3Q9O | pdb_00003q9o

Full-length Cholix toxin from Vibrio cholerae in complex with NAD

• PDB DOI: https://doi.org/10.2210/pdb3Q9O/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio cholerae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-01-09 Released: 2012-01-04 
• Deposition Author(s): Merrill, A.R., Jorgensen, R., Fieldhouse, R.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.203 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

The 1.8 a cholix toxin crystal structure in complex with NAD+ and evidence for a new kinetic model.

Fieldhouse, R.J., Jorgensen, R., Lugo, M.R., Merrill, A.R.

(2012) J Biological Chem 287: 21176-21188

• PubMed: 22535961 
• DOI: https://doi.org/10.1074/jbc.M111.337311
• Primary Citation Related Structures: 
  3Q9O


• PubMed Abstract: 
  

  Certain Vibrio cholerae strains produce cholix, a potent protein toxin that has diphthamide-specific ADP-ribosyltransferase activity against eukaryotic elongation factor 2. Here we present a 1.8 Å crystal structure of cholix in complex with its natural substrate, nicotinamide adenine dinucleotide (NAD(+)). We also substituted hallmark catalytic residues by site-directed mutagenesis and analyzed both NAD(+) binding and ADP-ribosyltransferase activity using a fluorescence-based assay. These data are the basis for a new kinetic model of cholix toxin activity. Further, the new structural data serve as a reference for continuing inhibitor development for this toxin class.

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Organizational Affiliation: 
• Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 72.81 kDa 
• Atom Count: 5,317 
• Modeled Residue Count: 605 
• Deposited Residue Count: 642 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
exotoxin A	A	642	Vibrio cholerae	Mutation(s): 0  Gene Names: chxa, toxA EC: 2.4.2.36
UniProt
Find proteins for Q5EK40 (Vibrio cholerae) Explore Q5EK40  Go to UniProtKB:  Q5EK40

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	B [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.203 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.929	α = 90
b = 89.083	β = 95.11
c = 80.283	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
Macromolecular	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-04 
Deposition Author(s): Merrill, A.R., Jorgensen, R., Fieldhouse, R.J.

Revision History  

• Version 1.0: 2012-01-04
  Type: Initial release
  
• Version 1.1: 2012-05-09
  Changes: Database references
• Version 1.2: 2012-07-04
  Changes: Database references
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary