1DTP

THE STRUCTURE OF THE ISOLATED CATALYTIC DOMAIN OF DIPHTHERIA TOXIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the isolated catalytic domain of diphtheria toxin.

Weiss, M.S.Blanke, S.R.Collier, R.J.Eisenberg, D.

(1995) Biochemistry 34: 773-781


  • PubMed Abstract: 
  • The structure of the isolated catalytic domain of diphtheria toxin at pH 5.0 was determined by X-ray crystallography at 2.5 A resolution and refined to an R-factor of 19.7%. The domain is bound to its endogenous inhibitor adenylyl(3'-->5')uridine 3'- ...

    The structure of the isolated catalytic domain of diphtheria toxin at pH 5.0 was determined by X-ray crystallography at 2.5 A resolution and refined to an R-factor of 19.7%. The domain is bound to its endogenous inhibitor adenylyl(3'-->5')uridine 3'-monophosphate (ApUp). The structure of this 190-residue domain, which was expressed in and isolated from Escherichia coli, is essentially identical to the structure of the catalytic domain within whole diphtheria toxin determined at pH 7.5. However, there are two adjacent surface loops (loop 66-78 and loop 169-176) that exhibit clear differences when compared to the structure of the catalytic domain in whole diphtheria toxin. Although both loops are at the surface of the protein and are relatively flexible, the chain trace is well-defined in the electron density. The main structural difference is the closer approach of loops 66-78 and 169-176. We ascribe this structural change mainly to the absence of the neighboring transmembrane domain in the isolated catalytic domain as compared to whole diphtheria toxin. We suggest that this change represents the first step of the structural transition from the catalytic domain in whole diphtheria toxin to the translocated form of the domain. The changes are described in detail, and their implications for membrane translocation are discussed.


    Related Citations: 
    • Three Domains for Three Functions: The Crystal Structure of Diphtheria Toxin
      Choe, S.,Bennett, M.J.,Fujii, G.,Curmi, P.M.G.,Kantardjeff, K.A.,Collier, R.J.,Eisenberg, D.
      (1992) Nature 357: 216
    • The Refined Structure of Monomeric Diphtheria Toxin
      Bennett, M.J.,Eisenberg, D.
      () TO BE PUBLISHED --: --
    • Domain Swapping: Entangling Alliances between Proteins
      Bennett, M.J.,Choe, S.,Eisenberg, D.
      (1994) Proc.Natl.Acad.Sci.USA 91: 3127
    • X-Ray Grade Crystals of the Enzymatic Fragment of Diphtheria Toxin
      Kantardjeff, K.,Collier, R.J.,Eisenberg, D.
      (1989) J.Biol.Chem. 264: 10402
    • The Refined Structure of Dimeric Diphtheria Toxin at 2.0 Angstroms Resolution
      Bennett, M.J.,Choe, S.,Eisenberg, D.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Molecular Biology Institute, University of California, Los Angeles 90024-1570.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIPHTHERIA TOXIN
A
190Corynephage betaEC: 2.4.2.36
Find proteins for P00588 (Corynephage beta)
Go to UniProtKB:  P00588
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
APU
Query on APU

Download SDF File 
Download CCD File 
A
ADENYLYL-3'-5'-PHOSPHO-URIDINE-3'-MONOPHOSPHATE
C19 H25 N7 O15 P2
FZCSEXOMUJFOHQ-KPKSGTNCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 55.700α = 90.00
b = 43.900β = 101.50
c = 73.900γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-11-01
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance