Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.34 kDa 
• Atom Count: 2765 
• Modelled Residue Count: 300 
• Deposited Residue Count: 303 
• Unique protein chains: 1

5A3H

2-DEOXY-2-FLURO-B-D-CELLOBIOSYL/ENZYME INTERMEDIATE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHEARANS AT 1.8 ANGSTROMS RESOLUTION

• PDB DOI: 10.2210/pdb5A3H/pdb

• Classification: HYDROLASE
• Organism(s): Salipaludibacillus agaradhaerens
• Expression System: Bacillus subtilis
• Mutation(s): No 


• Deposited: 1998-07-23 Released: 1999-07-24 
• Deposition Author(s): Davies, G.J., Varrot, A., Dauter, M., Brzozowski, A.M., Schulein, M., Mackenzie, L., Withers, S.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.186 
• R-Value Work: 0.144 

Literature

Snapshots along an enzymatic reaction coordinate: analysis of a retaining beta-glycoside hydrolase.

Davies, G.J., Mackenzie, L., Varrot, A., Dauter, M., Brzozowski, A.M., Schulein, M., Withers, S.G.

(1998) Biochemistry 37: 11707-11713

• PubMed: 9718293 
• DOI: 10.1021/bi981315i
• Primary Citation of Related Structures:  
  3A3H, 4A3H, 5A3H, 6A3H, 7A3H


• PubMed Abstract: 
  

The enzymatic hydrolysis of O-glycosidic linkages is one of the most diverse and widespread reactions in nature and involves a classic "textbook" enzyme mechanism. A multidisciplinary analysis of a beta-glycoside hydrolase, the Cel5A from Bacillus agaradhaerens, is presented in which the structures of each of the native, substrate, covalent-intermediate, and product complexes have been determined and their interconversions analyzed kinetically, providing unprecedented insights into the mechanism of this enzyme class. Substrate is bound in a distorted 1S3 skew-boat conformation, thereby presenting the anomeric carbon appropriately for nucleophilic attack as well as satisfying the stereoelectronic requirements for an incipient oxocarbenium ion. Leaving group departure results in the trapping of a covalent alpha-glycosyl-enzyme intermediate in which the sugar adopts an undistorted 4C1 conformation. Finally, hydrolysis of this intermediate yields a product complex in which the sugar is bound in a partially disordered mode, consistent with unfavorable interactions and low product affinity.

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Related Citations: 

• Structure of the Bacillus Agaradherans Family 5 Endoglucanase at 1.6 A and its Cellobiose Complex at 2.0 A Resolution
  Davies, G.J., Dauter, M., Brzozowski, A.M., Bjornvad, M.E., Andersen, K.V., Schulein, M.
  (1998) Biochemistry 37: 1926

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Organizational Affiliation: 

Department of Chemistry, University of York, Heslington, U.K. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDOGLUCANASE	A	303	Salipaludibacillus agaradhaerens	Mutation(s): 0  Gene Names: cel5A EC: 3.2.1.4
UniProt
Find proteins for O85465 (Salipaludibacillus agaradhaerens) Explore O85465  Go to UniProtKB:  O85465

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-glucopyranose-(1-4)-2-deoxy-2-fluoro-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G29564OM GlyCosmos:  G29564OM

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900050	B	2-deoxy-2-fluoro-beta-cellobiose	Oligosaccharide / Substrate analog		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.186 
• R-Value Work: 0.144 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.71	α = 90
b = 69.57	β = 90
c = 77.04	γ = 90

Software Package:

Software Name	Purpose
CCP4	model building
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-07-23 
• Released Date: 1999-07-24 
Deposition Author(s): Davies, G.J., Varrot, A., Dauter, M., Brzozowski, A.M., Schulein, M., Mackenzie, L., Withers, S.G.

Revision History  

• Version 1.0: 1999-07-24
  Type: Initial release
  
• Version 1.1: 2008-03-25
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary