2bvm - Revision history

OCA at 13:56, 13 December 2023

2023-12-13T13:56:41Z

← Older revision		Revision as of 13:56, 13 December 2023
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	<StructureSection load='2bvm' size='340' side='right'caption='[[2bvm]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='2bvm' size='340' side='right'caption='[[2bvm]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2bvm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_difficilis"_hall_and_o'toole_1935 "bacillus difficilis" hall and o'toole 1935~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BVM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BVM FirstGlance]. <br>		<table><tr><td colspan='2'>[[2bvm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridioides_difficile Clostridioides difficile]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BVM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BVM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene~~></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]] 2.55Å</td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2bvl\|2bvl]]</div~~></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2bvm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bvm OCA], [https://pdbe.org/2bvm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bvm RCSB], [https://www.ebi.ac.uk/pdbsum/2bvm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bvm ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2bvm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bvm OCA], [https://pdbe.org/2bvm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bvm RCSB], [https://www.ebi.ac.uk/pdbsum/2bvm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bvm ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/TCDB_CLODI TCDB_CLODI] Precursor of a cytotoxin that targets and disrupts the colonic epithelium, inducing the host inflammatory and innate immune responses and resulting in diarrhea and pseudomembranous colitis (PubMed:20844489, PubMed:24919149). TcdB constitutes the main toxin that mediates the pathology of C.difficile infection, an opportunistic pathogen that colonizes the colon when the normal gut microbiome is disrupted (PubMed:19252482, PubMed:20844489). Compared to TcdA, TcdB is more virulent and more important for inducing the host inflammatory and innate immune responses (PubMed:19252482, PubMed:24919149). This form constitutes the precursor of the toxin: it enters into host cells and mediates autoprocessing to release the active toxin (Glucosyltransferase TcdB) into the host cytosol (PubMed:10768933, PubMed:11152463, PubMed:12941936, PubMed:17334356, PubMed:20498856). Targets colonic epithelia by binding to the frizzled receptors FZD1, FZD2 and FZD7, and enters host cells via clathrin-mediated endocytosis (PubMed:27680706). Frizzled receptors constitute the major host receptors in the colonic epithelium, but other receptors, such as CSPG4 or NECTIN3/PVRL3, have been identified (PubMed:25547119, PubMed:26038560, PubMed:27680706). Binding to carbohydrates and sulfated glycosaminoglycans on host cell surface also contribute to entry into cells (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 (PubMed:11152463, PubMed:12941936, PubMed:24567384). This activates the peptidase C80 domain and autocatalytic processing, releasing the N-terminal part (Glucosyltransferase TcdB), which constitutes the active part of the toxin, in the cytosol (PubMed:17334356, PubMed:27571750).[UniProtKB:P16154]<ref>PMID:10768933</ref> <ref>PMID:11152463</ref> <ref>PMID:12941936</ref> <ref>PMID:17334356</ref> <ref>PMID:19252482</ref> <ref>PMID:20498856</ref> <ref>PMID:20844489</ref> <ref>PMID:24567384</ref> <ref>PMID:24919149</ref> <ref>PMID:25547119</ref> <ref>PMID:26038560</ref> <ref>PMID:27571750</ref> <ref>PMID:27680706</ref> Active form of the toxin, which is released into the host cytosol following autoprocessing and inactivates small GTPases (PubMed:8144660, PubMed:7777059, PubMed:16157585, PubMed:17901056, PubMed:24905543, PubMed:24919149). Acts by mediating monoglucosylation of small GTPases of the Rho family (Rac1, RhoA, RhoB, RhoC, RhoG and Cdc42) in host cells at the conserved threonine residue located in the switch I region ('Thr-37/35'), using UDP-alpha-D-glucose as the sugar donor (PubMed:7777059, PubMed:16157585, PubMed:17901056, PubMed:24905543, PubMed:24919149). Monoglucosylation 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, resulting in the loss of colonic epithelial barrier function (PubMed:7777059, PubMed:24919149).<ref>PMID:16157585</ref> <ref>PMID:17901056</ref> <ref>PMID:24905543</ref> <ref>PMID:24919149</ref> <ref>PMID:7777059</ref> <ref>PMID:8144660</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Bacillus difficilis hall and o'toole 1935~~]]		[[Category: Clostridioides difficile]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Aktories, K]]		[[Category: Aktories K]]
	[[Category: Jank, T]]		[[Category: Jank T]]
	[[Category: Reinert~~, D J~~]]		[[Category: Reinert DJ]]
	[[Category: Schulz~~, G E]]~~		[[Category: Schulz GE]]
	~~[[Category: Glycosyltransferase]]~~
	~~[[Category: Toxin~~]]

OCA at 13:18, 24 November 2021

2021-11-24T13:18:52Z

← Older revision		Revision as of 13:18, 24 November 2021
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	<StructureSection load='2bvm' size='340' side='right'caption='[[2bvm]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='2bvm' size='340' side='right'caption='[[2bvm]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2bvm]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_difficilis"_hall_and_o'toole_1935 "bacillus difficilis" hall and o'toole 1935]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BVM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2BVM FirstGlance]. <br>		<table><tr><td colspan='2'>[[2bvm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_difficilis"_hall_and_o'toole_1935 "bacillus difficilis" hall and o'toole 1935]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BVM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BVM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2bvl\|2bvl]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2bvl\|2bvl]]</div></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2bvm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bvm OCA], [~~http~~://pdbe.org/2bvm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2bvm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2bvm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2bvm ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2bvm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bvm OCA], [https://pdbe.org/2bvm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bvm RCSB], [https://www.ebi.ac.uk/pdbsum/2bvm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bvm ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 08:10, 19 February 2020

2020-02-19T08:10:31Z

← Older revision		Revision as of 08:10, 19 February 2020
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	==Crystal structure of the catalytic domain of toxin B from Clostridium difficile in complex with UDP, Glc and manganese ion==		==Crystal structure of the catalytic domain of toxin B from Clostridium difficile in complex with UDP, Glc and manganese ion==
	<StructureSection load='2bvm' size='340' side='right' caption='[[2bvm]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='2bvm' size='340' side='right'caption='[[2bvm]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2bvm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_difficilis"_hall_and_o'toole_1935 "bacillus difficilis" hall and o'toole 1935]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BVM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BVM FirstGlance]. <br>		<table><tr><td colspan='2'>[[2bvm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_difficilis"_hall_and_o'toole_1935 "bacillus difficilis" hall and o'toole 1935]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BVM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BVM FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Bacillus difficilis hall and o'toole 1935]]		[[Category: Bacillus difficilis hall and o'toole 1935]]
			[[Category: Large Structures]]
	[[Category: Aktories, K]]		[[Category: Aktories, K]]
	[[Category: Jank, T]]		[[Category: Jank, T]]

OCA at 06:37, 16 May 2018

2018-05-16T06:37:46Z

← Older revision		Revision as of 06:37, 16 May 2018
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	==~~CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF TOXIN~~ B ~~FROM CLOSTRIDIUM DIFFICILE IN COMPLEX WITH~~ UDP, ~~GLC AND MANGANESE ION~~==
			==Crystal structure of the catalytic domain of toxin B from Clostridium difficile in complex with UDP, Glc and manganese ion==
	<StructureSection load='2bvm' size='340' side='right' caption='[[2bvm]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='2bvm' size='340' side='right' caption='[[2bvm]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2bvl\|2bvl]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2bvl\|2bvl]]</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2bvm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bvm OCA], [http://pdbe.org/2bvm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2bvm RCSB], [http://www.ebi.ac.uk/pdbsum/2bvm PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2bvm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bvm OCA], [http://pdbe.org/2bvm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2bvm RCSB], [http://www.ebi.ac.uk/pdbsum/2bvm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2bvm ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bv/2bvm_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bv/2bvm_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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=2bvm ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 11:30, 11 September 2015

2015-09-11T11:30:30Z

← Older revision		Revision as of 11:30, 11 September 2015
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	<StructureSection load='2bvm' size='340' side='right' caption='[[2bvm]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='2bvm' size='340' side='right' caption='[[2bvm]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2bvm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~[clostridium]_difficile [clostridium] difficile~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BVM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BVM FirstGlance]. <br>		<table><tr><td colspan='2'>[[2bvm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_difficilis"_hall_and_o'toole_1935 "bacillus difficilis" hall and o'toole 1935]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BVM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BVM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2bvl\|2bvl]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2bvl\|2bvl]]</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2bvm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bvm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2bvm RCSB], [http://www.ebi.ac.uk/pdbsum/2bvm PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2bvm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bvm OCA], [http://pdbe.org/2bvm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2bvm RCSB], [http://www.ebi.ac.uk/pdbsum/2bvm PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 2bvm" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Bacillus difficilis hall and o'toole 1935]]
	[[Category: Aktories, K]]		[[Category: Aktories, K]]
	[[Category: Jank, T]]		[[Category: Jank, T]]

OCA at 18:12, 15 January 2015

2015-01-15T18:12:25Z

← Older revision		Revision as of 18:12, 15 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2bvm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/[clostridium]_difficile [clostridium] difficile]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BVM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BVM FirstGlance]. <br>		<table><tr><td colspan='2'>[[2bvm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/[clostridium]_difficile [clostridium] difficile]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BVM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BVM FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2bvl\|2bvl]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2bvl\|2bvl]]</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=2bvm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bvm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2bvm RCSB], [http://www.ebi.ac.uk/pdbsum/2bvm PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2bvm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bvm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2bvm RCSB], [http://www.ebi.ac.uk/pdbsum/2bvm PDBsum]</span></td></tr>
	<table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 29:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Aktories, K.]]		[[Category: Aktories, K]]
	[[Category: Jank, T.]]		[[Category: Jank, T]]
	[[Category: Reinert, D J.]]		[[Category: Reinert, D J]]
	[[Category: Schulz, G E.]]		[[Category: Schulz, G E]]
	[[Category: Glycosyltransferase]]		[[Category: Glycosyltransferase]]
	[[Category: Toxin]]		[[Category: Toxin]]

OCA at 01:09, 30 September 2014

2014-09-30T01:09:58Z

← Older revision		Revision as of 01:09, 30 September 2014
Line 1:		Line 1:
	[[Image:~~2bvm~~.~~png~~\|~~left~~\|~~200px~~]]		==CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF TOXIN B FROM CLOSTRIDIUM DIFFICILE IN COMPLEX WITH UDP, GLC AND MANGANESE ION==
			<StructureSection load='2bvm' size='340' side='right' caption='[[2bvm]], [[Resolution\|resolution]] 2.55Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2bvm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/[clostridium]_difficile [clostridium] difficile]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BVM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BVM FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2bvl\|2bvl]]</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=2bvm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bvm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2bvm RCSB], [http://www.ebi.ac.uk/pdbsum/2bvm PDBsum]</span></td></tr>
			<table>
			== 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/bv/2bvm_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].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Toxin B is a member of the family of large clostridial cytotoxins which are of great medical importance. Its catalytic fragment was crystallized in the presence of UDP-glucose and Mn2+. The structure was determined at 2.2 A resolution, showing that toxin B belongs to the glycosyltransferase type A family. However, toxin B contains as many as 309 residues in addition to the common chainfold, which most likely contribute to the target specificity. A superposition with other glycosyltransferases shows the expected positions of the acceptor oxygen atom during glucosyl transfer and indicates further that the reaction proceeds probably along a single-displacement pathway. The C1'' donor carbon atom position is defined by the bound UDP and glucose. It assigns the surface area of toxin B that forms the interface to the target protein during the modifying reaction. A docking attempt brought the known acceptor atom, Thr37 O(gamma1) of the switch I region of the RhoA:GDP target structure, near the expected position. The relative orientation of the two proteins was consistent with both being attached to a membrane. Sequence comparisons between toxin B variants revealed that the highest exchange rate occurs around the active center at the putative docking interface, presumably due to a continuous hit-and-evasion struggle between Clostridia and their eukaryotic hosts.

