1EXP

BETA-1,4-GLYCANASE CEX-CD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Crystallographic observation of a covalent catalytic intermediate in a beta-glycosidase.

White, A.Tull, D.Johns, K.Withers, S.G.Rose, D.R.

(1996) Nat Struct Biol 3: 149-154

  • DOI: 10.1038/nsb0296-149
  • Primary Citation of Related Structures:  
    1EXP

  • PubMed Abstract: 
  • The three-dimensional structure of a catalytically competent glycosyl-enzyme intermediate of a retaining beta-1,4-glycanase has been determined at a resolution of 1.8 A by X-ray diffraction. A fluorinated slow substrate forms an alpha-D-glycopyranosyl linkage to one of the two invariant carboxylates, Glu 233, as supported in solution by 19F-NMR studies ...

    The three-dimensional structure of a catalytically competent glycosyl-enzyme intermediate of a retaining beta-1,4-glycanase has been determined at a resolution of 1.8 A by X-ray diffraction. A fluorinated slow substrate forms an alpha-D-glycopyranosyl linkage to one of the two invariant carboxylates, Glu 233, as supported in solution by 19F-NMR studies. The resulting ester linkage is coplanar with the cyclic oxygen of the proximal saccharide and is inferred to form a strong hydrogen bond with the 2-hydroxyl of that saccharide unit in natural substrates. The active-site architecture of this covalent intermediate gives insights into both the classical double-displacement catalytic mechanism and the basis for the enzyme's specificity.


    Related Citations: 
    • Crystal Structure of the Catalytic Domain of the Beta-1,4-Glycanase Cex from Cellulomonas Fimi
      White, A., Withers, S.G., Gilkes, N.R., Rose, D.R.
      (1994) Biochemistry 33: 12546
    • Crystallization and Preliminary X-Ray Diffraction Analysis of the Catalytic Domain of Cex, an Exo-Beta-1,4-Glucanase and Beta-1,4-Xylanase from the Bacterium Cellulomonas Fimi
      Bedarkar, S., Gilkes, N.R., Kilburn, D.G., Kwan, E., Rose, D.R., Miller Junior, R.C., Warren, R.A., Withers, S.G.
      (1992) J Mol Biol 228: 693

    Organizational Affiliation

    Protein Engineering Network of Centres of Excellence, Ontario Cancer Institute, Toronto, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BETA-1,4-D-GLYCANASE CEX-CDA312Cellulomonas fimiMutation(s): 0 
Gene Names: cexxynB
EC: 3.2.1.91 (PDB Primary Data), 3.2.1.8 (PDB Primary Data)
UniProt
Find proteins for P07986 (Cellulomonas fimi)
Explore P07986 
Go to UniProtKB:  P07986
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-glucopyranose-(1-4)-2-deoxy-2-fluoro-alpha-D-glucopyranoseB2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G29564OM
GlyCosmos:  G29564OM
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.172α = 90
b = 88.172β = 90
c = 81.097γ = 90
Software Package:
Software NamePurpose
SDMWdata collection
X-PLORmodel building
X-PLORrefinement
SDMSdata reduction
XENGENdata reduction
NIELSENdata reduction
XUONG)data reduction
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-01-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary