7A3H

NATIVE ENDOGLUCANASE CEL5A CATALYTIC CORE DOMAIN AT 0.95 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.130 
  • R-Value Work: 0.110 

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 agaradhaerensGene Names: cel5A
EC: 3.2.1.4
Find proteins for O85465 (Salipaludibacillus agaradhaerens)
Go to UniProtKB:  O85465
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EOH
Query on EOH

Download SDF File 
Download CCD File 
A
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.130 
  • R-Value Work: 0.110 
  • 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
CCP4model building
REFMACrefinement
DENZOdata reduction
CCP4phasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-08-06
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance