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PDBsum entry 1xez

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Toxin PDB id
1xez
Jmol
Contents
Protein chain
663 a.a. *
Ligands
BOG
Waters ×300
* Residue conservation analysis
PDB id:
1xez
Name: Toxin
Title: Crystal structure of the vibrio cholerae cytolysin (hlya) pro-toxin with octylglucoside bound
Structure: Hemolysin. Chain: a. Synonym: cytolysin. Engineered: yes. Mutation: yes
Source: Vibrio cholerae. Organism_taxid: 666. Strain: o1 el tor 8731. Gene: hlya. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.30Å     R-factor:   0.207     R-free:   0.246
Authors: R.Olson,E.Gouaux
Key ref:
R.Olson and E.Gouaux (2005). Crystal structure of the Vibrio cholerae cytolysin (VCC) pro-toxin and its assembly into a heptameric transmembrane pore. J Mol Biol, 350, 997. PubMed id: 15978620 DOI: 10.1016/j.jmb.2005.05.045
Date:
13-Sep-04     Release date:   14-Jun-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P09545  (HLYA_VIBCH) -  Hemolysin
Seq:
Struc:
 
Seq:
Struc:
741 a.a.
663 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 8 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   5 terms 
  Biological process     hemolysis in other organism   3 terms 
  Biochemical function     carbohydrate binding     2 terms  

 

 
DOI no: 10.1016/j.jmb.2005.05.045 J Mol Biol 350:997 (2005)
PubMed id: 15978620  
 
 
Crystal structure of the Vibrio cholerae cytolysin (VCC) pro-toxin and its assembly into a heptameric transmembrane pore.
R.Olson, E.Gouaux.
 
  ABSTRACT  
 
Pathogenic Vibrio cholerae secrete V. cholerae cytolysin (VCC), an 80 kDa pro-toxin that assembles into an oligomeric pore on target cell membranes following proteolytic cleavage and interaction with cell surface receptors. To gain insight into the activation and targeting activities of VCC, we solved the crystal structure of the pro-toxin at 2.3A by X-ray diffraction. The core cytolytic domain of VCC shares a fold similar to the staphylococcal pore-forming toxins, but in VCC an amino-terminal pro-domain and two carboxy-terminal lectin domains decorate the cytolytic domain. The pro-domain masks a protomer surface that likely participates in inter-protomer interactions in the cytolytic oligomer, thereby explaining why proteolytic cleavage and movement of the pro-domain is necessary for toxin activation. A single beta-octyl glucoside molecule outlines a possible receptor binding site on one lectin domain, and removal of this domain leads to a tenfold decrease in lytic activity toward rabbit erythrocytes. VCC activated by proteolytic cleavage assembles into an oligomeric species upon addition of soybean asolectin/cholesterol liposomes and this oligomer was purified in detergent micelles. Analytical ultracentrifugation and crystallographic analysis indicate that the resulting VCC oligomer is a heptamer. Taken together, these studies define the architecture of a pore forming toxin and associated lectin domains, confirm the stoichiometry of the assembled oligomer as heptameric, and suggest a common mechanism of assembly for staphylococcal and Vibrio cytolytic toxins.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. VCC and Staph pore-forming toxins have a similar cytolysin domain. (a) Stereoview of the superposition of the VCC cytolysin domain (blue) and the LukF structure (PDB code 3LKF, orange). Four loops (red arrows) within the membrane-interacting rim domain are longer in VCC than in LukF and contain a unique disulfide bond not seen in the Staph toxins (yellow arrow). A lipid-headgroup binding pocket (LBP) in LukF is defined by a loop structure that is missing in VCC. LukF has an additional b-strand at the amino and carboxy termini. The LukF pre-stem (red) consists of three b-strands folded against the central b-sandwich, while the VCC pre-stem (green) is composed of two extended b-strands held in place by a bracketing loop. (b) The interface between the pre-stem and b-sheet domains in VCC is composed of patches of hydrophobic (gray) and polar (magenta) residues in contrast to the entirely hydrophobic character of the corresponding LukF interface.
Figure 10.
Figure 10. Proposed mechanism for VCC and staphylococcal PFT assembly. In VCC, the monomer (1) binds to cell surfaces via interactions with the cytolysin (dark blue) domain and binding of carbohydrate receptors (orange, only shown in (1), but may remain associated throughout) by the b-prism (light blue) and/or b-trefoil (purple) domains. The red pro-region prevents assembly into the oligomeric form until proteolytic cleavage releases the domain (red arrow). Oligomerization is also blocked by steric overlap between the b-prism domains (2), which must rearrange (3) to allow the stem (green) to unfold for membrane insertion (4). Only two of seven protomers in the pre-pore intermediate are shown in (3) for clarity. The Staph toxins are also secreted as water-soluble monomers (5, LukF structure shown), and bind to membranes via hydrophobic interactions and a specific lipid headgroup binding pocket12 (6) leading to reduced proteolytic sensitivity of the pre-stem loop17 (green). Monomers diffuse laterally and assemble into a transient heptameric pre-pore structure83 (7, hypothetical model: five of seven subunits shown). In this metastable state, the amino-latches (red) are nudged away from the protomer core and become accessible to proteases.83 A final irreversible transformation leads to the insertion of the pre-stems into the membrane to form a 14-stranded b-barrel pore (8).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 350, 997-0) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21502531 S.De, and R.Olson (2011).
Crystal structure of the Vibrio cholerae cytolysin heptamer reveals common features among disparate pore-forming toxins.
  Proc Natl Acad Sci U S A, 108, 7385-7390.
PDB code: 3o44
21426913 S.Miyoshi, Y.Abe, M.Senoh, T.Mizuno, Y.Maehara, and H.Nakao (2011).
Inactivation of Vibrio vulnificus hemolysin through mutation of the N- or C-terminus of the lectin-like domain.
  Toxicon, 57, 904-908.  
20644623 H.N.Cinar, M.Kothary, A.R.Datta, B.D.Tall, R.Sprando, K.Bilecen, F.Yildiz, and B.McCardell (2010).
Vibrio cholerae hemolysin is required for lethality, developmental delay, and intestinal vacuolation in Caenorhabditis elegans.
  PLoS One, 5, e11558.  
19854900 S.Dutta, B.Mazumdar, K.K.Banerjee, and A.N.Ghosh (2010).
Three-dimensional structure of different functional forms of the Vibrio cholerae hemolysin oligomer: a cryo-electron microscopic study.
  J Bacteriol, 192, 169-178.  
19897654 T.Kashimoto, S.Ueno, T.Koga, S.Fukudome, H.Ehara, M.Komai, H.Sugiyama, and N.Susa (2010).
The aromatic ring of phenylalanine 334 is essential for oligomerization of Vibrio vulnificus hemolysin.
  J Bacteriol, 192, 568-574.  
20043185 U.Hinz, R.Apweiler, M.J.Martin, C.O'Donovan, M.Magrane, Y.Alam-Faruque, R.Antunes, D.Barrell, B.Bely, M.Bingley, D.Binns, L.Bower, P.Browne, W.M.Chan, E.Dimmer, R.Eberhardt, A.Fedotov, R.Foulger, J.Garavelli, R.Huntley, J.Jacobsen, M.Kleen, K.Laiho, R.Leinonen, D.Legge, Q.Lin, W.Liu, J.Luo, S.Orchard, S.Patient, D.Poggioli, M.Pruess, M.Corbett, G.di Martino, M.Donnelly, P.van Rensburg, A.Bairoch, L.Bougueleret, I.Xenarios, S.Altairac, A.Auchincloss, G.Argoud-Puy, K.Axelsen, D.Baratin, M.C.Blatter, B.Boeckmann, J.Bolleman, L.Bollondi, E.Boutet, S.B.Quintaje, L.Breuza, A.Bridge, E.de Castro, L.Ciapina, D.Coral, E.Coudert, I.Cusin, F.David, G.Delbard, M.Doche, D.Dornevil, P.D.Roggli, S.Duvaud, A.Estreicher, L.Famiglietti, M.Feuermann, S.Gehant, N.Farriol-Mathis, S.Ferro, E.Gasteiger, A.Gateau, V.Gerritsen, A.Gos, N.Gruaz-Gumowski, U.Hinz, C.Hulo, N.Hulo, J.James, S.Jimenez, F.Jungo, T.Kappler, G.Keller, C.Lachaize, L.Lane-Guermonprez, P.Langendijk-Genevaux, V.Lara, P.Lemercier, D.Lieberherr, T.d.e. .O.Lima, V.Mangold, X.Martin, P.Masson, M.Moinat, A.Morgat, A.Mottaz, S.Paesano, I.Pedruzzi, S.Pilbout, V.Pillet, and S.Poux (2010).
From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase.
  Cell Mol Life Sci, 67, 1049-1064.  
19907657 G.Ou, P.K.Rompikuntal, A.Bitar, B.Lindmark, K.Vaitkevicius, S.N.Wai, and M.L.Hammarström (2009).
Vibrio cholerae cytolysin causes an inflammatory response in human intestinal epithelial cells that is modulated by the PrtV protease.
  PLoS One, 4, e7806.  
19494904 H.Bayley (2009).
Membrane-protein structure: Piercing insights.
  Nature, 459, 651-652.  
  19309687 S.Berne, L.Lah, and K.Sepcińá (2009).
Aegerolysins: structure, function, and putative biological role.
  Protein Sci, 18, 694-706.  
19143841 T.Mizuno, S.Z.Sultan, Y.Kaneko, T.Yoshimura, Y.Maehara, H.Nakao, T.Tsuchiya, S.Shinoda, and S.Miyoshi (2009).
Modulation of Vibrio mimicus hemolysin through limited proteolysis by an endogenous metalloprotease.
  FEBS J, 276, 825-834.  
18713007 A.Valeva, I.Siegel, M.Wylenzek, T.M.Wassenaar, S.Weis, N.Heinz, R.Schmitt, C.Fischer, R.Reinartz, S.Bhakdi, and I.Walev (2008).
Putative identification of an amphipathic alpha-helical sequence in hemolysin of Escherichia coli (HlyA) involved in transmembrane pore formation.
  Biol Chem, 389, 1201-1207.  
17882454 A.Valeva, I.Walev, S.Weis, F.Boukhallouk, T.M.Wassenaar, and S.Bhakdi (2008).
Pro-inflammatory feedback activation cycle evoked by attack of Vibrio cholerae cytolysin on human neutrophil granulocytes.
  Med Microbiol Immunol, 197, 285-293.  
18440555 D.J.Slade, L.L.Lovelace, M.Chruszcz, W.Minor, L.Lebioda, and J.M.Sodetz (2008).
Crystal structure of the MACPF domain of human complement protein C8 alpha in complex with the C8 gamma subunit.
  J Mol Biol, 379, 331-342.
PDB code: 2rd7
18778941 G.Anderluh, and J.H.Lakey (2008).
Disparate proteins use similar architectures to damage membranes.
  Trends Biochem Sci, 33, 482-490.  
18390598 P.Schön, A.J.García-Sáez, P.Malovrh, K.Bacia, G.Anderluh, and P.Schwille (2008).
Equinatoxin II permeabilizing activity depends on the presence of sphingomyelin and lipid phase coexistence.
  Biophys J, 95, 691-698.  
18553932 S.Farrand, E.Hotze, P.Friese, S.K.Hollingshead, D.F.Smith, R.D.Cummings, G.L.Dale, and R.K.Tweten (2008).
Characterization of a streptococcal cholesterol-dependent cytolysin with a lewis y and b specific lectin domain.
  Biochemistry, 47, 7097-7107.  
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 code is shown on the right.