2VKD

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

Summary for 2VKD

• Entry DOI: 10.2210/pdb2vkd/pdb
• Related: 2VKH 2VL8
• Descriptor: CYTOTOXIN L, MANGANESE (II) ION, URIDINE-5'-DIPHOSPHATE-GLUCOSE, ... (4 entities in total)
• Functional Keywords: toxin, glycosyltransferase
• Biological source: CLOSTRIDIUM SORDELLII
• Total number of polymer chains: 3
• Total formula weight: 192793.76

Authors

Ziegler, M.O.P.,Jank, T.,Aktories, K.,Schulz, G.E. (deposition date: 2007-12-18, release date: 2008-03-18, Last modification date: 2024-05-08)

Primary citation

Ziegler, M.O.P.,Jank, T.,Aktories, K.,Schulz, G.E.
Conformational Changes and Reaction of Clostridial Glycosylating Toxins.
J.Mol.Biol., 377:1346-, 2008

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.

PubMed: 18325534
DOI: 10.1016/J.JMB.2007.12.065

Experimental method

X-RAY DIFFRACTION (2.53 Å)