2C8B | pdb_00002c8b

Structure of the ARTT motif Q212A mutant C3bot1 Exoenzyme (Free state, crystal form II)

• PDB DOI: https://doi.org/10.2210/pdb2C8B/pdb

• Classification: TRANSFERASE
• Organism(s): Clostridium botulinum D phage
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2005-12-03 Released: 2007-02-27 
• Deposition Author(s): Stura, E.A., Menetrey, J., Flatau, G., Boquet, P., Menez, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.218 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Structural Basis for the Nad-Hydrolysis Mechanism and the Artt-Loop Plasticity of C3 Exoenzymes.

Menetrey, J., Flatau, G., Boquet, P., Menez, A., Stura, E.A.

(2008) Protein Sci 17: 878

• PubMed: 18369192 
• DOI: https://doi.org/10.1110/ps.073398508
• Primary Citation Related Structures: 
  2C89, 2C8A, 2C8B, 2C8C, 2C8D, 2C8E, 2C8F


• PubMed Abstract: 
  

  C3-like exoenzymes are ADP-ribosyltransferases that specifically modify some Rho GTPase proteins, leading to their sequestration in the cytoplasm, and thus inhibiting their regulatory activity on the actin cytoskeleton. This modification process goes through three sequential steps involving NAD-hydrolysis, Rho recognition, and binding, leading to Rho ADP-ribosylation. Independently, three distinct residues within the ARTT loop of the C3 exoenzymes are critical for each of these steps. Supporting the critical role of the ARTT loop, we have shown previously that it adopts a distinct conformation upon NAD binding. Here, we present seven wild-type and ARTT loop-mutant structures of C3 exoenzyme of Clostridium botulinum free and bound to its true substrate, NAD, and to its NAD-hydrolysis product, nicotinamide. Altogether, these structures expand our understanding of the conformational diversity of the C3 exoenzyme, mainly within the ARTT loop.

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Organizational Affiliation: 
• Institut Curie, Centre de Recherche, Paris F-75248, France. [e-mail]

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: 23.73 kDa 
• Atom Count: 1,830 
• Modeled Residue Count: 201 
• Deposited Residue Count: 211 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MONO-ADP-RIBOSYLTRANSFERASE C3	A [auth X]	211	Clostridium botulinum D phage	Mutation(s): 1  EC: 2.4.2
UniProt
Find proteins for P15879 (Clostridium botulinum D phage) Explore P15879  Go to UniProtKB:  P15879

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth X], C [auth X]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.218 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.941	α = 90
b = 86.884	β = 117.31
c = 42.896	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-27 
Deposition Author(s): Stura, E.A., Menetrey, J., Flatau, G., Boquet, P., Menez, A.

Revision History  

• Version 1.0: 2007-02-27
  Type: Initial release
  
• Version 1.1: 2011-06-02
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description