Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.33 kDa 
• Atom Count: 3215 
• Residue Count: 360 
• Unique protein chains: 1

4A05

Structure of the catalytic core domain of the cellobiohydrolase, Cel6A, from Chaetomium thermophilum

• DOI: 10.2210/pdb4A05/pdb

• Classification: HYDROLASE
• Organism(s): Chaetomium thermophilum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-09-08 Released: 2012-07-25 
• Deposition Author(s): Thompson, A.J., Wilson, K.S., Davies, G.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.197 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 

Literature

Structure of the Catalytic Core Module of the Chaetomium Thermophilum Family Gh6 Cellobiohydrolase Cel6A.

Thompson, A.J., Heu, T., Shaghasi, T., Benyamino, R., Jones, A., Friis, E.P., Wilson, K.S., Davies, G.J.

(2012) Acta Crystallogr D Biol Crystallogr 68: 875

• PubMed: 22868752 
• DOI: 10.1107/S0907444912016496
• Primary Citation of Related Structures:  
  4A05


• PubMed Abstract: 
  

Cellulases, including cellobiohydrolases and endoglucanases, are important enzymes involved in the breakdown of the polysaccharide cellulose. These catalysts have found widescale industrial applications, particularly in the paper and textile industries, and are now finding use in `second-generation' conversion of biomass to biofuels. Despite this considerable biotechnological application, and undoubted future potential, uncertainty remains as to the exact reaction mechanism of the inverting cellulases found in the GH6 family of carbohydrate-active enzymes. In order to gain additional understanding as to how these societally beneficial biocatalysts function, the crystal structure of a GH6 cellobiohydrolase from Chaetomium thermophilum, CtCel6A, has been solved. This structure reveals a distorted α/β-barrel fold comprising a buried tunnel-like active site quite typical of Cel6A enzymes. Analysis of an enzyme-product complex (cellobiose in the -3 and -2 subsites and cellotetraose in subsites +1 to +4) supports the hypothesis that this group of enzymes act via an atypical single-displacement mechanism. Of particular note in this analysis is an active-centre metal ion, Li(+), the position of which matches the position of the positively charged anomeric carbon of the oxocarbenium-ion-like transition state.

---

Organizational Affiliation: 

Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CELLOBIOHYDROLASE FAMILY 6	A	364	Chaetomium thermophilum	Mutation(s): 0  EC: 3.2.1.91 (PDB Primary Data), 3.2.1 (UniProt)
Find proteins for G0SD43 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0SD43  Go to UniProtKB:  G0SD43

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	C	2		N/A

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	D	4		N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LI	A	LITHIUM ION Li HBBGRARXTFLTSG-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 2 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900005	C	beta-cellobiose	Oligosaccharide /  Metabolism		--

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900011	D	beta-cellotetraose	Oligosaccharide /  Metabolism		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.197 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.71	α = 90
b = 76.06	β = 90
c = 107.24	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-09-08 
• Released Date: 2012-07-25 
Deposition Author(s): Thompson, A.J., Wilson, K.S., Davies, G.J.

Revision History 

• Version 1.0: 2012-07-25
  Type: Initial release
  
• Version 1.1: 2012-08-01
  Changes: Structure summary
• Version 1.2: 2012-08-15
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary