5fx3 - Revision history

OCA at 13:30, 26 July 2023

OCA — Wed, 26 Jul 2023 13:30:10 GMT

←Older revision		Revision as of 13:30, 26 July 2023
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	<StructureSection load='5fx3' size='340' side='right'caption='[[5fx3]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5fx3' size='340' side='right'caption='[[5fx3]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fx3]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FX3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5FX3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fx3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FX3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FX3 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=EDT:{~~[~~-(BIS-CARBOXYMETHYL-AMINO)-ETHYL~~]~~-CARBOXYMETHYL-AMINO}-ACETIC+ACID'>EDT</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]] 1.9Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALY:N(6)-ACETYLLYSINE'>ALY</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ALY:N(6)-ACETYLLYSINE'>ALY</scene>, <scene name='pdbligand=EDT:{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC+ACID'>EDT</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat">~~[~~[5fwr\|5fwr~~]~~]</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=5fx3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fx3 OCA], [https://pdbe.org/5fx3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fx3 RCSB], [https://www.ebi.ac.uk/pdbsum/5fx3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fx3 ProSAT]</span></td></tr>
-	~~<tr id='gene~~'>~~<td class="sblockLbl"><b>[[Gene\|Gene:]]~~</b>~~</td><td class="sblockDat">fimH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])~~</td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5fx3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fx3 OCA], [~~http~~://pdbe.org/5fx3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5fx3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5fx3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5fx3 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/FIMH_ECOLI FIMH_ECOLI] Involved in regulation of length and mediation of adhesion of type 1 fimbriae (but not necessary for the production of fimbriae). Adhesin responsible for the binding to D-mannose. It is laterally positioned at intervals in the structure of the type 1 fimbriae. In order to integrate FimH in the fimbriae FimF and FimG are needed.
	<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~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bouckaert, J]]	+	[[Category: Bouckaert J]]
-	~~[[Category: Bacterial adhesin]]~~	+
-	~~[[Category: Cell adhesion]]~~	+
-	~~[[Category: Type 1 fimbriae]]~~	+
-	~~[[Category: Urinary tract infection]]~~	+
-	~~[[Category: Variable immunoglobulin fold~~]]	+

OCA at 07:41, 6 May 2020

OCA — Wed, 06 May 2020 07:41:21 GMT

←Older revision		Revision as of 07:41, 6 May 2020
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	==Breaking down the wall: mutation of the tyrosine gate of the universal Escherichia coli fimbrial adhesin FimH==		==Breaking down the wall: mutation of the tyrosine gate of the universal Escherichia coli fimbrial adhesin FimH==
-	<StructureSection load='5fx3' size='340' side='right' caption='[[5fx3]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='5fx3' size='340' side='right'caption='[[5fx3]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fx3]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FX3 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5FX3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fx3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FX3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5FX3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDT:{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC+ACID'>EDT</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDT:{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC+ACID'>EDT</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALY:N(6)-ACETYLLYSINE'>ALY</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALY:N(6)-ACETYLLYSINE'>ALY</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fwr\|5fwr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fwr\|5fwr]]</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=5fx3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fx3 OCA], [http://pdbe.org/5fx3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fx3 RCSB], [http://www.ebi.ac.uk/pdbsum/5fx3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fx3 ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fimH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5fx3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fx3 OCA], [http://pdbe.org/5fx3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fx3 RCSB], [http://www.ebi.ac.uk/pdbsum/5fx3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fx3 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5fx3" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5fx3" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Adhesin 3D structures\|Adhesin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Bouckaert, J]]		[[Category: Bouckaert, J]]
	[[Category: Bacterial adhesin]]		[[Category: Bacterial adhesin]]

OCA at 13:21, 15 March 2017

OCA — Wed, 15 Mar 2017 13:21:36 GMT

←Older revision		Revision as of 13:21, 15 March 2017
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	<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=5fx3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fx3 OCA], [http://pdbe.org/5fx3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fx3 RCSB], [http://www.ebi.ac.uk/pdbsum/5fx3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fx3 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=5fx3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fx3 OCA], [http://pdbe.org/5fx3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fx3 RCSB], [http://www.ebi.ac.uk/pdbsum/5fx3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fx3 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The most prevalent diseases manifested by Escherichia coli are acute and recurrent bladder infections and chronic inflammatory bowel diseases such as Crohn's disease. E. coli clinical isolates express the FimH adhesin, which consists of a mannose-specific lectin domain connected via a pilin domain to the tip of type 1 pili. Although the isolated FimH lectin domain has affinities in the nanomolar range for all high-mannosidic glycans, differentiation between these glycans is based on their capacity to form predominantly hydrophobic interactions within the tyrosine gate at the entrance to the binding pocket. In this study, novel crystal structures of tyrosine-gate mutants of FimH, ligand-free or in complex with heptyl alpha-d-O-mannopyranoside or 4-biphenyl alpha-d-O-mannopyranoside, are combined with quantum-mechanical calculations and molecular-dynamics simulations. In the Y48A FimH crystal structure, a large increase in the dynamics of the alkyl chain of heptyl alpha-d-O-mannopyranoside attempts to compensate for the absence of the aromatic ring; however, the highly energetic and stringent mannose-binding pocket of wild-type FimH is largely maintained. The Y137A mutation, on the other hand, is the most detrimental to FimH affinity and specificity: (i) in the absence of ligand the FimH C-terminal residue Thr158 intrudes into the mannose-binding pocket and (ii) ethylenediaminetetraacetic acid interacts strongly with Glu50, Thr53 and Asn136, in spite of multiple dialysis and purification steps. Upon mutation, pre-ligand-binding relaxation of the backbone dihedral angles at position 137 in the tyrosine gate and their coupling to Tyr48 via the interiorly located Ile52 form the basis of the loss of affinity of the FimH adhesin in the Y137A mutant.
		+
		+	Mutation of Tyr137 of the universal Escherichia coli fimbrial adhesin FimH relaxes the tyrosine gate prior to mannose binding.,Rabbani S, Krammer EM, Roos G, Zalewski A, Preston R, Eid S, Zihlmann P, Prevost M, Lensink MF, Thompson A, Ernst B, Bouckaert J IUCrJ. 2017 Jan 1;4(Pt 1):7-23. doi: 10.1107/S2052252516016675. eCollection 2017 , Jan 1. PMID:28250938<ref>PMID:28250938</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5fx3" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 00:38, 19 January 2017

OCA — Thu, 19 Jan 2017 00:38:10 GMT

←Older revision		Revision as of 00:38, 19 January 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5fx3 is ON HOLD until Feb 22 2018~~	+	==Breaking down the wall: mutation of the tyrosine gate of the universal Escherichia coli fimbrial adhesin FimH==
-		+	<StructureSection load='5fx3' size='340' side='right' caption='[[5fx3]], [[Resolution\|resolution]] 1.90Å' scene=''>
-	~~Authors: Bouckaert, J.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5fx3]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FX3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FX3 FirstGlance]. <br>
-	~~Description:~~ Breaking down the wall: mutation of the tyrosine gate of the universal Escherichia coli fimbrial adhesin FimH	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDT:{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC+ACID'>EDT</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALY:N(6)-ACETYLLYSINE'>ALY</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fwr\|5fwr]]</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=5fx3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fx3 OCA], [http://pdbe.org/5fx3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fx3 RCSB], [http://www.ebi.ac.uk/pdbsum/5fx3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fx3 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
	[[Category: Bouckaert, J]]		[[Category: Bouckaert, J]]
		+	[[Category: Bacterial adhesin]]
		+	[[Category: Cell adhesion]]
		+	[[Category: Type 1 fimbriae]]
		+	[[Category: Urinary tract infection]]
		+	[[Category: Variable immunoglobulin fold]]

OCA at 23:12, 10 May 2016

OCA — Tue, 10 May 2016 23:12:32 GMT

←Older revision		Revision as of 23:12, 10 May 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5fx3 is ON HOLD	+	The entry 5fx3 is ON HOLD until Feb 22 2018

	Authors: Bouckaert, J.		Authors: Bouckaert, J.

OCA: Protected "5fx3" [edit=sysop:move=sysop]

OCA — Wed, 02 Mar 2016 12:18:37 GMT

Protected "5fx3" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:18, 2 March 2016

OCA: New page: '''Unreleased structure''' The entry 5fx3 is ON HOLD Authors: Bouckaert, J. Description: Breaking down the wall: mutation of the tyrosine gate of the universal Escherichia coli fimbria...

OCA — Wed, 02 Mar 2016 12:18:36 GMT

New page: '''Unreleased structure''' The entry 5fx3 is ON HOLD Authors: Bouckaert, J. Description: Breaking down the wall: mutation of the tyrosine gate of the universal Escherichia coli fimbria...

New page

'''Unreleased structure'''

The entry 5fx3 is ON HOLD

Authors: Bouckaert, J.

Description: Breaking down the wall: mutation of the tyrosine gate of the universal Escherichia coli fimbrial adhesin FimH
[[Category: Unreleased Structures]]
[[Category: Bouckaert, J]]