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PDBsum entry 1ikp

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protein metals links
Transferase PDB id
1ikp
Jmol
Contents
Protein chain
599 a.a.
Metals
_NA ×2
_CL ×2
Waters ×540
PDB id:
1ikp
Name: Transferase
Title: Pseudomonas aeruginosa exotoxin a, p201q, w281a mutant
Structure: Exotoxin a. Chain: a. Synonym: NAD-dependent adp-ribosyltransferase. Engineered: yes. Mutation: yes
Source: Pseudomonas aeruginosa. Organism_taxid: 287. Gene: pe. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.45Å     R-factor:   0.205     R-free:   0.228
Authors: D.B.Mckay,J.E.Wedekind,C.B.Trame
Key ref:
J.E.Wedekind et al. (2001). Refined crystallographic structure of Pseudomonas aeruginosa exotoxin A and its implications for the molecular mechanism of toxicity. J Mol Biol, 314, 823-837. PubMed id: 11734000 DOI: 10.1006/jmbi.2001.5195
Date:
04-May-01     Release date:   12-Dec-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P11439  (TOXA_PSEAE) -  Exotoxin A
Seq:
Struc:
 
Seq:
Struc:
638 a.a.
599 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 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: 10.1006/jmbi.2001.5195 J Mol Biol 314:823-837 (2001)
PubMed id: 11734000  
 
 
Refined crystallographic structure of Pseudomonas aeruginosa exotoxin A and its implications for the molecular mechanism of toxicity.
J.E.Wedekind, C.B.Trame, M.Dorywalska, P.Koehl, T.M.Raschke, M.McKee, D.FitzGerald, R.J.Collier, D.B.McKay.
 
