5uqn - Revision history

OCA at 13:32, 4 October 2023

OCA — Wed, 04 Oct 2023 13:32:44 GMT

←Older revision		Revision as of 13:32, 4 October 2023
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	<StructureSection load='5uqn' size='340' side='right'caption='[[5uqn]], [[Resolution\|resolution]] 2.06Å' scene=''>		<StructureSection load='5uqn' size='340' side='right'caption='[[5uqn]], [[Resolution\|resolution]] 2.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5uqn]] 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=5UQN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5UQN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5uqn]] 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=5UQN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UQN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=U2F:URIDINE-5-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE'>U2F</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]] 2.06Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uqk\|5uqk]], [[5uql\|5uql]], [[5uqm\|5uqm]], [[5uqt\|5uqt]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=U2F:URIDINE-5-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE'>U2F</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">toxB, tcdB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1496 "Bacillus difficilis" Hall and O'Toole 1935])</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=5uqn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uqn OCA], [https://pdbe.org/5uqn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5uqn RCSB], [https://www.ebi.ac.uk/pdbsum/5uqn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5uqn ProSAT]</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=5uqn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uqn OCA], [~~http~~://pdbe.org/5uqn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5uqn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5uqn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5uqn ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~TOXB_CLODI TOXB_CLODI~~]] ~~Cytotoxin~~.	+	[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>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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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: Alvin~~, J W~~]]	+	[[Category: Alvin JW]]
-	[[Category: Lacy~~, D B]]~~	+	[[Category: Lacy DB]]
-	~~[[Category: Glucosyltransferase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Toxin]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 17:10, 11 December 2019

OCA — Wed, 11 Dec 2019 17:10:33 GMT

←Older revision		Revision as of 17:10, 11 December 2019
Line 1:		Line 1:

	==Clostridium difficile Toxin B (TcdB) glucosyltransferase domain in complex with U2F==		==Clostridium difficile Toxin B (TcdB) glucosyltransferase domain in complex with U2F==
-	<StructureSection load='5uqn' size='340' side='right' caption='[[5uqn]], [[Resolution\|resolution]] 2.06Å' scene=''>	+	<StructureSection load='5uqn' size='340' side='right'caption='[[5uqn]], [[Resolution\|resolution]] 2.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5uqn]] 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=5UQN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UQN FirstGlance]. <br>		<table><tr><td colspan='2'>[[5uqn]] 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=5UQN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UQN FirstGlance]. <br>
Line 25:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus difficilis hall and o'toole 1935]]		[[Category: Bacillus difficilis hall and o'toole 1935]]
		+	[[Category: Large Structures]]
	[[Category: Alvin, J W]]		[[Category: Alvin, J W]]
	[[Category: Lacy, D B]]		[[Category: Lacy, D B]]

OCA at 19:45, 15 November 2017

OCA — Wed, 15 Nov 2017 19:45:02 GMT

←Older revision		Revision as of 19:45, 15 November 2017
Line 3:		Line 3:
	<StructureSection load='5uqn' size='340' side='right' caption='[[5uqn]], [[Resolution\|resolution]] 2.06Å' scene=''>		<StructureSection load='5uqn' size='340' side='right' caption='[[5uqn]], [[Resolution\|resolution]] 2.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5uqn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UQN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UQN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5uqn]] 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=5UQN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UQN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=U2F:URIDINE-5-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE'>U2F</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=U2F:URIDINE-5-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE'>U2F</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uqk\|5uqk]], [[5uql\|5uql]], [[5uqm\|5uqm]], [[5uqt\|5uqt]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uqk\|5uqk]], [[5uql\|5uql]], [[5uqm\|5uqm]], [[5uqt\|5uqt]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">toxB, tcdB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1496 "Bacillus difficilis" Hall and O'Toole 1935])</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=5uqn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uqn OCA], [http://pdbe.org/5uqn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uqn RCSB], [http://www.ebi.ac.uk/pdbsum/5uqn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uqn ProSAT]</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=5uqn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uqn OCA], [http://pdbe.org/5uqn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uqn RCSB], [http://www.ebi.ac.uk/pdbsum/5uqn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uqn ProSAT]</span></td></tr>
	</table>		</table>
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus difficilis hall and o'toole 1935]]
	[[Category: Alvin, J W]]		[[Category: Alvin, J W]]
	[[Category: Lacy, D B]]		[[Category: Lacy, D B]]

OCA at 12:53, 10 May 2017

OCA — Wed, 10 May 2017 12:53:08 GMT

←Older revision		Revision as of 12:53, 10 May 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5uqn is ~~ON HOLD until Paper~~ Publication	+	==Clostridium difficile Toxin B (TcdB) glucosyltransferase domain in complex with U2F==
		+	<StructureSection load='5uqn' size='340' side='right' caption='[[5uqn]], [[Resolution\|resolution]] 2.06Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5uqn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UQN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UQN FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=U2F:URIDINE-5-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE'>U2F</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uqk\|5uqk]], [[5uql\|5uql]], [[5uqm\|5uqm]], [[5uqt\|5uqt]]</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=5uqn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uqn OCA], [http://pdbe.org/5uqn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uqn RCSB], [http://www.ebi.ac.uk/pdbsum/5uqn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uqn ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TOXB_CLODI TOXB_CLODI]] Cytotoxin.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Clostridium difficile is the leading cause of hospital-acquired diarrhea and pseudomembranous colitis worldwide. The organism produces two homologous toxins, TcdA and TcdB, which enter and disrupt host cell function by glucosylating and thereby inactivating key signalling molecules within the host. As a toxin-mediated disease, there has been a significant interest in identifying small molecule inhibitors of the toxins' glucosyltransferase activities. This study was initiated as part of an effort to identify the mode of inhibition for a small molecule inhibitor of glucosyltransferase activity called apigenin. In the course of trying to get co-crystals with this inhibitor, we determined five different structures of the TcdA and TcdB glucosyltransferase domains and made use of a non-hydrolyzable UDP-glucose substrate. While we were able to visualize apigenin bound in one of our structures, the site was a crystal packing interface and not likely to explain the mode of inhibition. Nevertheless, the structure allowed us to capture an apo-state (one without the sugar nucleotide substrate) of the TcdB glycosyltransferase domain that had not been previously observed. Comparison of this structure with structures obtained in the presence of a non-hydrolyzable UDP-glucose analogue have allowed us to document multiple conformations of a C-terminal loop important for catalysis. We present our analysis of these five new structures with the hope that it will advance inhibitor design efforts for this important class of biological toxins.

-	~~Authors~~:	+	Clostridium difficile toxin glucosyltransferase domains in complex with a non-hydrolyzable UDP-glucose analogue.,Alvin JW, Lacy DB J Struct Biol. 2017 Apr 19. pii: S1047-8477(17)30059-X. doi:, 10.1016/j.jsb.2017.04.006. PMID:28433497<ref>PMID:28433497</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5uqn" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Alvin, J W]]
		+	[[Category: Lacy, D B]]
		+	[[Category: Glucosyltransferase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Toxin]]
		+	[[Category: Transferase]]

OCA at 19:17, 15 March 2017

OCA — Wed, 15 Mar 2017 19:17:53 GMT

←Older revision		Revision as of 19:17, 15 March 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5uqn is ON HOLD	+	The entry 5uqn is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5uqn" [edit=sysop:move=sysop]

OCA — Thu, 09 Mar 2017 14:47:51 GMT

Protected "5uqn" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:47, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5uqn is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Thu, 09 Mar 2017 14:47:50 GMT

New page: '''Unreleased structure''' The entry 5uqn is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5uqn is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]