Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | 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: 75.44 kDa 
• Atom Count: 6750 
• Modelled Residue Count: 636 
• Deposited Residue Count: 642 
• Unique protein chains: 1

4JJJ

The structure of T. fusca GH48 D224N mutant

• PDB DOI: 10.2210/pdb4JJJ/pdb

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


• Deposited: 2013-03-07 Released: 2014-07-30 
• Deposition Author(s): Alahuhta, P.M., Lunin, V.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.164 
• R-Value Work: 0.121 
• R-Value Observed: 0.124 

Literature

Cel48A from Thermobifida fusca: structure and site directed mutagenesis of key residues.

Kostylev, M., Alahuhta, M., Chen, M., Brunecky, R., Himmel, M.E., Lunin, V.V., Brady, J., Wilson, D.B.

(2014) Biotechnol Bioeng 111: 664-673

• PubMed: 24264519 
• DOI: 10.1002/bit.25139
• Primary Citation of Related Structures:  
  4JJJ


• PubMed Abstract: 
  

Lignocellulosic biomass is a potential source of sustainable transportation fuels, but efficient enzymatic saccharification of cellulose is a key challenge in its utilization. Cellulases from the glycoside hydrolase (GH) family 48 constitute an important component of bacterial biomass degrading systems and structures of three enzymes from this family have been previously published. We report a new crystal structure of TfCel48A, a reducing end directed exocellulase from Thermobifida fusca, which shows that this enzyme shares important structural features with the other members of the GH48 family. The active site tunnel entrance of the known GH48 exocellulases is enriched in aromatic residues, which are known to interact well with anhydroglucose units of cellulose. We carried out site-directed mutagenesis studies of these aromatic residues (Y97, F195, Y213, and W313) along with two non-aromatic residues (N212 and S311) also located around the tunnel entrance and a W315 residue inside the active site tunnel. Only the aromatic residues located around the tunnel entrance appear to be important for the ability of TfCel48A to access individual cellulose chains on bacterial cellulose (BC), a crystalline substrate. Both Trp residues were found to be important for the processivity of TfCel48A on BC and phosphoric acid swollen cellulose (PASC), but only W313 appears to play a role in the ability of the enzyme to access individual cellulose chains in BC. When acting on BC, reduced processivity was found to correlate with reduced enzyme activity. The reverse, however, is true when PASC is the substrate. Presumably, higher density of available cellulose chain ends and the amorphous nature of PASC explain the increased initial activity of mutants with lower processivity.

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Organizational Affiliation: 

Department of Molecular Biology and Genetics, Cornell University, 458 Biotechnology Building, Ithaca, New York, 14853. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellulose 1,4-beta-cellobiosidase	A	642	Thermobifida fusca	Mutation(s): 1  Gene Names: Tfu_1959 EC: 3.2.1.91
UniProt
Find proteins for Q47NH7 (Thermobifida fusca (strain YX)) Explore Q47NH7  Go to UniProtKB:  Q47NH7

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G84824ZO GlyCosmos:  G84824ZO

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C	2		N/A
Glycosylation Resources
GlyTouCan:  G86802XL GlyCosmos:  G86802XL

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-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	D	6		N/A
Glycosylation Resources
GlyTouCan:  G09454VW GlyCosmos:  G09454VW GlyGen:  G09454VW

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A], HA [auth A], IA [auth A], JA [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	MA [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	KA [auth A], LA [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FE	L [auth A], M [auth A], N [auth A], O [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
CA	E [auth A], F [auth A], G [auth A], H [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	I [auth A], J [auth A], K [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 3 Unique

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

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900023	C	alpha-cellobiose	Oligosaccharide / Metabolism		Ligand Interaction

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900020	D	beta-cellohexaose	Oligosaccharide / Metabolism		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.164 
• R-Value Work: 0.121 
• R-Value Observed: 0.124 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.458	α = 90
b = 88.494	β = 113.72
c = 66.753	γ = 90

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
MOLREP	phasing
REFMAC	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-03-07 
• Released Date: 2014-07-30 
Deposition Author(s): Alahuhta, P.M., Lunin, V.V.

Revision History  

• Version 1.0: 2014-07-30
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary