1EEI

CHOLERA TOXIN B-PENTAMER COMPLEXED WITH METANITROPHENYL-ALPHA-D-GALACTOSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Exploration of the GM1 receptor-binding site of heat-labile enterotoxin and cholera toxin by phenyl-ring-containing galactose derivatives.

Fan, E.Merritt, E.A.Zhang, Z.Pickens, J.C.Roach, C.Ahn, M.Hol, W.G.

(2001) Acta Crystallogr D Biol Crystallogr 57: 201-212

  • DOI: 10.1107/s0907444900016814
  • Primary Citation of Related Structures:  
    1EEF, 1EEI, 1EFI, 1FD7

  • PubMed Abstract: 
  • Cholera toxin (CT) and the closely related heat-labile enterotoxin of Escherichia coli (LT) are responsible for numerous cases of diarrhea worldwide, leading to considerable morbidity and mortality. The B subunits of these heterohexameric AB(5) toxins form a pentameric arrangement which is responsible for binding to the receptor GM1 of the target epithelial cells of the host ...

    Cholera toxin (CT) and the closely related heat-labile enterotoxin of Escherichia coli (LT) are responsible for numerous cases of diarrhea worldwide, leading to considerable morbidity and mortality. The B subunits of these heterohexameric AB(5) toxins form a pentameric arrangement which is responsible for binding to the receptor GM1 of the target epithelial cells of the host. Blocking these B pentamer-receptor interactions forms an avenue for therapeutic intervention. Here, the structural characterization of potential receptor-blocking compounds are described based on the previously identified inhibitor m-nitrophenyl-alpha-D-galactoside (MNPG). The structure of a CTB-MNPG complex confirms that the binding mode of this inhibitor is identical in the two homologous toxins CT and LT and is characterized by a glycosyl linkage geometry that leads to displacement of a well ordered water molecule near the amide group of Gly33 by the O1-substituent of MNPG. This glycosyl geometry is not maintained in the absence of a substituent that can displace this water, as shown by a complex of LTB with p-aminophenyl-alpha-D-galactoside (PAPG). New compounds were synthesized to investigate the feasibility of maintaining the favorable binding interactions exhibited by MNPG while gaining increased affinity through the addition of hydrophobic substituents complementary to either of two hydrophobic regions of the receptor-binding site. The structural characterization of complexes of LTB with two of these compounds, 3-benzylaminocarbonylphenyl-alpha-D-galactoside (BAPG) and 2-phenethyl-7-(2,3-dihydrophthalazine-1,4-dione)-alpha-D-galactoside (PEPG), demonstrates a partial success in this goal. Both compounds exhibit a mixture of binding modes, some of which are presumably influenced by the local packing environment at multiple crystallographically independent binding sites. The terminal phenyl ring of BAPG associates either with the phenyl group of Tyr12 or with the hydrophobic patch formed by Lys34 and Ile58. The latter interaction is also made by the terminal phenyl substituent of PEPG, despite a larger ring system linking the galactose moiety to the terminal phenyl. However, neither BAPG nor PEPG displaces the intended target water molecule. Both of the designed compounds exhibit increased affinity relative to the galactose and to PAPG notwithstanding the failure to displace a bound water, confirming that additional favorable hydrophobic interactions can be gained by extending the starting inhibitor by a hydrophobic tail. The insight gained from these structures should allow the design of additional candidate inhibitors that retain both the glycosyl geometry and water displacement exhibited by MNPG and the favorable hydrophobic interactions exhibited by BAPG and PEPG.


    Related Citations: 
    • The 1.25 A Resolution Refinement of the Cholera Toxin B-Pentamer: Evidence of Peptide Backbone Strain at the Receptor-binding Site.
      Merritt, E.A., Kuhn, P., Sarfaty, S., Erbe, J.L., Holmes, R.K., Hol, W.G.
      (1998) J Mol Biol 282: 1043
    • Structural Foundation for the Design of Receptor Antagonists Targeting Escherichia Heat-Labile Enterotoxin
      Merritt, E.A., Sarfaty, S., Feil, I.K., Hol, W.G.J.
      (1997) Structure 5: 1485

    Organizational Affiliation

    Department of Biological Structure, University of Washington, Seattle 98195, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (CHOLERA TOXIN B)A [auth D], B [auth E], C [auth F], D [auth G], E [auth H]103Vibrio choleraeMutation(s): 0 
Gene Names: ctxBC9J66_18955ERS013165_03981ERS013197_06217ERS013202_03762ERS013206_03003
Find proteins for Q57193 (Vibrio cholerae)
Explore Q57193 
Go to UniProtKB:  Q57193
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GAA
Query on GAA

Download Ideal Coordinates CCD File 
F [auth D], G [auth E], H [auth F], I [auth G], J [auth H]3-nitrophenyl alpha-D-galactopyranoside
C12 H15 N O8
VCCMGHVCRFMITI-IIRVCBMXSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GAAIC50 :  700000   nM  PDBBind
GAAIC50:  700000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.9α = 90
b = 69.55β = 90
c = 130.66γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-02-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary