5A3H

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1021/bi981315i
  • Primary Citation of Related Structures:  

  • 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 ag ...

    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.


    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


    Organizational Affiliation

    Department of Chemistry, University of York, Heslington, U.K. davies@yorvic.york.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENDOGLUCANASE
A
303Salipaludibacillus agaradhaerensMutation(s): 0 
Gene Names: cel5A
EC: 3.2.1.4
Find proteins for O85465 (Salipaludibacillus agaradhaerens)
Go to UniProtKB:  O85465
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FFC
Query on FFC

Download SDF File 
Download CCD File 
A
2-DEOXY-2-FLUORO-B-D-CELLOBIOSIDE
C12 H21 F O10
CHZBROHNUFSPPZ-FINXQLPQSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FFCKd: 26700 nM PDBBIND
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 = 54.710α = 90.00
b = 69.570β = 90.00
c = 77.040γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
CCP4model building
CCP4phasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-07-24
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance