1DDT

THE REFINED STRUCTURE OF DIMERIC DIPHTHERIA TOXIN AT 2.0 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 

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This is version 1.3 of the entry. See complete history


Literature

Refined structure of dimeric diphtheria toxin at 2.0 A resolution.

Bennett, M.J.Choe, S.Eisenberg, D.

(1994) Protein Sci 3: 1444-1463

  • DOI: 10.1002/pro.5560030911
  • Primary Citation of Related Structures:  
    1DDT

  • PubMed Abstract: 
  • The refined structure of dimeric diphtheria toxin (DT) at 2.0 A resolution, based on 37,727 unique reflections (F > 1 sigma (F)), yields a final R factor of 19.5% with a model obeying standard geometry. The refined model consists of 523 amino acid residues, 1 molecule of the bound dinucleotide inhibitor adenylyl 3'-5' uridine 3' monophosphate (ApUp), and 405 well-ordered water molecules ...

    The refined structure of dimeric diphtheria toxin (DT) at 2.0 A resolution, based on 37,727 unique reflections (F > 1 sigma (F)), yields a final R factor of 19.5% with a model obeying standard geometry. The refined model consists of 523 amino acid residues, 1 molecule of the bound dinucleotide inhibitor adenylyl 3'-5' uridine 3' monophosphate (ApUp), and 405 well-ordered water molecules. The 2.0-A refined model reveals that the binding motif for ApUp includes residues in the catalytic and receptor-binding domains and is different from the Rossmann dinucleotide-binding fold. ApUp is bound in part by a long loop (residues 34-52) that crosses the active site. Several residues in the active site were previously identified as NAD-binding residues. Glu 148, previously identified as playing a catalytic role in ADP-ribosylation of elongation factor 2 by DT, is about 5 A from uracil in ApUp. The trigger for insertion of the transmembrane domain of DT into the endosomal membrane at low pH may involve 3 intradomain and 4 interdomain salt bridges that will be weakened at low pH by protonation of their acidic residues. The refined model also reveals that each molecule in dimeric DT has an "open" structure unlike most globular proteins, which we call an open monomer. Two open monomers interact by "domain swapping" to form a compact, globular dimeric DT structure. The possibility that the open monomer resembles a membrane insertion intermediate is discussed.


    Related Citations: 
    • Domain Swapping: Entangling Alliances between Proteins
      Bennett, M.J., Choe, S., Eisenberg, D.
      (1994) Proc Natl Acad Sci U S A 91: 3127
    • The Crystal Structure of Diphtheria Toxin
      Choe, S., Bennett, M.J., Fujii, G., Curmi, P.M.G., Kantardjieff, K.A., Collier, R.J., Eisenberg, D.
      (1992) Nature 357: 216

    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California at Los Angeles 90024-1570.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DIPHTHERIA TOXINA535Corynephage 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
Expand
  • 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: 2.00 Å
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.64α = 90
b = 92.56β = 94.6
c = 65.58γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-07-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other