4CJ0

Crystal structure of CelD in complex with affitin E12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.125 
  • R-Value Work: 0.107 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Potent and Specific Inhibition of Glycosidases by Small Artificial Binding Proteins (Affitins)

Correa, A.Pacheco, S.Mechaly, A.E.Obal, G.Behar, G.Mouratou, B.Oppezzo, P.Alzari, P.M.Pecorari, F.

(2014) Plos One 9: 97438

  • DOI: 10.1371/journal.pone.0097438
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glycosidases are associated with various human diseases. The development of efficient and specific inhibitors may provide powerful tools to modulate their activity. However, achieving high selectivity is a major challenge given that glycosidases with ...

    Glycosidases are associated with various human diseases. The development of efficient and specific inhibitors may provide powerful tools to modulate their activity. However, achieving high selectivity is a major challenge given that glycosidases with different functions can have similar enzymatic mechanisms and active-site architectures. As an alternative approach to small-chemical compounds, proteinaceous inhibitors might provide a better specificity by involving a larger surface area of interaction. We report here the design and characterization of proteinaceous inhibitors that specifically target endoglycosidases representative of the two major mechanistic classes; retaining and inverting glycosidases. These inhibitors consist of artificial affinity proteins, Affitins, selected against the thermophilic CelD from Clostridium thermocellum and lysozyme from hen egg. They were obtained from libraries of Sac7d variants, which involve either the randomization of a surface or the randomization of a surface and an artificially-extended loop. Glycosidase binders exhibited affinities in the nanomolar range with no cross-recognition, with efficient inhibition of lysozyme (Ki = 45 nM) and CelD (Ki = 95 and 111 nM), high expression yields in Escherichia coli, solubility, and thermal stabilities up to 81.1°C. The crystal structures of glycosidase-Affitin complexes validate our library designs. We observed that Affitins prevented substrate access by two modes of binding; covering or penetrating the catalytic site via the extended loop. In addition, Affitins formed salt-bridges with residues essential for enzymatic activity. These results lead us to propose the use of Affitins as versatile selective glycosidase inhibitors and, potentially, as enzymatic inhibitors in general.


    Organizational Affiliation

    Institut Pasteur de Montevideo, Recombinant Protein Unit, Montevideo, Uruguay; Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528, Paris, France.,Institut Pasteur de Montevideo, Recombinant Protein Unit, Montevideo, Uruguay.,Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528, Paris, France.,Institut Pasteur de Montevideo, Protein Biophysics Unit, Montevideo, Uruguay.,Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528, Paris, France; INSERM UMR 892 - CRCNA, Nantes, France; CNRS UMR 6299, Nantes, France; University of Nantes, Nantes, France.,INSERM UMR 892 - CRCNA, Nantes, France; CNRS UMR 6299, Nantes, France; University of Nantes, Nantes, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENDOGLUCANASE D
A
625Clostridium thermocellumMutation(s): 0 
Gene Names: celD
EC: 3.2.1.4
Find proteins for P0C2S4 (Clostridium thermocellum)
Go to UniProtKB:  P0C2S4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
E12 AFFITIN
B
81N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.125 
  • R-Value Work: 0.107 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 87.633α = 90.00
b = 87.633β = 90.00
c = 97.426γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
REFMACrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-21
    Type: Initial release
  • Version 1.1: 2014-05-28
    Type: Database references
  • Version 1.2: 2018-05-16
    Type: Data collection