Structure of the Clostridium botulinum C3 exoenzyme (wild-type) in complex with NAD

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Nad Binding Induces Conformational Changes in Rho Adp-Ribosylating Clostridium Botulinum C3 Exoenzyme

Menetrey, J.Flatau, G.Stura, E.A.Charbonnier, J.B.Gas, F.Teulon, J.M.Le Du, M.H.Boquet, P.Menez, A.

(2002) J Biol Chem 277: 30950

  • DOI: https://doi.org/10.1074/jbc.M201844200
  • Primary Citation of Related Structures:  
    1GZE, 1GZF

  • PubMed Abstract: 

    We have solved the crystal structures of Clostridium botulinum C3 exoenzyme free and complexed to NAD in the same crystal form, at 2.7 and 1.95 A, respectively. The asymmetric unit contains four molecules, which, in the free form, share the same conformation. Upon NAD binding, C3 underwent various conformational changes, whose amplitudes were differentially limited in the four molecules of the crystal unit. A major rearrangement concerns the loop that contains the functionally important ARTT motif (ADP-ribosyltransferase toxin turn-turn). The ARTT loop undergoes an ample swinging motion to adopt a conformation that covers the nicotinamide moiety of NAD. In particular, Gln-212, which belongs to the ARTT motif, flips over from a solvent-exposed environment to a buried conformation in the NAD binding pocket. Mutational experiments showed that Gln-212 is neither involved in NAD binding nor in the NAD-glycohydrolase activity of C3, whereas it plays a critical role in the ADP-ribosyl transfer to the substrate Rho. We observed additional NAD-induced movements, including a crab-claw motion of a subdomain that closes the NAD binding pocket. The data emphasized a remarkable NAD-induced plasticity of the C3 binding pocket and suggest that the NAD-induced ARTT loop conformation may be favored by the C3-NAD complex to bind to the substrate Rho. Our structural observations, together with a number of mutational experiments suggest that the mechanisms of Rho ADP-ribosylation by C3-NAD may be more complex than initially anticipated.

  • Organizational Affiliation

    Département d'Ingénierie et d'Etudes des Protéines, Commissariat à l'Energie Atomique, CE Saclay, F91191 Gif-sur-Yvette Cedex, France. julie.menetrey@cea.fr

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
211Clostridium botulinumMutation(s): 0 
EC: 2.4.2
Find proteins for P15879 (Clostridium botulinum D phage)
Explore P15879 
Go to UniProtKB:  P15879
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15879
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAD

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B]
C21 H27 N7 O14 P2
Query on ADP

Download Ideal Coordinates CCD File 
J [auth C],
K [auth D]
C10 H15 N5 O10 P2
Query on NIR

Download Ideal Coordinates CCD File 
C11 H18 N2 O4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B]
O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
NAD Binding MOAD:  1GZF Kd: 6.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.947α = 90
b = 74.191β = 102.1
c = 119.68γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-08-29
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance