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2vk9

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CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF ALPHA-TOXIN FROM CLOSTRIDIUM NOVYI

Structural highlights

2vk9 is a 1 chain structure with sequence from Clostridium novyi. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.85Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TCDA_CLONO Precursor of a cytotoxin, which enters into host cells and mediates autoprocessing to release the active toxin (N-acetylglucosaminyltransferase TcdA) into the host cytosol (By similarity). Once entered into host cells, acidification in the endosome promotes the membrane insertion of the translocation region and formation of a pore, leading to translocation of the GT44 and peptidase C80 domains across the endosomal membrane (By similarity). This activates the peptidase C80 domain and autocatalytic processing, releasing the N-terminal part (N-acetylglucosaminyltransferase TcdA), which constitutes the active part of the toxin, in the cytosol (PubMed:17334356).[UniProtKB:P18177]^[1] Active form of the toxin, which is released into the host cytosol following autoprocessing and inactivates small GTPases (PubMed:8810274, PubMed:16157585). Acts by mediating monoglycosylation of small GTPases of the Rho family (Rac1, RhoA, RhoG and Cdc42) in host cells at the conserved threonine residue located in the switch I region ('Thr-37/35'), using UDP-N-acetyl-alpha-D-glucosamine as the sugar donor (PubMed:8810274, PubMed:16157585). Monoglycosylation of host small GTPases completely prevents the recognition of the downstream effector, blocking the GTPases in their inactive form, leading to actin cytoskeleton disruption and cell death (PubMed:8810274).^[2] ^[3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

Conformational changes and reaction of clostridial glycosylating toxins.,Ziegler MO, Jank T, Aktories K, Schulz GE J Mol Biol. 2008 Apr 11;377(5):1346-56. Epub 2008 Jan 5. PMID:18325534^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Reineke J, Tenzer S, Rupnik M, Koschinski A, Hasselmayer O, Schrattenholz A, Schild H, von Eichel-Streiber C. Autocatalytic cleavage of Clostridium difficile toxin B. Nature. 2007 Mar 22;446(7134):415-9. doi: 10.1038/nature05622. Epub 2007 Mar 4. PMID:17334356 doi:http://dx.doi.org/10.1038/nature05622
↑ Jank T, Reinert DJ, Giesemann T, Schulz GE, Aktories K. Change of the donor substrate specificity of Clostridium difficile toxin B by site-directed mutagenesis. J Biol Chem. 2005 Nov 11;280(45):37833-8. doi: 10.1074/jbc.M506836200. Epub 2005 , Sep 12. PMID:16157585 doi:http://dx.doi.org/10.1074/jbc.M506836200
↑ Selzer J, Hofmann F, Rex G, Wilm M, Mann M, Just I, Aktories K. Clostridium novyi alpha-toxin-catalyzed incorporation of GlcNAc into Rho subfamily proteins. J Biol Chem. 1996 Oct 11;271(41):25173-7. PMID:8810274 doi:10.1074/jbc.271.41.25173
↑ Ziegler MO, Jank T, Aktories K, Schulz GE. Conformational changes and reaction of clostridial glycosylating toxins. J Mol Biol. 2008 Apr 11;377(5):1346-56. Epub 2008 Jan 5. PMID:18325534 doi:10.1016/j.jmb.2007.12.065

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2vk9"

@@ Line 1: / Line 1: @@
 ==CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF ALPHA-TOXIN FROM CLOSTRIDIUM NOVYI==
-<StructureSection load='2vk9' size='340' side='right' caption='[[2vk9]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
+<StructureSection load='2vk9' size='340' side='right'caption='[[2vk9]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2vk9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_novyi Clostridium novyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VK9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VK9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2vk9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_novyi Clostridium novyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VK9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VK9 FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2vk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vk9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vk9 RCSB], [http://www.ebi.ac.uk/pdbsum/2vk9 PDBsum]</span></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.85&#8491;</td></tr>
-<table>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vk9 OCA], [https://pdbe.org/2vk9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vk9 RCSB], [https://www.ebi.ac.uk/pdbsum/2vk9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vk9 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TCDA_CLONO TCDA_CLONO] Precursor of a cytotoxin, which enters into host cells and mediates autoprocessing to release the active toxin (N-acetylglucosaminyltransferase TcdA) into the host cytosol (By similarity). Once entered into host cells, acidification in the endosome promotes the membrane insertion of the translocation region and formation of a pore, leading to translocation of the GT44 and peptidase C80 domains across the endosomal membrane (By similarity). This activates the peptidase C80 domain and autocatalytic processing, releasing the N-terminal part (N-acetylglucosaminyltransferase TcdA), which constitutes the active part of the toxin, in the cytosol (PubMed:17334356).[UniProtKB:P18177]<ref>PMID:17334356</ref>   Active form of the toxin, which is released into the host cytosol following autoprocessing and inactivates small GTPases (PubMed:8810274, PubMed:16157585). Acts by mediating monoglycosylation of small GTPases of the Rho family (Rac1, RhoA, RhoG and Cdc42) in host cells at the conserved threonine residue located in the switch I region ('Thr-37/35'), using UDP-N-acetyl-alpha-D-glucosamine as the sugar donor (PubMed:8810274, PubMed:16157585). Monoglycosylation of host small GTPases completely prevents the recognition of the downstream effector, blocking the GTPases in their inactive form, leading to actin cytoskeleton disruption and cell death (PubMed:8810274).<ref>PMID:16157585</ref> <ref>PMID:8810274</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vk/2vk9_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vk/2vk9_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2vk9 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 23: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2vk9" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Alpha-toxin|Alpha-toxin]]
+*[[Hemolysin 3D structures|Hemolysin 3D structures]]
 == References ==
 <references/>
@@ Line 31: / Line 36: @@
 </StructureSection>
 [[Category: Clostridium novyi]]
-[[Category: Aktories, K.]]
+[[Category: Large Structures]]
-[[Category: Jank, T.]]
+[[Category: Aktories K]]
-[[Category: Schulz, G E.]]
+[[Category: Jank T]]
-[[Category: Ziegler, M O.P.]]
+[[Category: Schulz GE]]
-[[Category: Glycosyltransferase]]
+[[Category: Ziegler MOP]]
-[[Category: Toxin]]

2vk9

From Proteopedia

Current revision

CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF ALPHA-TOXIN FROM CLOSTRIDIUM NOVYI

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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