1SGK

NUCLEOTIDE-FREE DIPHTHERIA TOXIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of nucleotide-free diphtheria toxin.

Bell, C.E.Eisenberg, D.

(1997) Biochemistry 36: 481-488

  • DOI: 10.1021/bi962214s
  • Primary Citation of Related Structures:  
    1SGK

  • PubMed Abstract: 
  • The crystal structure of diphtheria toxin (DT) in the absence of nucleotide (nucleotide-free DT) has been determined at 2.3 A resolution to a crystallographic R factor and free R factor of 18.2 and 28.2%, respectively. A comparison of this structure to the previously determined structures of DT in complex with adenyly(3'-5')uridine monophosphate (ApUp) and DT in complex with nicotinamide adenine dinucleotide (NAD) reveals that there are no significant movements of the two subdomains of the catalytic (C) domain associated with dinucleotide binding ...

    The crystal structure of diphtheria toxin (DT) in the absence of nucleotide (nucleotide-free DT) has been determined at 2.3 A resolution to a crystallographic R factor and free R factor of 18.2 and 28.2%, respectively. A comparison of this structure to the previously determined structures of DT in complex with adenyly(3'-5')uridine monophosphate (ApUp) and DT in complex with nicotinamide adenine dinucleotide (NAD) reveals that there are no significant movements of the two subdomains of the catalytic (C) domain associated with dinucleotide binding. The side chains of six residues within the active-site cleft, including Tyr65, Pro38, Tyr27, Thr23, Glu148, and Tyr54, show movements of up to 3 A upon dinucleotide binding. In the structure of nucleotide-free DT, the active-site loop residues 39-47 of the C domain are well ordered and extend over the active-site cleft in approximately the same position as in the structure of DT in complex with ApUp. This is in contrast to the structure of the DT-NAD complex, in which the active-site loop is disordered. On the basis of a comparison of the nucleotide-free and NAD-bound DT structures, we suggest that the interaction of NAD with Pro38 and also possibly Tyr54 and Trp153 could disrupt the network of hydrogen bonds that stabilizes the position of the active-site loop over the active-site cleft, allowing this loop to become disordered. This may be an important step in binding of the C domain of DT to its substrate, elongation factor-2.


    Related Citations: 
    • Crystal Structure of Diphtheria Toxin Bound to Nicotinamide Adenine Dinucleotide
      Bell, C.E., Eisenberg, D.
      (1996) Biochemistry 35: 1137
    • Domain Swapping: Entangling Alliances between Proteins
      Bennett, M.J., Choe, S., Eisenberg, D.
      (1994) Proc Natl Acad Sci U S A 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DIPHTHERIA TOXIN (DIMERIC)A535Corynephage betaMutation(s): 0 
EC: 2.4.2.36
UniProt
Find proteins for P00588 (Corynephage beta)
Explore P00588 
Go to UniProtKB:  P00588
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.2α = 90
b = 91.2β = 94.2
c = 65.3γ = 90
Software Package:
Software NamePurpose
R-AXISdata collection
R-AXISdata reduction
X-PLORmodel building
X-PLORrefinement
R-AXISdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-12-23
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance