Conformational Changes and Reaction of Clostridial Glycosylating Toxins.

Ziegler, M.O.P.; Jank, T.; Aktories, K.; Schulz, G.E.

doi:10.2210/pdb2vkh/pdb

Macromolecule Content

Total Structure Weight: 192639.31
Atom Count: 13312
Residue Count: 1638
Unique protein chains: 1

2VKH

CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF LETHAL TOXIN FROM CLOSTRIDIUM SORDELLII IN COMPLEX WITH UDP-GLC AND CALCIUM ION

DOI: 10.2210/pdb2VKH/pdb

Classification: TOXIN
Organism(s): Paeniclostridium sordellii
Expression System: Escherichia coli
Mutation(s): 2

Deposited: 2007-12-19 Released: 2008-03-18
Deposition Author(s): Ziegler, M.O.P., Jank, T., Aktories, K., Schulz, G.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.3 Å
R-Value Free: 0.273
R-Value Work: 0.235

wwPDB Validation3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Conformational Changes and Reaction of Clostridial Glycosylating Toxins.

Ziegler, M.O.P., Jank, T., Aktories, K., Schulz, G.E.

(2008) J.Mol.Biol. 377: 1346

PubMed: 18325534 Search on PubMed
DOI: 10.1016/j.jmb.2007.12.065
Primary Citation of Related Structures:
2VKD, 2VK9

PubMed Abstract:

The crystal structures of the catalytic fragments of 'lethal toxin' from Clostridium sordellii and of 'alpha-toxin' from Clostridium novyi have been established. Almost half of the residues follow the chain fold of the glycosyl-transferase type A family of enzymes; the other half forms large alpha-helical protrusions that are likely to confer specificity for the respective targeted subgroup of Rho proteins in the cell. In the crystal, the active center of alpha-toxin contained no substrates and was disassembled, whereas that of lethal toxin, which was ligated with the donor substrate UDP-glucose and cofactor Mn2+, was catalytically competent. Surprisingly, the structure of lethal toxin with Ca2+ (instead of Mn2+) at the cofactor position showed a bound donor substrate with a disassembled active center, indicating that the strictly octahedral coordination sphere of Mn2+ is indispensable to the integrity of the enzyme. The homologous structures of alpha-toxin without substrate, distorted lethal toxin with Ca2+ plus donor, active lethal toxin with Mn2+ plus donor and the homologous Clostridium difficile toxin B with a hydrolyzed donor have been lined up to show the geometry of several reaction steps. Interestingly, the structural refinement of one of the three crystallographically independent molecules of Ca2+-ligated lethal toxin resulted in the glucosyl half-chair conformation expected for glycosyl-transferases that retain the anomeric configuration at the C1'' atom. A superposition of six acceptor substrates bound to homologous enzymes yielded the position of the nucleophilic acceptor atom with a deviation of <1 A. The resulting donor-acceptor geometry suggests that the reaction runs as a circular electron transfer in a six-membered ring, which involves the deprotonation of the nucleophile by the beta-phosphoryl group of the donor substrate UDP-glucose.

Organizational Affiliation:

Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Albertstr. 21, D-79104 Freiburg im Breisgau, Germany.

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
CYTOTOXIN L	A, B, C	546	Paeniclostridium sordellii	Mutation(s): 2
Find proteins for Q46342 (Paeniclostridium sordellii) Go to UniProtKB: Q46342
Protein Feature View Full Protein Feature View for Q46342

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
UPG Query on UPG Download SDF File Download CCD File	A, B, C	URIDINE-5'-DIPHOSPHATE-GLUCOSE URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER C₁₅ H₂₄ N₂ O₁₇ P₂ HSCJRCZFDFQWRP-JZMIEXBBSA-N		Ligand Interaction
CA Query on CA Download SDF File Download CCD File	A, B, C	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Ligand Interaction