PDBsum entry: 2vkd

Toxin

PDB-id: 2vkd

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Description

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Header records

References

PROCHECK

Protein chains

542 a.a. *

Ligands

UPG ×3

Metal ions

_MN ×5

Waters ×148

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

2vkd

Name:

Toxin

Title:

Crystal structure of the catalytic domain of lethal toxin from clostridium sordellii in complex with udp-glc and manganese ion

Structure:

Cytotoxin l. Chain: a, b, c. Fragment: catalytic domain, residues 1-546. Synonym: lethal toxin. Engineered: yes. Mutation: yes

Source:

Clostridium sordellii. Organism_taxid: 1505. Strain: 6018. Expressed in: escherichia coli. Expression_system_taxid: 562

UniProt:

Chains A, B, C: Q46342 (Q46342_CLOSO)

Seq:

Struc:

Seq:

Struc:

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Struc:

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Struc:

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Struc:

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Struc:

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Struc:

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Struc:

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Struc:

Seq:

2364 a.a.

Struc:

542 a.a.*

Key:	PfamA domain	PfamB domain
Secondary structure

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Resolution:

2.53Å

R-factor:

0.247

R-free:

0.288

Authors:

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

Key ref:

M.O.Ziegler et al. (2008). Conformational changes and reaction of clostridial glycosylating toxins.. J Mol Biol, 377, 1346-1356. [PubMed id: 18325534] [DOI: 10.1016/j.jmb.2007.12.065]

Date:

18-Dec-07

Release date:

18-Mar-08

Related entries:

2vl8 crystal structure of the catalytic domain of lethal toxin from clostridium sordellii in complex with udp, castanospermine and calcium ion
2vkh crystal structure of the catalytic domain of lethal toxin from clostridium sordellii in complex with udp-glc and calcium ion

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Key reference

DOI no: 10.1016/j.jmb.2007.12.065

J Mol Biol 377:1346-1356 (2008)

PubMed id: 18325534

Conformational changes and reaction of clostridial glycosylating toxins.

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

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.

Selected figure(s)

Figure 1.
Fig. 1. Stereoview showing the Cα backbones of LT (blue) with bound UDP-Glc (gray) and Mn^2 + (pink), αTox (green) and ToxB without the ligands (red). The common GT-A chain fold is indicated by lighter colors. The view presents the active center pocket.

Figure 6.
Fig. 6. Proposed scheme for the reaction of clostridial glycosylating toxins. One of the β-phosphoryl oxygen atoms is the only available base. The developing plane of the suggested half-chair intermediate is indicated by dots. The half-chair opens the space around the C1″ atom for nucleophilic attack (see Fig. 5a). The suggested reaction is a circular electron transfer that does not directly involve any residues of the toxin. Most likely, the transfers start with the split of the glycosidic bond (step a) because it seems to result in the most stable transient state. This split increases the pK of the phosphoryl oxygen, facilitating deprotonation of the acceptor; and it provides more space for the nucleophilic attack.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 377, 1346-1356) copyright 2008.

Figures were selected by the author.