	~~{{STRUCTURE_2bvm\| PDB=2bvm \| SCENE= }}~~		Structural basis for the function of Clostridium difficile toxin B.,Reinert DJ, Jank T, Aktories K, Schulz GE J Mol Biol. 2005 Sep 2;351(5):973-81. PMID:16054646<ref>PMID:16054646</ref>

	~~===CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF TOXIN B FROM CLOSTRIDIUM DIFFICILE IN COMPLEX WITH UDP~~, ~~GLC AND MANGANESE ION===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_16054646}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2bvm]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/[clostridium]_difficile [clostridium] difficile]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2BVM OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:016054646<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Aktories, K.]]		[[Category: Aktories, K.]]
	[[Category: Jank, T.]]		[[Category: Jank, T.]]

OCA: Protected "2bvm" [edit=sysop:move=sysop]

2013-01-06T10:25:41Z

Protected "2bvm" [edit=sysop:move=sysop]

← Older revision	Revision as of 10:25, 6 January 2013
(No difference)

OCA at 10:25, 6 January 2013

2013-01-06T10:25:37Z

← Older revision		Revision as of 10:25, 6 January 2013
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	~~{{Seed}}~~
	[[Image:2bvm.png\|left\|200px]]		[[Image:2bvm.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2bvm", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_2bvm\| PDB=2bvm \| SCENE= }}		{{STRUCTURE_2bvm\| PDB=2bvm \| SCENE= }}

	===CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF TOXIN B FROM CLOSTRIDIUM DIFFICILE IN COMPLEX WITH UDP, GLC AND MANGANESE ION===		===CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF TOXIN B FROM CLOSTRIDIUM DIFFICILE IN COMPLEX WITH UDP, GLC AND MANGANESE ION===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_16054646}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 16054646 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_16054646}}		{{ABSTRACT_PUBMED_16054646}}

	==About this Structure==		==About this Structure==
	~~2BVM~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/~~Clostridium_difficile Clostridium~~ difficile]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BVM OCA].		[[2bvm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/[clostridium]_difficile [clostridium] difficile]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BVM OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~16054646~~</ref><references group="xtra"/>		<ref group="xtra">PMID:016054646</ref><references group="xtra"/>
	~~[[Category: Clostridium difficile]]~~
	[[Category: Aktories, K.]]		[[Category: Aktories, K.]]
	[[Category: Jank, T.]]		[[Category: Jank, T.]]
	[[Category: Reinert, D J.]]		[[Category: Reinert, D J.]]
	[[Category: Schulz, G E.]]		[[Category: Schulz, G E.]]
	[[Category: ~~Toxin,glycosyltransferase~~]]		[[Category: Glycosyltransferase]]
			[[Category: Toxin]]
	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 20:58:44 2009''~~

OCA at 18:58, 17 February 2009

2009-02-17T18:58:45Z

← Older revision		Revision as of 18:58, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
	2BVM is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Clostridium_difficile Clostridium difficile]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BVM OCA].		2BVM is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Clostridium_difficile Clostridium difficile]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BVM OCA].

	==Reference==		==Reference==
	~~Structural basis for the function of Clostridium difficile toxin B., Reinert DJ, Jank T, Aktories K, Schulz GE, J Mol Biol. 2005 Sep 2;351(5):973-81.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16054646 16054646]~~		<ref group="xtra">PMID:16054646</ref><references group="xtra"/>
	[[Category: Clostridium difficile]]		[[Category: Clostridium difficile]]
	~~[[Category: Single protein]]~~
	[[Category: Aktories, K.]]		[[Category: Aktories, K.]]
	[[Category: Jank, T.]]		[[Category: Jank, T.]]
Line 32:		Line 31:
	[[Category: Toxin,glycosyltransferase]]		[[Category: Toxin,glycosyltransferase]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 04~~:59:~~03 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 20:58:44 2009''