2vkd
From Proteopedia
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|PDB= 2vkd |SIZE=350|CAPTION= <scene name='initialview01'>2vkd</scene>, resolution 2.53Å | |PDB= 2vkd |SIZE=350|CAPTION= <scene name='initialview01'>2vkd</scene>, resolution 2.53Å | ||
|SITE= <scene name='pdbsite=AC1:Mn+Binding+Site+For+Chain+A'>AC1</scene>, <scene name='pdbsite=AC2:Upg+Binding+Site+For+Chain+A'>AC2</scene>, <scene name='pdbsite=AC3:Mn+Binding+Site+For+Chain+A'>AC3</scene>, <scene name='pdbsite=AC4:Mn+Binding+Site+For+Chain+A'>AC4</scene>, <scene name='pdbsite=AC5:Mn+Binding+Site+For+Chain+B'>AC5</scene>, <scene name='pdbsite=AC6:Upg+Binding+Site+For+Chain+B'>AC6</scene>, <scene name='pdbsite=AC7:Mn+Binding+Site+For+Chain+C'>AC7</scene> and <scene name='pdbsite=AC8:Upg+Binding+Site+For+Chain+C'>AC8</scene> | |SITE= <scene name='pdbsite=AC1:Mn+Binding+Site+For+Chain+A'>AC1</scene>, <scene name='pdbsite=AC2:Upg+Binding+Site+For+Chain+A'>AC2</scene>, <scene name='pdbsite=AC3:Mn+Binding+Site+For+Chain+A'>AC3</scene>, <scene name='pdbsite=AC4:Mn+Binding+Site+For+Chain+A'>AC4</scene>, <scene name='pdbsite=AC5:Mn+Binding+Site+For+Chain+B'>AC5</scene>, <scene name='pdbsite=AC6:Upg+Binding+Site+For+Chain+B'>AC6</scene>, <scene name='pdbsite=AC7:Mn+Binding+Site+For+Chain+C'>AC7</scene> and <scene name='pdbsite=AC8:Upg+Binding+Site+For+Chain+C'>AC8</scene> | ||
| - | |LIGAND= <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene> | + | |LIGAND= <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UPG:URIDINE-5'-DIPHOSPHATE-GLUCOSE'>UPG</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[2vl8|2VL8]], [[2vkh|2VKH]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2vkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vkd OCA], [http://www.ebi.ac.uk/pdbsum/2vkd PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2vkd RCSB]</span> | ||
}} | }} | ||
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[[Category: Schulz, G E.]] | [[Category: Schulz, G E.]] | ||
[[Category: Ziegler, M O.P.]] | [[Category: Ziegler, M O.P.]] | ||
| - | [[Category: MN]] | ||
| - | [[Category: UPG]] | ||
[[Category: glycosyltransferase]] | [[Category: glycosyltransferase]] | ||
[[Category: toxin]] | [[Category: toxin]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:13:16 2008'' |
Revision as of 02:13, 31 March 2008
| |||||||
| , resolution 2.53Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | , , , , , , and | ||||||
| Ligands: | , | ||||||
| Related: | 2VL8, 2VKH
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF LETHAL TOXIN FROM CLOSTRIDIUM SORDELLII IN COMPLEX WITH UDP-GLC AND MANGANESE ION
Overview
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 Mn(2+), was catalytically competent. Surprisingly, the structure of lethal toxin with Ca(2+) (instead of Mn(2+)) at the cofactor position showed a bound donor substrate with a disassembled active center, indicating that the strictly octahedral coordination sphere of Mn(2+) is indispensable to the integrity of the enzyme. The homologous structures of alpha-toxin without substrate, distorted lethal toxin with Ca(2+) plus donor, active lethal toxin with Mn(2+) 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 Ca(2+)-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.
About this Structure
2VKD is a Single protein structure of sequence from Clostridium sordellii. Full crystallographic information is available from OCA.
Reference
Conformational Changes and Reaction of Clostridial Glycosylating Toxins., Ziegler MO, Jank T, Aktories K, Schulz GE, J Mol Biol. 2008 Jan 5;. PMID:18325534
Page seeded by OCA on Mon Mar 31 05:13:16 2008
