1yg8 - Revision history

OCA at 06:56, 23 August 2023

OCA — Wed, 23 Aug 2023 06:56:54 GMT

←Older revision		Revision as of 06:56, 23 August 2023
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	<StructureSection load='1yg8' size='340' side='right'caption='[[1yg8]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='1yg8' size='340' side='right'caption='[[1yg8]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yg8]] is a 28 chain structure with sequence from [https://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=1YG8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YG8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yg8]] is a 28 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=1YG8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YG8 FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[1yg6\|1yg6]]</div></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]] 2.6Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">clpP, lopP ([https://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Endopeptidase_Clp Endopeptidase Clp], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.92 3.4.21.92] </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=1yg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yg8 OCA], [https://pdbe.org/1yg8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yg8 RCSB], [https://www.ebi.ac.uk/pdbsum/1yg8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yg8 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=1yg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yg8 OCA], [https://pdbe.org/1yg8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yg8 RCSB], [https://www.ebi.ac.uk/pdbsum/1yg8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yg8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/CLPP_ECOLI CLPP_ECOLI]] Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins. May play the role of a master protease which is attracted to different substrates by different specificity factors such as ClpA or ClpX.	+	[https://www.uniprot.org/uniprot/CLPP_ECOLI CLPP_ECOLI] Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins. May play the role of a master protease which is attracted to different substrates by different specificity factors such as ClpA or ClpX.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 31:
	==See Also==		==See Also==
	*[[Clp protease 3D structures\|Clp protease 3D structures]]		*[[Clp protease 3D structures\|Clp protease 3D structures]]
		+	*[[Heat Shock Protein structures\|Heat Shock Protein structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895]]~~	+	[[Category: Escherichia coli]]
-	~~[[Category: Endopeptidase Clp~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bewley~~, M C~~]]	+	[[Category: Bewley MC]]
-	[[Category: Flanagan~~, J M~~]]	+	[[Category: Flanagan JM]]
-	[[Category: Graziano, V]]	+	[[Category: Graziano V]]
-	[[Category: Griffin, K]]	+	[[Category: Griffin K]]
-	~~[[Category: Caseinolytic protease]]~~	+
-	~~[[Category: Endopeptidase clp]]~~	+
-	~~[[Category: Heat shock protein f21 5]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Protease ti~~]]	+

OCA at 16:52, 20 October 2021

OCA — Wed, 20 Oct 2021 16:52:12 GMT

←Older revision		Revision as of 16:52, 20 October 2021
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	<StructureSection load='1yg8' size='340' side='right'caption='[[1yg8]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='1yg8' size='340' side='right'caption='[[1yg8]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yg8]] is a 28 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=1YG8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1YG8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yg8]] is a 28 chain structure with sequence from [https://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=1YG8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YG8 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1yg6\|1yg6]]</div></td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1yg6\|1yg6]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">clpP, lopP ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">clpP, lopP ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Endopeptidase_Clp Endopeptidase Clp], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.92 3.4.21.92] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Endopeptidase_Clp Endopeptidase Clp], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.92 3.4.21.92] </span></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=1yg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yg8 OCA], [~~http~~://pdbe.org/1yg8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1yg8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1yg8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1yg8 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=1yg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yg8 OCA], [https://pdbe.org/1yg8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yg8 RCSB], [https://www.ebi.ac.uk/pdbsum/1yg8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yg8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/CLPP_ECOLI CLPP_ECOLI]] Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins. May play the role of a master protease which is attracted to different substrates by different specificity factors such as ClpA or ClpX.	+	[[https://www.uniprot.org/uniprot/CLPP_ECOLI CLPP_ECOLI]] Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins. May play the role of a master protease which is attracted to different substrates by different specificity factors such as ClpA or ClpX.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 08:45, 20 January 2021

OCA — Wed, 20 Jan 2021 08:45:09 GMT

←Older revision		Revision as of 08:45, 20 January 2021
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	==The structure of a V6A variant of ClpP.==		==The structure of a V6A variant of ClpP.==
-	<StructureSection load='1yg8' size='340' side='right' caption='[[1yg8]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='1yg8' size='340' side='right'caption='[[1yg8]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yg8]] is a 28 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=1YG8 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1YG8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yg8]] is a 28 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=1YG8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1YG8 FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yg6\|1yg6]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1yg6\|1yg6]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">clpP, lopP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">clpP, lopP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endopeptidase_Clp Endopeptidase Clp], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.92 3.4.21.92] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endopeptidase_Clp Endopeptidase Clp], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.92 3.4.21.92] </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=1yg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yg8 OCA], [http://pdbe.org/1yg8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yg8 RCSB], [http://www.ebi.ac.uk/pdbsum/1yg8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yg8 ProSAT]</span></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=1yg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yg8 OCA], [http://pdbe.org/1yg8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yg8 RCSB], [http://www.ebi.ac.uk/pdbsum/1yg8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yg8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 32:		Line 32:

