2bvl - Revision history

OCA at 09:19, 9 May 2024

OCA — Thu, 09 May 2024 09:19:48 GMT

←Older revision		Revision as of 09:19, 9 May 2024
Line 3:		Line 3:
	<StructureSection load='2bvl' size='340' side='right'caption='[[2bvl]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2bvl' size='340' side='right'caption='[[2bvl]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2bvl]] 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=2BVL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BVL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2bvl]] 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=2BVL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BVL 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=TBR:HEXATANTALUM+DODECABROMIDE'>TBR</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]] 2.2Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2bvm\|2bvm]]</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=TBR:HEXATANTALUM+DODECABROMIDE'>TBR</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=2bvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bvl OCA], [https://pdbe.org/2bvl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bvl RCSB], [https://www.ebi.ac.uk/pdbsum/2bvl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bvl 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=2bvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bvl OCA], [https://pdbe.org/2bvl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bvl RCSB], [https://www.ebi.ac.uk/pdbsum/2bvl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bvl 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

OCA — Wed, 24 Nov 2021 13:18:51 GMT

←Older revision		Revision as of 13:18, 24 November 2021
Line 3:		Line 3:
	<StructureSection load='2bvl' size='340' side='right'caption='[[2bvl]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2bvl' size='340' side='right'caption='[[2bvl]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2bvl]] 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=2BVL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2BVL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2bvl]] 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=2BVL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BVL 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=TBR:HEXATANTALUM+DODECABROMIDE'>TBR</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=TBR:HEXATANTALUM+DODECABROMIDE'>TBR</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">[[2bvm\|2bvm]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2bvm\|2bvm]]</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=2bvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bvl OCA], [~~http~~://pdbe.org/2bvl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2bvl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2bvl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2bvl 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=2bvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bvl OCA], [https://pdbe.org/2bvl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bvl RCSB], [https://www.ebi.ac.uk/pdbsum/2bvl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bvl ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 08:13, 19 February 2020

OCA — Wed, 19 Feb 2020 08:13:04 GMT

←Older revision		Revision as of 08:13, 19 February 2020
Line 1:		Line 1:

	==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='2bvl' size='340' side='right' caption='[[2bvl]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='2bvl' size='340' side='right'caption='[[2bvl]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2bvl]] 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=2BVL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BVL FirstGlance]. <br>		<table><tr><td colspan='2'>[[2bvl]] 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=2BVL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BVL FirstGlance]. <br>
Line 32:		Line 32:
	</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 06:41, 16 May 2018

OCA — Wed, 16 May 2018 06:41:57 GMT

←Older revision		Revision as of 06:41, 16 May 2018
Line 1:		Line 1:
-	==~~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='2bvl' size='340' side='right' caption='[[2bvl]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2bvl' size='340' side='right' caption='[[2bvl]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 5:		Line 6:
	</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=TBR:HEXATANTALUM+DODECABROMIDE'>TBR</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=TBR:HEXATANTALUM+DODECABROMIDE'>TBR</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">[[2bvm\|2bvm]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2bvm\|2bvm]]</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=2bvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bvl OCA], [http://pdbe.org/2bvl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2bvl RCSB], [http://www.ebi.ac.uk/pdbsum/2bvl 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=2bvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bvl OCA], [http://pdbe.org/2bvl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2bvl RCSB], [http://www.ebi.ac.uk/pdbsum/2bvl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2bvl ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 11:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bv/2bvl_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bv/2bvl_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>

OCA at 15:24, 7 February 2016

OCA — Sun, 07 Feb 2016 15:24:35 GMT

←Older revision		Revision as of 15:24, 7 February 2016
Line 15:		Line 15:
	<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=2bvl ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 02:46, 10 September 2015

OCA — Thu, 10 Sep 2015 02:46:29 GMT

←Older revision		Revision as of 02:46, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2bvl' size='340' side='right' caption='[[2bvl]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2bvl' size='340' side='right' caption='[[2bvl]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2bvl]] 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=2BVL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BVL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2bvl]] 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=2BVL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BVL 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=TBR:HEXATANTALUM+DODECABROMIDE'>TBR</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=TBR:HEXATANTALUM+DODECABROMIDE'>TBR</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">[[2bvm\|2bvm]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2bvm\|2bvm]]</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=2bvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bvl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2bvl RCSB], [http://www.ebi.ac.uk/pdbsum/2bvl 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=2bvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bvl OCA], [http://pdbe.org/2bvl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2bvl RCSB], [http://www.ebi.ac.uk/pdbsum/2bvl PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 25:		Line 25:
	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 2bvl" 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 16:54, 15 January 2015

OCA — Thu, 15 Jan 2015 16:54:19 GMT

←Older revision		Revision as of 16:54, 15 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2bvl]] 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=2BVL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BVL FirstGlance]. <br>		<table><tr><td colspan='2'>[[2bvl]] 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=2BVL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BVL 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=TBR:HEXATANTALUM+DODECABROMIDE'>TBR</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=TBR:HEXATANTALUM+DODECABROMIDE'>TBR</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">[[2bvm\|2bvm]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2bvm\|2bvm]]</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=2bvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bvl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2bvl RCSB], [http://www.ebi.ac.uk/pdbsum/2bvl 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=2bvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bvl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2bvl RCSB], [http://www.ebi.ac.uk/pdbsum/2bvl 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 02:01, 30 September 2014

OCA — Tue, 30 Sep 2014 02:01:40 GMT

←Older revision		Revision as of 02:01, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2bvl.~~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='2bvl' size='340' side='right' caption='[[2bvl]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2bvl]] 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=2BVL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BVL 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=TBR:HEXATANTALUM+DODECABROMIDE'>TBR</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2bvm\|2bvm]]</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=2bvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bvl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2bvl RCSB], [http://www.ebi.ac.uk/pdbsum/2bvl 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/2bvl_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_2bvl\| PDB=2bvl \| 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__
-	~~[[2bvl]] 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=2BVL 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 "2bvl" [edit=sysop:move=sysop]

OCA — Sun, 06 Jan 2013 11:15:09 GMT

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

←Older revision

Revision as of 11:15, 6 January 2013

OCA at 11:15, 6 January 2013

OCA — Sun, 06 Jan 2013 11:15:06 GMT

←Older revision		Revision as of 11:15, 6 January 2013
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-	{{Seed}}
	[[Image:2bvl.png\|left\|200px]]		[[Image:2bvl.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2bvl", 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_2bvl\| PDB=2bvl \| SCENE= }}		{{STRUCTURE_2bvl\| PDB=2bvl \| 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==
-	~~2BVL~~ 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=2BVL OCA].	+	[[2bvl]] 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=2BVL 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 Mon Feb 16 14:45:45 2009''~~	+