3A9B

CcCel6C, a glycoside hydrolase family 6 enzyme, complexed with cellobiose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of a glycoside hydrolase family 6 enzyme, CcCel6C, a cellulase constitutively produced by Coprinopsis cinerea

Liu, Y.Yoshida, M.Kurakata, Y.Miyazaki, T.Igarashi, K.Samejima, M.Fukuda, K.Nishikawa, A.Tonozuka, T.

(2010) Febs J. 277: 1532-1542

  • DOI: 10.1111/j.1742-4658.2010.07582.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The basidiomycete Coprinopsis cinerea produces the glycoside hydrolase family 6 enzyme CcCel6C at low and constitutive levels. CcCel6C exhibits unusual cellobiohydrolase activity; it hydrolyses carboxymethyl cellulose, which is a poor substrate for t ...

    The basidiomycete Coprinopsis cinerea produces the glycoside hydrolase family 6 enzyme CcCel6C at low and constitutive levels. CcCel6C exhibits unusual cellobiohydrolase activity; it hydrolyses carboxymethyl cellulose, which is a poor substrate for typical cellobiohydrolases. Here, we determined the crystal structures of CcCel6C unbound and in complex with p-nitrophenyl beta-D-cellotrioside and cellobiose. CcCel6C consists of a distorted seven-stranded beta/alpha barrel and has an enclosed tunnel, which is observed in other cellobiohydrolases from ascomecetes Hypocrea jecorina (HjeCel6A) and Humicola insolens (HinCel6A). In HjeCel6A and HinCel6A, ligand binding produces a conformational change that narrows this tunnel. In contrast, the tunnel remains wide in CcCel6C and the conformational change appears to be less favourable than in HjeCel6A and HinCel6A. The ligand binding cleft for subsite -3 of CcCel6C is also wide and is rather similar to that of endoglucanase. These results suggest that the open tunnel and the wide cleft are suitable for the hydrolysis of carboxymethyl cellulose.


    Related Citations: 
    • Heterologous expression, crystallization and preliminary X-ray characterization of CcCel6C, a glycoside hydrolase family 6 enzyme from the basidiomycete Coprinopsis cinerea
      Kurakata, Y.,Tonozuka, T.,Liu, Y.,Kaneko, S.,Nishikawa, A.,Fukuda, K.,Yoshida, M.
      (2009) Acta Crystallogr.,Sect.F 65: 140


    Organizational Affiliation

    Department of Environmental and Natural Resource Science, Tokyo University of Agriculture and Technology, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cellobiohydrolase
A
395Coprinopsis cinereaMutation(s): 0 
Gene Names: CcCel6C
EC: 3.2.1.-
Find proteins for B7X9Z2 (Coprinopsis cinerea)
Go to UniProtKB:  B7X9Z2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CBI
Query on CBI

Download SDF File 
Download CCD File 
A
CELLOBIOSE
C12 H22 O11
GUBGYTABKSRVRQ-QRZGKKJRSA-N
 Ligand Interaction
BGC
Query on BGC

Download SDF File 
Download CCD File 
A
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.148 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 44.168α = 77.57
b = 45.395β = 86.91
c = 49.128γ = 68.60
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
MOLREPphasing
HKL-2000data scaling
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance