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: 46.30 kDa 
• Atom Count: 3549 
• Residue Count: 420 
• Unique protein chains: 1

4AVN

Thermobifida fusca cellobiohydrolase Cel6B catalytic mutant D226A- S232A cocrystallized with cellobiose

• DOI: 10.2210/pdb4AVN/pdb

• Classification: HYDROLASE
• Organism(s): Thermobifida fusca YX
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-05-28 Released: 2013-06-12 
• Deposition Author(s): Wu, M., Vuong, T.V., Wilson, D.B., Sandgren, M., Stahlberg, J., Hansson, H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.198 
• R-Value Work: 0.154 
• R-Value Observed: 0.157 

Literature

Loop Motions Important to Product Expulsion in the Thermobifida Fusca Glycoside Hydrolase Family 6 Cellobiohydrolase from Structural and Computational Studies.

Wu, M., Bu, L., Vuong, T.V., Wilson, D.B., Crowley, M.F., Sandgren, M., Stahlberg, J., Beckham, G.T., Hansson, H.

(2013) J Biol Chem 288: 33107

• PubMed: 24085303 
• DOI: 10.1074/jbc.M113.502765
• Primary Citation of Related Structures:  
  4AVN, 4AVO


• PubMed Abstract: 
  

Cellobiohydrolases (CBHs) are typically major components of natural enzyme cocktails for biomass degradation. Their active sites are enclosed in a tunnel, enabling processive hydrolysis of cellulose chains. Glycoside hydrolase Family 6 (GH6) CBHs act from nonreducing ends by an inverting mechanism and are present in many cellulolytic fungi and bacteria. The bacterial Thermobifida fusca Cel6B (TfuCel6B) exhibits a longer and more enclosed active site tunnel than its fungal counterparts. Here, we determine the structures of two TfuCel6B mutants co-crystallized with cellobiose, D274A (catalytic acid), and the double mutant D226A/S232A, which targets the putative catalytic base and a conserved serine that binds the nucleophilic water. The ligand binding and the structure of the active site are retained when compared with the wild type structure, supporting the hypothesis that these residues are directly involved in catalysis. One structure exhibits crystallographic waters that enable construction of a model of the α-anomer product after hydrolysis. Interestingly, the product sites of TfuCel6B are completely enclosed by an "exit loop" not present in fungal GH6 CBHs and by an extended "bottom loop". From the structures, we hypothesize that either of the loops enclosing the product subsites in the TfuCel6B active site tunnel must open substantially for product release. With simulation, we demonstrate that both loops can readily open to allow product release with equal probability in solution or when the enzyme is engaged on cellulose. Overall, this study reveals new structural details of GH6 CBHs likely important for functional differences among enzymes from this important family.

---

Organizational Affiliation: 

From the Department of Molecular Biology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CELLOBIOHYDROLASE. GLYCOSYL HYDROLASE FAMILY 6	A	420	Thermobifida fusca YX	Mutation(s): 2  Gene Names: Tfu_0620 EC: 3.2.1.91 (PDB Primary Data), 3.2.1 (UniProt)
Find proteins for Q47SA9 (Thermobifida fusca (strain YX)) Explore Q47SA9  Go to UniProtKB:  Q47SA9

Oligosaccharides

Help

Entity ID: 2
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	B	4		N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC	A	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.198 
• R-Value Work: 0.154 
• R-Value Observed: 0.157 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.52	α = 90
b = 92.08	β = 111.85
c = 49.78	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-05-28 
• Released Date: 2013-06-12 
Deposition Author(s): Wu, M., Vuong, T.V., Wilson, D.B., Sandgren, M., Stahlberg, J., Hansson, H.

Revision History 

• Version 1.0: 2013-06-12
  Type: Initial release
  
• Version 1.1: 2013-10-16
  Changes: Database references
• Version 1.2: 2013-11-27
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary