1DTP

THE STRUCTURE OF THE ISOLATED CATALYTIC DOMAIN OF DIPHTHERIA TOXIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 

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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

  • DOI: 10.1021/bi00003a010
  • Primary Citation of Related Structures:  
    1DTP

  • 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'-monophosphate (ApUp) ...

    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: 
    • The Refined Structure of Dimeric Diphtheria Toxin at 2.0 Angstroms Resolution
      Bennett, M.J., Choe, S., Eisenberg, D.
      () To be published --: --
    • 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 U S A 91: 3127
    • 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
    • X-Ray Grade Crystals of the Enzymatic Fragment of Diphtheria Toxin
      Kantardjeff, K., Collier, R.J., Eisenberg, D.
      (1989) J Biol Chem 264: 10402

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DIPHTHERIA TOXINA190Corynephage betaMutation(s): 0 
EC: 2.4.2.36
UniProt
Find proteins for P00588 (Corynephage beta)
Explore P00588 
Go to UniProtKB:  P00588
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00588
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
APU
Query on APU

Download Ideal Coordinates CCD File 
B [auth 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: 2.50 Å
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.7α = 90
b = 43.9β = 101.5
c = 73.9γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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