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PDBsum entry 2q5t

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protein ligands metals links
Toxin PDB id
2q5t
Jmol
Contents
Protein chain
605 a.a.
Ligands
EDO ×9
Metals
_CL ×2
Waters ×406
PDB id:
2q5t
Name: Toxin
Title: Full-length cholix toxin from vibrio cholerae
Structure: Cholix toxin. Chain: a. Engineered: yes
Source: Vibrio cholerae. Organism_taxid: 666. Strain: tp. Gene: toxa. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.10Å     R-factor:   0.194     R-free:   0.239
Authors: R.Jorgensen,R.J.Fieldhouse,A.R.Merrill
Key ref:
R.Jørgensen et al. (2008). Cholix toxin, a novel ADP-ribosylating factor from Vibrio cholerae. J Biol Chem, 283, 10671-10678. PubMed id: 18276581 DOI: 10.1074/jbc.M710008200
Date:
01-Jun-07     Release date:   12-Feb-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q5EK40  (CHXA_VIBCL) -  Cholix toxin
Seq:
Struc:
 
Seq:
Struc:
666 a.a.
605 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!
  Biological process     metabolic process   1 term 
  Biochemical function     transferase activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1074/jbc.M710008200 J Biol Chem 283:10671-10678 (2008)
PubMed id: 18276581  
 
 
Cholix toxin, a novel ADP-ribosylating factor from Vibrio cholerae.
R.Jørgensen, A.E.Purdy, R.J.Fieldhouse, M.S.Kimber, D.H.Bartlett, A.R.Merrill.
 
  ABSTRACT  
 
The ADP-ribosyltransferases are a class of enzymes that display activity in a variety of bacterial pathogens responsible for causing diseases in plants and animals, including those affecting mankind, such as diphtheria, cholera, and whooping cough. We report the characterization of a novel toxin from Vibrio cholerae, which we call cholix toxin. The toxin is active against mammalian cells (IC(50) = 4.6 +/- 0.4 ng/ml) and crustaceans (Artemia nauplii LD(50) = 10 +/- 2 mug/ml). Here we show that this toxin is the third member of the diphthamide-specific class of ADP-ribose transferases and that it possesses specific ADP-ribose transferase activity against ribosomal eukaryotic elongation factor 2. We also describe the high resolution crystal structures of the multidomain toxin and its catalytic domain at 2.1- and 1.25-A resolution, respectively. The new structural data show that cholix toxin possesses the necessary molecular features required for infection of eukaryotes by receptor-mediated endocytosis, translocation to the host cytoplasm, and inhibition of protein synthesis by specific modification of elongation factor 2. The crystal structures also provide important insight into the structural basis for activation of toxin ADP-ribosyltransferase activity. These results indicate that cholix toxin may be an important virulence factor of Vibrio cholerae that likely plays a significant role in the survival of the organism in an aquatic environment.
 
  Selected figure(s)  
 
Figure 3.
FIGURE 3. The structure of cholix toxin. a, ribbon drawing of the cholix toxin structure (PDB entry 2Q5T): domain Ia, blue (1–264); domain II (265–386), red; domain Ib (387–423), orange; and domain III (424–634), green. Disulfides and furin cut sites are shown as light green and blue spheres, respectively. b, superposition of ExoA onto the cholix toxin structure. Disulfides are indicated by light green and yellow spheres for cholix toxin and ExoA, respectively. c, ribbon drawing of the catalytic domain structure (PDB entry 2Q6M). The two PJ34 inhibitors are shown in black and grey ball-and-stick representation, and the catalytic loops (L1–L4) are shown in yellow, cyan, orange, and red, respectively. d, binding of PJ34 to the NAD^+ binding pocket. The phenyl moiety of Tyr-504 forms stacking interactions with PJ34 (4 Å), and Tyr-493 is also adjacent to the hetero-ring system.
Figure 4.
FIGURE 4. The structure of cholix toxin. a, superposition of the catalytic fragment from cholix toxin with the cholix[c] toxin structure (blue). Catalytic loops (L1–L4 in cholix toxin) are colored as in Fig. 3c and PJ34 (black) in the active site is shown in ball-and-stick representation. b, L1 interactions in the cholix toxin. Asn-481 and Asn-481 (yellow) in L1 form H-bonds to Arg-362 and Asn-366 in -helix E of domain II (red). Ethylene glycol (purple) mediates contact between L1 and domain II. c, binding of NAD^+ (black) to cholix[c] toxin from superposition of cholix[c] toxin onto the eEF2-ExoA-NAD^+ complex.^7 The electrostatic surface potential of the cholix toxin binding site was calculated using the APBS PyMOL plugin. d, superposition of catalytic fragments of DT and ExoA from eEF2-ExoA-NAD^+ onto cholix[c] toxin. Cholix[c] toxin, ExoA, and DT residues are shown as green, yellow, and black sticks, respectively, and NAD^+ in grey ball-and-stick representation. e, superposition of the furin-cleaved C-terminal fragment of full-length cholix toxin onto ExoA of the eEF2-ExoA-NAD^+ complex structure. Catalytic fragment (green) and domains Ib and II (brown) are shown as ribbons. L1–L4 are colored as before, and NAD^+ is in black spheres. eEF2 is depicted as a white transparent surface with the diphthamide shown in purple spheres. f, residues in L1 of cholix toxin with the potential to interact with the diphthamide and NAD^+. Same superposition and coloring as in e.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 10671-10678) copyright 2008.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20822442 M.Morar, and G.D.Wright (2010).
The genomic enzymology of antibiotic resistance.
  Annu Rev Genet, 44, 25-51.  
20106667 M.O.Hottiger, P.O.Hassa, B.Lüscher, H.Schüler, and F.Koch-Nolte (2010).
Toward a unified nomenclature for mammalian ADP-ribosyltransferases.
  Trends Biochem Sci, 35, 208-219.  
20140093 P.K.Gupta, S.Liu, and S.H.Leppla (2010).
Characterization of a Chinese hamster ovary cell mutant having a mutation in elongation factor-2.
  PLoS One, 5, e9078.  
20091030 R.Sarnovsky, T.Tendler, M.Makowski, M.Kiley, A.Antignani, R.Traini, J.Zhang, R.Hassan, and D.J.FitzGerald (2010).
Initial characterization of an immunotoxin constructed from domains II and III of cholera exotoxin.
  Cancer Immunol Immunother, 59, 737-746.  
21203470 V.Roy, K.Ghani, and M.Caruso (2010).
A dominant-negative approach that prevents diphthamide formation confers resistance to Pseudomonas exotoxin a and diphtheria toxin.
  PLoS One, 5, e15753.  
18583986 R.Jørgensen, Y.Wang, D.Visschedyk, and A.R.Merrill (2008).
The nature and character of the transition state for the ADP-ribosyltransferase reaction.
  EMBO Rep, 9, 802-809.
PDB codes: 2zit 3b78 3b82 3b8h
18815047 R.J.Fieldhouse, and A.R.Merrill (2008).
Needle in the haystack: structure-based toxin discovery.
  Trends Biochem Sci, 33, 546-556.  
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.