1TOX

DIPHTHERIA TOXIN DIMER COMPLEXED WITH NAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of diphtheria toxin bound to nicotinamide adenine dinucleotide.

Bell, C.E.Eisenberg, D.

(1996) Biochemistry 35: 1137-1149

  • DOI: 10.1021/bi9520848

  • PubMed Abstract: 
  • Diphtheria toxin (DT), a 58 kDa protein secreted by lysogenic strains of Corynebacterium diphtheriae, causes the disease diphtheria in humans by gaining entry into the cytoplasm of cells and inhibiting protein synthesis. Specifically, the catalytic ( ...

    Diphtheria toxin (DT), a 58 kDa protein secreted by lysogenic strains of Corynebacterium diphtheriae, causes the disease diphtheria in humans by gaining entry into the cytoplasm of cells and inhibiting protein synthesis. Specifically, the catalytic (C) domain of DT transfers the ADP-ribose group of NAD to elongation factor-2 (EF-2), rendering EF-2 inactive. In order to investigate how the C-domain of DT binds NAD and catalyzes the ADP-ribosylation of EF-2, the crystal structure of DT in complex with NAD has been determined to 2.3 A resolution. This is the first crystal structure of an ADP-ribosyltransferase (ADP-RT) enzyme in complex with NAD and suggests the features of the ADP-RT fold which are important for NAD binding. The conformation of NAD in the complex and the proximity of the Glu148 carboxylate group of the C-domain to the scissile, N-glycosidic bond of NAD suggest plausible modes of catalysis of the ADP-ribosylation reaction. Residues 39-46 of the active-site loop of the C-domain become disordered upon NAD binding, suggesting a potential role for this loop in the recognition of the ADP-ribose acceptor substrate, EF-2. The negatively charged phosphates and two ribose hydroxyls of NAD are not in direct contact with any atoms of the C-domain. Instead, they form an exposed surface which appears to be presented for recognition by EF-2. Structural alignments of the DT-NAD complex with the structures of other members of the ADP-RT family suggest how NAD may bind to these other enzymes.


    Related Citations: 
    • Domain Swapping: Entangling Alliances between Proteins
      Bennett, M.J.,Choe, S.,Eisenberg, D.
      (1994) Proc.Natl.Acad.Sci.USA 91: 3127
    • Refined Structure of Monomeric Diphtheria Toxin at 2.3 A Resolution
      Bennett, M.J.,Eisenberg, D.
      (1994) Protein Sci. 3: 1464
    • Refined Structure of Dimeric Diphtheria Toxin at 2.0 A Resolution
      Bennett, M.J.,Choe, S.,Eisenberg, D.
      (1994) Protein Sci. 3: 1444
    • The Crystal Structure of Diphtheria Toxin
      Choe, S.,Bennett, M.J.,Fujii, G.,Curmi, P.M.,Kantardjieff, K.A.,Collier, R.J.,Eisenberg, D.
      (1992) Nature 357: 216


    Organizational Affiliation

    UCLA-DOE Laboratory of Structural Biology and Molecular Medicine, Molecular Biology Institute, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIPHTHERIA TOXIN (DIMERIC)
A, B
535Corynephage betaMutation(s): 0 
Find proteins for P00588 (Corynephage beta)
Go to UniProtKB:  P00588
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NADKd: 10000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.227 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 105.000α = 90.00
b = 89.500β = 94.00
c = 130.100γ = 90.00
Software Package:
Software NamePurpose
R-AXISdata collection
X-PLORphasing
X-PLORrefinement
R-AXISdata reduction
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-06-10
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance