1H2J

ENDOGLUCANASE CEL5A IN COMPLEX WITH UNHYDROLYSED AND COVALENTLY LINKED 2,4-DINITROPHENYL-2-DEOXY-2-FLUORO-CELLOBIOSIDE AT 1.15 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.136 
  • R-Value Work: 0.117 
  • R-Value Observed: 0.118 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Direct Experimental Observation of the Hydrogen-Bonding Network of a Glycosidase Along its Reaction Coordinate Revealed by Atomic Resolution Analyses of Endoglucanase Cel5A

Varrot, A.Davies, G.J.

(2003) Acta Crystallogr D Biol Crystallogr 59: 447

  • DOI: 10.1107/s0907444902023405
  • Primary Citation of Related Structures:  
    1H11, 1H2J, 1HF6

  • PubMed Abstract: 
  • Non-covalent interactions between protein and ligand at the active centre of glycosidases play an enormous role in catalysis. Dissection of these hydrogen-bonding networks is not merely important for an understanding of enzymatic catalysis, but is al ...

    Non-covalent interactions between protein and ligand at the active centre of glycosidases play an enormous role in catalysis. Dissection of these hydrogen-bonding networks is not merely important for an understanding of enzymatic catalysis, but is also increasingly relevant for the design of transition-state mimics, whose tautomeric state, hydrogen-bonding interactions and protonation contribute to tight binding. Here, atomic resolution ( approximately 1 A) analysis of a series of complexes of the 34 kDa catalytic core domain of the Bacillus agaradhaerens endoglucanase Cel5A is presented. Cel5A is a 'retaining' endoglucanase which performs catalysis via the formation and subsequent breakdown of a covalent glycosyl-enzyme intermediate via oxocarbenium-ion-like transition states. Previous medium-resolution analyses of a series of enzymatic snapshots has revealed conformational changes in the substrate along the reaction coordinate (Davies et al., 1998). Here, atomic resolution analyses of the series of complexes along the pathway are presented, including the 'Michaelis' complex of the unhydrolysed substrate, the covalent glycosyl-enzyme intermediate and the complex with the reaction product, cellotriose. These structures reveal intimate details of the protein-ligand interactions, including most of the carbohydrate-associated H atoms and the tautomeric state of crucial active-centre groups in the pH 5 orthorhombic crystal form and serve to illustrate the potential for atomic resolution analyses to inform strategies for enzyme inhibition.


    Organizational Affiliation

    Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5YW, England.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ENDOGLUCANASE 5AA303Salipaludibacillus agaradhaerensMutation(s): 0 
Gene Names: cel5A
EC: 3.2.1.4
Find proteins for O85465 (Salipaludibacillus agaradhaerens)
Explore O85465 
Go to UniProtKB:  O85465
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DCB
Query on DCB

Download CCD File 
A
2,4-DINITROPHENYL-2-DEOXY-2-FLUORO-BETA-D-CELLOBIOSIDE
C18 H23 F N2 O14
WFVCNOHOODVBQK-IUBYCILNSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.136 
  • R-Value Work: 0.117 
  • R-Value Observed: 0.118 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.355α = 90
b = 69.572β = 90
c = 77.091γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2002-08-09 
  • Released Date: 2002-08-15 
  • Deposition Author(s): Varrot, A., Davies, G.J.
  • This entry supersedes: 1HF7

Revision History 

  • Version 1.0: 2002-08-15
    Type: Initial release
  • Version 1.1: 2011-10-19
    Changes: Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 2.0: 2018-12-19
    Changes: Advisory, Atomic model, Data collection, Derived calculations
  • Version 2.1: 2019-07-10
    Changes: Data collection
  • Version 2.2: 2019-07-24
    Changes: Data collection