1GZF

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1074/jbc.M201844200
  • Primary Citation of Related Structures:  
  • Also Cited By: 2C8H, 2C8G, 2C8F, 2C8E, 2C8D, 2C8C, 2C8B, 2C8A, 2C89

  • 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 conf ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MONO-ADP-RIBOSYLTRANSFERASE C3
A, B, C, D
211Clostridium botulinum D phageMutation(s): 0 
Gene Names: C3
EC: 2.4.2.-
Find proteins for P15879 (Clostridium botulinum D phage)
Go to Gene View: C3
Go to UniProtKB:  P15879
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ADP
Query on ADP

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Download CCD File 
C, D
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
NAD
Query on NAD

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Download CCD File 
A, B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
NIR
Query on NIR

Download SDF File 
Download CCD File 
C
3-(AMINOCARBONYL)-1-[(3R,4S,5R)-3,4-DIHYDROXY-5-METHYLTETRAHYDRO-2-FURANYL]PYRIDINIUM
C11 H18 N2 O4
MYKCTORFOIHUSG-LALMQGGXSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NADKd: 60000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.234 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 103.947α = 90.00
b = 74.191β = 102.10
c = 119.680γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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