriose and one cellotetraose complex structures, the cello-oligosaccharide also spanned over the cleavage site (-1/+1). There were surprisingly large variations in the amino acid side chain conformations and in the positions of glycosyl units in the different cello-oligomer complexes, particularly at subsites near the catalytic site. However, in each complex structure, all glycosyl residues were in the chair (4C(1)) conformation. Implications in relation to the complex structures with respect to the reaction mechanism are discussed.


    Organizational Affiliation

    Department of Chemistry, University of Joensuu, 80101 Joensuu, Finland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cellulose 1,4-beta-cellobiosidase
A, B, C, D
430Melanocarpus albomycesMutation(s): 1 
Gene Names: cel7B (gh7)
EC: 3.2.1.-
Find proteins for Q8J0K6 (Melanocarpus albomyces)
Go to UniProtKB:  Q8J0K6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CTR
Query on CTR

Download SDF File 
Download CCD File 
A, B, C, D
CELLOTRIOSE
Dextrin
C18 H32 O16
FYGDTMLNYKFZSV-RZDZXANRSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A, B, C, D
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.237 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 50.800α = 90.00
b = 94.370β = 90.19
c = 189.910γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
SHELXL-97refinement
PDB_EXTRACTdata extraction
XDSdata reduction
SHELXrefinement
MAR345dtbdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2018-08-01
    Type: Data collection, Structure summary
  • Version 1.3: 2018-08-15
    Type: Data collection, Source and taxonomy, Structure summary