  ABSTRACT  
 
Exotoxin A of Pseudomonas aeruginosa asserts its cellular toxicity through ADP-ribosylation of translation elongation factor 2, predicated on binding to specific cell surface receptors and intracellular trafficking via a complex pathway that ultimately results in translocation of an enzymatic activity into the cytoplasm. In early work, the crystallographic structure of exotoxin A was determined to 3.0 A resolution, revealing a tertiary fold having three distinct structural domains; subsequent work has shown that the domains are individually responsible for the receptor binding (domain I), transmembrane targeting (domain II), and ADP-ribosyl transferase (domain III) activities, respectively. Here, we report the structures of wild-type and W281A mutant toxin proteins at pH 8.0, refined with data to 1.62 A and 1.45 A resolution, respectively. The refined models clarify several ionic interactions within structural domains I and II that may modulate an obligatory conformational change that is induced by low pH. Proteolytic cleavage by furin is also obligatory for toxicity; the W281A mutant protein is substantially more susceptible to cleavage than the wild-type toxin. The tertiary structures of the furin cleavage sites of the wild-type and W281 mutant toxins are similar; however, the mutant toxin has significantly higher B-factors around the cleavage site, suggesting that the greater susceptibility to furin cleavage is due to increased local disorder/flexibility at the site, rather than to differences in static tertiary structure. Comparison of the refined structures of full-length toxin, which lacks ADP-ribosyl transferase activity, to that of the enzymatic domain alone reveals a salt bridge between Arg467 of the catalytic domain and Glu348 of domain II that restrains the substrate binding cleft in a conformation that precludes NAD+ binding. The refined structures of exotoxin A provide precise models for the design and interpretation of further studies of the mechanism of intoxication.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. PE and the domain I - domain II interface. (a) Ribbon drawing of the tri-partite domain organization: domain Ia (1-252), purple b-sheet, yellow a-helices and coils; domain Ib (365-404), green b-sheet and coil; domain II (253-364), light blue b-sheet and coil; and domain III (405-613), red a-helix and coil, blue b-sheet. Cyan CPK spheres represent Na ions; yellow CPK spheres represent Cl ions; disulfide positions are indicated as green spheres. (b) Ribbon drawing rotated 90° from orientation in (a). (c) Stereographic C^a representation. Spherical main-chain atom positions are numbered every 20 amino acid residues. Color scheme and orientation based on (a). Disulfide positions are indicated as ball-and-stick side-chains. An arrow indicates the site of furin cleavage. (d) Stereographic representation of the ionic (salt-bridge) interactions at the interface between domains I and II. Broken lines indicate potential ionic interactions between side-chains that are likely to be disrupted under acidic conditions (shown in Table 1). An arrowhead indicates the site of furin cleavage. The orientation and color scheme are similar to that of (a).
Figure 4.
Figure 4. The furin cleavage site of PE. (a) Schematic stereo ribbon representation with selected amino acid residues depicted as ball-and-stick models. Side-chains that would bind to the P1-P4 sites of furin are labeled; an arrow indicates the site of cleavage. Broken lines indicate hydrogen bond or ionic interactions. The color scheme and molecular orientation are identical to those in Figure 1(a). (b) Sequence alignment of the PE furin cleavage site with that of diphtheria toxin (DT). A star ( filled ) indicates the site of peptide bond cleavage.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 314, 823-837) copyright 2001.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22466878 K.V.Korotkov, M.Sandkvist, and W.G.Hol (2012).
The type II secretion system: biogenesis, molecular architecture and mechanism.
  Nat Rev Microbiol, 10, 336-351.  
18988862 J.E.Weldon, L.Xiang, O.Chertov, I.Margulies, R.J.Kreitman, D.J.FitzGerald, and I.Pastan (2009).
A protease-resistant immunotoxin against CD22 with greatly increased activity against CLL and diminished animal toxicity.
  Blood, 113, 3792-3800.  
18785839 Q.Deng, and J.T.Barbieri (2008).
Molecular mechanisms of the cytotoxicity of ADP-ribosylating toxins.
  Annu Rev Microbiol, 62, 271-288.  
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
  16603059 R.A.Spooner, D.C.Smith, A.J.Easton, L.M.Roberts, and J.M.Lord (2006).
Retrograde transport pathways utilised by viruses and protein toxins.
  Virol J, 3, 26.  
15838025 A.Purdy, F.Rohwer, R.Edwards, F.Azam, and D.H.Bartlett (2005).
A glimpse into the expanded genome content of Vibrio cholerae through identification of genes present in environmental strains.
  J Bacteriol, 187, 2992-3001.  
16109954 G.Pretzer, J.Snel, D.Molenaar, A.Wiersma, P.A.Bron, J.Lambert, W.M.de Vos, R.van der Meer, M.A.Smits, and M.Kleerebezem (2005).
Biodiversity-based identification and functional characterization of the mannose-specific adhesin of Lactobacillus plantarum.
  J Bacteriol, 187, 6128-6136.  
16239575 J.C.Hsieh, D.M.Tham, W.Feng, F.Huang, S.Embaie, K.Liu, D.Dean, R.Hertle, D.J.Fitzgerald, and R.J.Mrsny (2005).
Intranasal immunization strategy to impede pilin-mediated binding of Pseudomonas aeruginosa to airway epithelial cells.
  Infect Immun, 73, 7705-7717.  
15799975 J.Méré, J.Morlon-Guyot, A.Bonhoure, L.Chiche, and B.Beaumelle (2005).
Acid-triggered membrane insertion of Pseudomonas exotoxin A involves an original mechanism based on pH-regulated tryptophan exposure.
  J Biol Chem, 280, 21194-21201.  
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
15311272 J.Sun, A.W.Maresso, J.J.Kim, and J.T.Barbieri (2004).
How bacterial ADP-ribosylating toxins recognize substrates.
  Nat Struct Mol Biol, 11, 868-876.  
12360192 G.Thomas (2002).
Furin at the cutting edge: from protein traffic to embryogenesis and disease.
  Nat Rev Mol Cell Biol, 3, 753-766.  
12029083 J.Ménétrey, G.Flatau, E.A.Stura, J.B.Charbonnier, F.Gas, J.M.Teulon, M.H.Le Du, P.Boquet, and A.Menez (2002).
NAD binding induces conformational changes in Rho ADP-ribosylating clostridium botulinum C3 exoenzyme.
  J Biol Chem, 277, 30950-30957.
PDB codes: 1gze 1gzf
12270928 S.Armstrong, S.P.Yates, and A.R.Merrill (2002).
Insight into the catalytic mechanism of Pseudomonas aeruginosa exotoxin A. Studies of toxin interaction with eukaryotic elongation factor-2.
  J Biol Chem, 277, 46669-46675.  
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.