3blc - Revision history

OCA at 18:58, 20 October 2021

OCA — Wed, 20 Oct 2021 18:58:46 GMT

←Older revision		Revision as of 18:58, 20 October 2021
Line 1:		Line 1:

	==Crystal structure of the periplasmic domain of the Escherichia Coli YIDC==		==Crystal structure of the periplasmic domain of the Escherichia Coli YIDC==
-	<StructureSection load='3blc' size='340' side='right' caption='[[3blc]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='3blc' size='340' side='right'caption='[[3blc]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3blc]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3BLC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3blc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BLC FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">oxaA, yidC ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">oxaA, yidC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3blc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3blc OCA], [~~http~~://pdbe.org/3blc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3blc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3blc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3blc 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=3blc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3blc OCA], [https://pdbe.org/3blc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3blc RCSB], [https://www.ebi.ac.uk/pdbsum/3blc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3blc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/YIDC_ECOLI YIDC_ECOLI]] Inner membrane protein required for the insertion and/or proper folding and/or complex formation of integral inner membrane proteins. Involved in integration of membrane proteins that insert dependently and independently of the Sec translocase complex, as well as at least 2 lipoproteins. Its own insertion requires SRP and is Sec translocase-dependent. Essential for the integration of Sec-dependent subunit a of the F(0)ATP synthase, FtsQ and SecE proteins and for Sec-independent subunit c of the F(0)ATP synthase, M13 phage procoat and the N-terminus of leader peptidase Lep. Probably interacts directly with Sec-independent substrates. Sec-dependent protein FtsQ interacts first with SecY then subsequently with YidC. Sec-dependent LacY and MalF require YidC to acquire tertiary structure and stability, a chaperone-like function, but not for membrane insertion. Stable maltose transport copmplex formation (MalFGK(2)) also requires YidC. Partially complements a Streptococcus mutans yidC2 disruption mutant.<ref>PMID:10675323</ref> <ref>PMID:10949305</ref> <ref>PMID:12724529</ref> <ref>PMID:12950181</ref> <ref>PMID:15140892</ref> <ref>PMID:15067017</ref> <ref>PMID:17073462</ref> <ref>PMID:18456666</ref>	+	[[https://www.uniprot.org/uniprot/YIDC_ECOLI YIDC_ECOLI]] Inner membrane protein required for the insertion and/or proper folding and/or complex formation of integral inner membrane proteins. Involved in integration of membrane proteins that insert dependently and independently of the Sec translocase complex, as well as at least 2 lipoproteins. Its own insertion requires SRP and is Sec translocase-dependent. Essential for the integration of Sec-dependent subunit a of the F(0)ATP synthase, FtsQ and SecE proteins and for Sec-independent subunit c of the F(0)ATP synthase, M13 phage procoat and the N-terminus of leader peptidase Lep. Probably interacts directly with Sec-independent substrates. Sec-dependent protein FtsQ interacts first with SecY then subsequently with YidC. Sec-dependent LacY and MalF require YidC to acquire tertiary structure and stability, a chaperone-like function, but not for membrane insertion. Stable maltose transport copmplex formation (MalFGK(2)) also requires YidC. Partially complements a Streptococcus mutans yidC2 disruption mutant.<ref>PMID:10675323</ref> <ref>PMID:10949305</ref> <ref>PMID:12724529</ref> <ref>PMID:12950181</ref> <ref>PMID:15140892</ref> <ref>PMID:15067017</ref> <ref>PMID:17073462</ref> <ref>PMID:18456666</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Ecoli]]		[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Oliver, D C]]		[[Category: Oliver, D C]]
	[[Category: Paetzel, M]]		[[Category: Paetzel, M]]

OCA at 07:42, 31 October 2018

OCA — Wed, 31 Oct 2018 07:42:18 GMT

←Older revision		Revision as of 07:42, 31 October 2018
Line 1:		Line 1:
		+
	==Crystal structure of the periplasmic domain of the Escherichia Coli YIDC==		==Crystal structure of the periplasmic domain of the Escherichia Coli YIDC==
	<StructureSection load='3blc' size='340' side='right' caption='[[3blc]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='3blc' size='340' side='right' caption='[[3blc]], [[Resolution\|resolution]] 2.50Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">oxaA, yidC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">oxaA, yidC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3blc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3blc OCA], [http://pdbe.org/3blc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3blc RCSB], [http://www.ebi.ac.uk/pdbsum/3blc 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=3blc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3blc OCA], [http://pdbe.org/3blc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3blc RCSB], [http://www.ebi.ac.uk/pdbsum/3blc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3blc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bl/3blc_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bl/3blc_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 20:13, 9 February 2016

OCA — Tue, 09 Feb 2016 20:13:19 GMT

←Older revision		Revision as of 20:13, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='3blc' size='340' side='right' caption='[[3blc]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='3blc' size='340' side='right' caption='[[3blc]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3blc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli_k-12 Escherichia coli k-12~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BLC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3blc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BLC FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">oxaA, yidC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ~~Escherichia coli K-12~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">oxaA, yidC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3blc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3blc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3blc RCSB], [http://www.ebi.ac.uk/pdbsum/3blc 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=3blc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3blc OCA], [http://pdbe.org/3blc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3blc RCSB], [http://www.ebi.ac.uk/pdbsum/3blc PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~OXAA_ECOLI OXAA_ECOLI~~]] Inner membrane protein required for the insertion and/or proper folding and/or complex formation of integral inner membrane proteins. Involved in integration of membrane proteins that insert dependently and independently of the Sec translocase complex, as well as at least 2 lipoproteins. Its own insertion requires SRP and is Sec translocase-dependent. Essential for the integration of Sec-dependent subunit a of the F(0)ATP synthase, FtsQ and SecE proteins and for Sec-independent subunit c of the F(0)ATP synthase, M13 phage procoat and the N-terminus of leader peptidase Lep. Probably interacts directly with Sec-independent substrates. Sec-dependent protein FtsQ interacts first with SecY then subsequently with YidC. Sec-dependent LacY and MalF require YidC to acquire tertiary structure and stability, a chaperone-like function, but not for membrane insertion. Stable maltose transport copmplex formation (MalFGK(2)) also requires YidC. Partially complements a Streptococcus mutans yidC2 disruption mutant.<ref>PMID:10675323</ref> <ref>PMID:10949305</ref> <ref>PMID:12724529</ref> <ref>PMID:12950181</ref> <ref>PMID:15140892</ref> <ref>PMID:15067017</ref> <ref>PMID:17073462</ref> <ref>PMID:18456666</ref>	+	[[http://www.uniprot.org/uniprot/YIDC_ECOLI YIDC_ECOLI]] Inner membrane protein required for the insertion and/or proper folding and/or complex formation of integral inner membrane proteins. Involved in integration of membrane proteins that insert dependently and independently of the Sec translocase complex, as well as at least 2 lipoproteins. Its own insertion requires SRP and is Sec translocase-dependent. Essential for the integration of Sec-dependent subunit a of the F(0)ATP synthase, FtsQ and SecE proteins and for Sec-independent subunit c of the F(0)ATP synthase, M13 phage procoat and the N-terminus of leader peptidase Lep. Probably interacts directly with Sec-independent substrates. Sec-dependent protein FtsQ interacts first with SecY then subsequently with YidC. Sec-dependent LacY and MalF require YidC to acquire tertiary structure and stability, a chaperone-like function, but not for membrane insertion. Stable maltose transport copmplex formation (MalFGK(2)) also requires YidC. Partially complements a Streptococcus mutans yidC2 disruption mutant.<ref>PMID:10675323</ref> <ref>PMID:10949305</ref> <ref>PMID:12724529</ref> <ref>PMID:12950181</ref> <ref>PMID:15140892</ref> <ref>PMID:15067017</ref> <ref>PMID:17073462</ref> <ref>PMID:18456666</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 17:		Line 17:
	<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=3blc ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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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 3blc" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia coli k-12~~]]	+	[[Category: Ecoli]]
	[[Category: Oliver, D C]]		[[Category: Oliver, D C]]
	[[Category: Paetzel, M]]		[[Category: Paetzel, M]]

OCA at 09:15, 25 December 2014

OCA — Thu, 25 Dec 2014 09:15:53 GMT

←Older revision		Revision as of 09:15, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3blc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BLC FirstGlance]. <br>		<table><tr><td colspan='2'>[[3blc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BLC FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">oxaA, yidC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">oxaA, yidC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</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=3blc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3blc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3blc RCSB], [http://www.ebi.ac.uk/pdbsum/3blc 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=3blc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3blc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3blc RCSB], [http://www.ebi.ac.uk/pdbsum/3blc PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/OXAA_ECOLI OXAA_ECOLI]] Inner membrane protein required for the insertion and/or proper folding and/or complex formation of integral inner membrane proteins. Involved in integration of membrane proteins that insert dependently and independently of the Sec translocase complex, as well as at least 2 lipoproteins. Its own insertion requires SRP and is Sec translocase-dependent. Essential for the integration of Sec-dependent subunit a of the F(0)ATP synthase, FtsQ and SecE proteins and for Sec-independent subunit c of the F(0)ATP synthase, M13 phage procoat and the N-terminus of leader peptidase Lep. Probably interacts directly with Sec-independent substrates. Sec-dependent protein FtsQ interacts first with SecY then subsequently with YidC. Sec-dependent LacY and MalF require YidC to acquire tertiary structure and stability, a chaperone-like function, but not for membrane insertion. Stable maltose transport copmplex formation (MalFGK(2)) also requires YidC. Partially complements a Streptococcus mutans yidC2 disruption mutant.<ref>PMID:10675323</ref> <ref>PMID:10949305</ref> <ref>PMID:12724529</ref> <ref>PMID:12950181</ref> <ref>PMID:15140892</ref> <ref>PMID:15067017</ref> <ref>PMID:17073462</ref> <ref>PMID:18456666</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli k-12]]		[[Category: Escherichia coli k-12]]
-	[[Category: Oliver, D C.]]	+	[[Category: Oliver, D C]]
-	[[Category: Paetzel, M.]]	+	[[Category: Paetzel, M]]
	[[Category: Chaperone]]		[[Category: Chaperone]]
	[[Category: Inner membrane]]		[[Category: Inner membrane]]

OCA at 20:58, 2 October 2014

OCA — Thu, 02 Oct 2014 20:58:34 GMT

←Older revision		Revision as of 20:58, 2 October 2014
Line 1:		Line 1:
-	[[~~Image:~~3blc.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the periplasmic domain of the Escherichia Coli YIDC==
		+	<StructureSection load='3blc' size='340' side='right' caption='[[3blc]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3blc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BLC FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">oxaA, yidC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</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=3blc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3blc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3blc RCSB], [http://www.ebi.ac.uk/pdbsum/3blc 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/bl/3blc_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 ==
		+	The essential bacterial membrane protein YidC facilitates insertion and assembly of proteins destined for integration into the inner membrane. It has homologues in both mitochondria and chloroplasts. Here we report the crystal structure of the Escherichia coli YidC major periplasmic domain (YidCECP1) at 2.5A resolution. This domain is present in YidC from Gram-negative bacteria and is more than half the size of the full-length protein. The structure reveals that YidCECP1 is made up of a large twisted beta-sandwich protein fold with a C-terminal alpha-helix that packs against one face of the beta-sandwich. Our structure and sequence analysis reveals that the C-terminal alpha-helix and the beta-sheet that it lays against are the most conserved regions of the domain. The region corresponding to the C-terminal alpha-helix was previously shown to be important for the protein insertase function of YidC and is conserved in other YidC-like proteins. The structure reveals that a region of YidC that was previously shown to be involved in binding to SecF maps to one edge of the beta-sandwich. Electrostatic analysis of the molecular surface for this region of YidC reveals a predominantly charged surface and suggests that the SecF-YidC interaction may be electrostatic in nature. Interestingly, YidCECP1 has significant structural similarity to galactose mutarotase from Lactococcus lactis, suggesting that this domain may have another function besides its role in membrane protein assembly.

-	~~{{STRUCTURE_3blc\| PDB=3blc \| SCENE= }}~~	+	Crystal structure of the major periplasmic domain of the bacterial membrane protein assembly facilitator YidC.,Oliver DC, Paetzel M J Biol Chem. 2008 Feb 22;283(8):5208-16. Epub 2007 Dec 19. PMID:18093969<ref>PMID:18093969</ref>

-	~~===Crystal structure~~ of the ~~periplasmic domain of the Escherichia Coli YIDC===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18093969}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3blc]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3BLC OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:018093969<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli k-12]]		[[Category: Escherichia coli k-12]]
	[[Category: Oliver, D C.]]		[[Category: Oliver, D C.]]

OCA: Protected "3blc" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 20:44:52 GMT

Protected "3blc" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:44, 7 January 2013

OCA at 20:44, 7 January 2013

OCA — Mon, 07 Jan 2013 20:44:50 GMT

←Older revision		Revision as of 20:44, 7 January 2013
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-	{{Seed}}
	[[Image:3blc.png\|left\|200px]]		[[Image:3blc.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3blc", 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_3blc\| PDB=3blc \| SCENE= }}		{{STRUCTURE_3blc\| PDB=3blc \| SCENE= }}

	===Crystal structure of the periplasmic domain of the Escherichia Coli YIDC===		===Crystal structure of the periplasmic domain of the Escherichia Coli YIDC===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18093969}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18093969 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18093969}}		{{ABSTRACT_PUBMED_18093969}}

	==About this Structure==		==About this Structure==
-	~~3BLC~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/~~Escherichia_coli~~ Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLC OCA].	+	[[3blc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLC OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18093969~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018093969</ref><references group="xtra"/>
-	[[Category: Escherichia coli]]	+	[[Category: Escherichia coli k-12]]
	[[Category: Oliver, D C.]]		[[Category: Oliver, D C.]]
	[[Category: Paetzel, M.]]		[[Category: Paetzel, M.]]
	[[Category: Chaperone]]		[[Category: Chaperone]]
-	[[Category: Chaperone,protein transport]]
	[[Category: Inner membrane]]		[[Category: Inner membrane]]
	[[Category: Membrane assembly facilitator]]		[[Category: Membrane assembly facilitator]]
	[[Category: Oxaa]]		[[Category: Oxaa]]
	[[Category: Periplasmic domain]]		[[Category: Periplasmic domain]]
		+	[[Category: Protein transport]]
	[[Category: Transmembrane]]		[[Category: Transmembrane]]
	[[Category: Yidc]]		[[Category: Yidc]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 12:26:27 2009''

OCA at 10:26, 17 February 2009

OCA — Tue, 17 Feb 2009 10:26:29 GMT

←Older revision		Revision as of 10:26, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3BLC is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLC OCA].	+	3BLC is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLC OCA].

	==Reference==		==Reference==
-	~~Crystal structure of the major periplasmic domain of the bacterial membrane protein assembly facilitator YidC., Oliver DC, Paetzel M, J Biol Chem. 2008 Feb 22;283(8):5208-16. Epub 2007 Dec 19.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18093969 18093969]~~	+	<ref group="xtra">PMID:18093969</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Single protein]]
	[[Category: Oliver, D C.]]		[[Category: Oliver, D C.]]
	[[Category: Paetzel, M.]]		[[Category: Paetzel, M.]]
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	[[Category: Yidc]]		[[Category: Yidc]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 16~~:46:~~24 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 12:26:27 2009''

OCA at 13:46, 28 July 2008

OCA — Mon, 28 Jul 2008 13:46:26 GMT

←Older revision		Revision as of 13:46, 28 July 2008
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-	[[Image:3blc.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:3blc.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_3blc\| PDB=3blc \| SCENE= }}		{{STRUCTURE_3blc\| PDB=3blc \| SCENE= }}

-	~~'''~~Crystal structure of the periplasmic domain of the Escherichia Coli YIDC~~'''~~	+	===Crystal structure of the periplasmic domain of the Escherichia Coli YIDC===


-	~~==Overview==~~	+	<!--
-	The ~~essential bacterial membrane protein YidC facilitates insertion and assembly of proteins destined for integration into~~ the ~~inner membrane. It has homologues in both mitochondria and chloroplasts. Here we report~~ the ~~crystal structure of the Escherichia coli YidC major periplasmic domain~~ (~~YidCECP1)~~ at 2.~~5A resolution~~. ~~This domain~~ is ~~present in YidC from Gram-negative bacteria and is more than half~~ the ~~size of the full-length protein~~. ~~The structure reveals that YidCECP1 is made up of a large twisted beta~~-~~sandwich protein fold with a C~~-terminal alpha-helix that packs against one face of the beta-sandwich. Our structure and sequence analysis reveals that the C-terminal alpha-helix and the beta-sheet that it lays against are the most conserved regions of the domain. The region corresponding to the C-terminal alpha-helix was previously shown to be important for the protein insertase function of YidC and is conserved in other YidC-like proteins. The structure reveals that a region of YidC that was previously shown to be involved in binding to SecF maps to one edge of the beta-sandwich. Electrostatic analysis of the molecular surface for this region of YidC reveals a predominantly charged surface and suggests that the SecF-YidC interaction may be electrostatic in nature. Interestingly, YidCECP1 has significant structural similarity to galactose mutarotase from Lactococcus lactis, suggesting that this domain may have another function besides its role in membrane protein assembly.	+	The line below this paragraph, {{ABSTRACT_PUBMED_18093969}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 18093969 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_18093969}}

	==About this Structure==		==About this Structure==
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	[[Category: Transmembrane]]		[[Category: Transmembrane]]
	[[Category: Yidc]]		[[Category: Yidc]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 20~~:54:01 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 16:46:24 2008''

OCA at 17:54, 4 May 2008

OCA — Sun, 04 May 2008 17:54:03 GMT

←Older revision		Revision as of 17:54, 4 May 2008
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	[[Image:3blc.jpg\|left\|200px]]		[[Image:3blc.jpg\|left\|200px]]

-	~~{{Structure~~	+	<!--
-	~~\|PDB= 3blc \|SIZE=350\|CAPTION= <scene name='initialview01'>3blc</scene>~~, ~~resolution 2~~.~~50Å~~	+	The line below this paragraph, containing "STRUCTURE_3blc", creates the "Structure Box" on the page.
-	~~\|SITE=~~	+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	~~\|LIGAND= <~~scene ~~name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>~~	+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	~~\|ACTIVITY=~~	+	or leave the SCENE parameter empty for the default display.
-	~~\|GENE= oxaA, yidC ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])~~	+	-->
-	~~\|DOMAIN=~~	+	{{STRUCTURE_3blc\| PDB=3blc \| SCENE= }}
-	\|~~RELATEDENTRY~~=	+
-	\|~~RESOURCES~~=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3blc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3blc OCA], [http://www.ebi.ac.uk/pdbsum/3blc PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3blc RCSB]</span>	+
-	}}	+

	'''Crystal structure of the periplasmic domain of the Escherichia Coli YIDC'''		'''Crystal structure of the periplasmic domain of the Escherichia Coli YIDC'''
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	[[Category: Oliver, D C.]]		[[Category: Oliver, D C.]]
	[[Category: Paetzel, M.]]		[[Category: Paetzel, M.]]
-	[[Category: ~~chaperone~~]]	+	[[Category: Chaperone]]
-	[[Category: ~~chaperone~~,protein transport]]	+	[[Category: Chaperone,protein transport]]
-	[[Category: ~~inner~~ membrane]]	+	[[Category: Inner membrane]]
-	[[Category: ~~membrane~~ assembly facilitator]]	+	[[Category: Membrane assembly facilitator]]
-	[[Category: ~~oxaa~~]]	+	[[Category: Oxaa]]
-	[[Category: ~~periplasmic~~ domain]]	+	[[Category: Periplasmic domain]]
-	[[Category: ~~transmembrane~~]]	+	[[Category: Transmembrane]]
-	[[Category: ~~yidc~~]]	+	[[Category: Yidc]]
-		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 20:54:01 2008''
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Mar 31 05~~:27:24 2008''	+