Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 46489.01 
• Atom Count: 3068 
• Residue Count: 410 
• Unique protein chains: 2

2A9K

Crystal structure of the C3bot-NAD-RalA complex reveals a novel type of action of a bacterial exoenzyme

• DOI: 10.2210/pdb2A9K/pdb

• Classification: PROTEIN BINDING/TRANSFERASE
• Organism(s): Clostridium botulinum D phage, Homo sapiens
• Expression System: Escherichia coli BL21


• Deposited: 2005-07-12 Released: 2005-10-11 
• Deposition Author(s): Pautsch, A., Vogelsgesang, M., Trankle, J., Herrmann, C., Aktories, K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.225 
• R-Value Work: 0.186 

Literature

Crystal structure of the C3bot-RalA complex reveals a novel type of action of a bacterial exoenzyme.

Pautsch, A., Vogelsgesang, M., Trankle, J., Herrmann, C., Aktories, K.

(2005) Embo J. 24: 3670-3680

• PubMed: 16177825 
• DOI: 10.1038/sj.emboj.7600813
• Primary Citation of Related Structures:  
  2A78


• PubMed Abstract: 
  

C3 exoenzymes from bacterial pathogens ADP-ribosylate and inactivate low-molecular-mass GTPases of the Rho subfamily. Ral, a Ras subfamily GTPase, binds the C3 exoenzymes from Clostridium botulinum and C. limosum with high affinity without being a substrate for ADP ribosylation. In the complex, the ADP-ribosyltransferase activity of C3 is blocked, while binding of NAD and NAD-glycohydrolase activity remain. Here we report the crystal structure of C3 from C. botulinum in a complex with GDP-bound RalA at 1.8 A resolution. C3 binds RalA with a helix-loop-helix motif that is adjacent to the active site. A quaternary complex with NAD suggests a mode for ADP-ribosyltransferase inhibition. Interaction of C3 with RalA occurs at a unique interface formed by the switch-II region, helix alpha3 and the P loop of the GTPase. C3-binding stabilizes the GDP-bound conformation of RalA and blocks nucleotide release. Our data indicate that C. botulinum exoenzyme C3 is a single-domain toxin with bifunctional properties targeting Rho GTPases by ADP ribosylation and Ral by a guanine nucleotide dissociation inhibitor-like effect, which blocks nucleotide exchange.

---

Related Citations: 

• Molecular recognition of an ADP-ribosylating Clostridium botulinum C3 exoenzyme by RalA GTPase.
  Holbourn, K.P.,Sutton, J.M.,Evans, H.R.,Shone, C.C.,Acharya, K.R.
  (2005) Proc.Natl.Acad.Sci.Usa 102: 5357




---

Organizational Affiliation: 

Structural Research, Department of Integrated Lead Discovery, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Ras-related protein Ral-A	A	187	Homo sapiens	Mutation(s): 0  Gene Names: RALA (RAL)
Find proteins for P11233 (Homo sapiens) Go to Gene View: RALA Go to UniProtKB:  P11233

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Mono-ADP-ribosyltransferase C3	B	223	Clostridium botulinum D phage	Mutation(s): 0  Gene Names: C3 EC: 2.4.2.-
Find proteins for P15879 (Clostridium botulinum D phage) Go to Gene View: C3 Go to UniProtKB:  P15879

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GDP	A	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
NAD	B	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.225 
• R-Value Work: 0.186 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 35.260	α = 90.00
b = 113.850	β = 106.40
c = 56.310	γ = 90.00

Software Package:

Software Name	Purpose
MAR345	data collection
REFMAC	refinement
MOLREP	phasing
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-07-12 
• Released Date: 2005-10-11 
• Deposition Author(s): Pautsch, A., Vogelsgesang, M., Trankle, J., Herrmann, C., Aktories, K.

Revision History 

• Version 1.0: 2005-10-11
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Advisory, Version format compliance
• Version 1.3: 2017-10-11
  Type: Refinement description