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PDBsum entry 1dtp

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protein ligands links
Toxin PDB id
1dtp
Jmol
Contents
Protein chain
190 a.a.
Ligands
APU
Waters ×8
PDB id:
1dtp
Name: Toxin
Title: The structure of the isolated catalytic domain of diphtheria toxin
Structure: Diphtheria toxin. Chain: a. Engineered: yes
Source: Corynephage beta. Organism_taxid: 10703
Resolution:
2.50Å     R-factor:   0.197    
Authors: M.S.Weiss,D.Eisenberg
Key ref:
M.S.Weiss et al. (1995). Structure of the isolated catalytic domain of diphtheria toxin. Biochemistry, 34, 773-781. PubMed id: 7827036 DOI: 10.1021/bi00003a010
Date:
08-Sep-94     Release date:   01-Nov-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00588  (DTX_CORBE) -  Diphtheria toxin
Seq:
Struc:
 
Seq:
Struc:
567 a.a.
190 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.4.2.36  - NAD(+)--diphthamide ADP-ribosyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: NAD+ + diphthamide-[translation elongation factor 2] = nicotinamide + N-(ADP-D-ribosyl)diphthamide-[translation elongation factor 2]
NAD(+)
+ diphthamide-[translation elongation factor 2]
= nicotinamide
+ N-(ADP-D-ribosyl)diphthamide-[translation elongation factor 2]
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     pathogenesis   1 term 
  Biochemical function     NAD+-diphthamide ADP-ribosyltransferase activity     1 term  

 

 
    Added reference    
 
 
DOI no: 10.1021/bi00003a010 Biochemistry 34:773-781 (1995)
PubMed id: 7827036  
 
 
Structure of the isolated catalytic domain of diphtheria toxin.
M.S.Weiss, S.R.Blanke, R.J.Collier, D.Eisenberg.
 
  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 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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18055530 M.S.Kent, H.Yim, J.K.Murton, S.Satija, J.Majewski, and I.Kuzmenko (2008).
Oligomerization of membrane-bound diphtheria toxin (CRM197) facilitates a transition to the open form and deep insertion.
  Biophys J, 94, 2115-2127.  
  16511307 S.Kernstock, F.Koch-Nolte, J.Mueller-Dieckmann, M.S.Weiss, and C.Mueller-Dieckmann (2006).
Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of human ARH3, the first eukaryotic protein-ADP-ribosylhydrolase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 224-227.  
16107839 R.Jørgensen, A.R.Merrill, S.P.Yates, V.E.Marquez, A.L.Schwan, T.Boesen, and G.R.Andersen (2005).
Exotoxin A-eEF2 complex structure indicates ADP ribosylation by ribosome mimicry.
  Nature, 436, 979-984.
PDB codes: 1zm2 1zm3 1zm4 1zm9
10657208 R.K.Holmes (2000).
Biology and molecular epidemiology of diphtheria toxin and the tox gene.
  J Infect Dis, 181, S156-S167.  
10572923 J.C.Epinat, and T.D.Gilmore (1999).
In vitro-translated diphtheria toxin A chain inhibits translation in wheat germ extracts: analysis of biologically active, caspase-3-resistant diphtheria toxin mutants.
  Biochim Biophys Acta, 1472, 34-41.  
9632679 P.R.D'Silva, and A.K.Lala (1998).
Unfolding of diphtheria toxin. Identification of hydrophobic sites exposed on lowering of pH by photolabeling.
  J Biol Chem, 273, 16216-16222.  
9012663 C.E.Bell, and D.Eisenberg (1997).
Crystal structure of nucleotide-free diphtheria toxin.
  Biochemistry, 36, 481-488.
PDB code: 1sgk
9208920 D.T.Crane, B.Bolgiano, and C.Jones (1997).
Comparison of the diphtheria mutant toxin, CRM197, with a Haemophilus influenzae type-b polysaccharide-CRM197 conjugate by optical spectroscopy.
  Eur J Biochem, 246, 320-327.  
8755499 A.Ruf, J.Mennissier de Murcia, G.de Murcia, and G.E.Schulz (1996).
Structure of the catalytic fragment of poly(AD-ribose) polymerase from chicken.
  Proc Natl Acad Sci U S A, 93, 7481-7485.
PDB codes: 1paw 1pax
8573568 C.E.Bell, and D.Eisenberg (1996).
Crystal structure of diphtheria toxin bound to nicotinamide adenine dinucleotide.
  Biochemistry, 35, 1137-1149.
PDB code: 1tox
8901875 G.S.Prasad, D.E.McRee, E.A.Stura, D.G.Levitt, H.C.Lee, and C.D.Stout (1996).
Crystal structure of Aplysia ADP ribosyl cyclase, a homologue of the bifunctional ectozyme CD38.
  Nat Struct Biol, 3, 957-964.
PDB code: 1lbe
7499200 D.Tortorella, D.Sesardic, C.S.Dawes, and E.London (1995).
Immunochemical analysis of the structure of diphtheria toxin shows all three domains undergo structural changes at low pH.
  J Biol Chem, 270, 27439-27445.  
7568123 M.Li, F.Dyda, I.Benhar, I.Pastan, and D.R.Davies (1995).
The crystal structure of Pseudomonas aeruginosa exotoxin domain III with nicotinamide and AMP: conformational differences with the intact exotoxin.
  Proc Natl Acad Sci U S A, 92, 9308-9312.
PDB code: 1dma
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.