	==See Also==		==See Also==
-	*[[Clp ~~Protease~~\|Clp ~~Protease~~]]	+	*[[Clp protease 3D structures\|Clp protease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 39:
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
	[[Category: Endopeptidase Clp]]		[[Category: Endopeptidase Clp]]
		+	[[Category: Large Structures]]
	[[Category: Bewley, M C]]		[[Category: Bewley, M C]]
	[[Category: Flanagan, J M]]		[[Category: Flanagan, J M]]

OCA at 07:06, 25 April 2018

OCA — Wed, 25 Apr 2018 07:06:32 GMT

←Older revision		Revision as of 07:06, 25 April 2018
Line 1:		Line 1:
		+
	==The structure of a V6A variant of ClpP.==		==The structure of a V6A variant of ClpP.==
	<StructureSection load='1yg8' size='340' side='right' caption='[[1yg8]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='1yg8' size='340' side='right' caption='[[1yg8]], [[Resolution\|resolution]] 2.60Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">clpP, lopP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">clpP, lopP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endopeptidase_Clp Endopeptidase Clp], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.92 3.4.21.92] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endopeptidase_Clp Endopeptidase Clp], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.92 3.4.21.92] </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=1yg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yg8 OCA], [http://pdbe.org/1yg8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yg8 RCSB], [http://www.ebi.ac.uk/pdbsum/1yg8 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=1yg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yg8 OCA], [http://pdbe.org/1yg8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yg8 RCSB], [http://www.ebi.ac.uk/pdbsum/1yg8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yg8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yg/1yg8_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yg/1yg8_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 23:50, 7 February 2016

OCA — Sun, 07 Feb 2016 23:50:49 GMT

←Older revision		Revision as of 23:50, 7 February 2016
Line 18:		Line 18:
	<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=1yg8 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 05:59, 10 September 2015

OCA — Thu, 10 Sep 2015 05:59:17 GMT

←Older revision		Revision as of 05:59, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1yg8' size='340' side='right' caption='[[1yg8]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='1yg8' size='340' side='right' caption='[[1yg8]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yg8]] is a 28 chain structure with 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=1YG8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YG8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yg8]] is a 28 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=1YG8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YG8 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yg6\|1yg6]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yg6\|1yg6]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">clpP, lopP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">clpP, lopP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endopeptidase_Clp Endopeptidase Clp], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.92 3.4.21.92] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endopeptidase_Clp Endopeptidase Clp], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.92 3.4.21.92] </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=1yg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yg8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yg8 RCSB], [http://www.ebi.ac.uk/pdbsum/1yg8 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=1yg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yg8 OCA], [http://pdbe.org/1yg8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yg8 RCSB], [http://www.ebi.ac.uk/pdbsum/1yg8 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 1yg8" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Clp Protease\|Clp Protease]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: Endopeptidase Clp]]		[[Category: Endopeptidase Clp]]
-	[[Category: Escherichia coli]]
	[[Category: Bewley, M C]]		[[Category: Bewley, M C]]
	[[Category: Flanagan, J M]]		[[Category: Flanagan, J M]]

OCA at 19:04, 24 December 2014

OCA — Wed, 24 Dec 2014 19:04:28 GMT

←Older revision		Revision as of 19:04, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1yg8]] is a 28 chain structure with 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=1YG8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YG8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1yg8]] is a 28 chain structure with 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=1YG8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YG8 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yg6\|1yg6]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yg6\|1yg6]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">clpP, lopP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">clpP, lopP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endopeptidase_Clp Endopeptidase Clp], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.92 3.4.21.92] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endopeptidase_Clp Endopeptidase Clp], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.92 3.4.21.92] </span></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=1yg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yg8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yg8 RCSB], [http://www.ebi.ac.uk/pdbsum/1yg8 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=1yg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yg8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yg8 RCSB], [http://www.ebi.ac.uk/pdbsum/1yg8 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CLPP_ECOLI CLPP_ECOLI]] Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins. May play the role of a master protease which is attracted to different substrates by different specificity factors such as ClpA or ClpX.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 26:		Line 28:
	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>
-
-	==See Also==
-	*[[Clp Protease\|Clp Protease]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 34:
	[[Category: Endopeptidase Clp]]		[[Category: Endopeptidase Clp]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Bewley, M C.]]	+	[[Category: Bewley, M C]]
-	[[Category: Flanagan, J M.]]	+	[[Category: Flanagan, J M]]
-	[[Category: Graziano, V.]]	+	[[Category: Graziano, V]]
-	[[Category: Griffin, K.]]	+	[[Category: Griffin, K]]
	[[Category: Caseinolytic protease]]		[[Category: Caseinolytic protease]]
	[[Category: Endopeptidase clp]]		[[Category: Endopeptidase clp]]

OCA at 21:24, 28 September 2014

OCA — Sun, 28 Sep 2014 21:24:27 GMT

←Older revision		Revision as of 21:24, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1yg8.~~png~~\|~~left~~\|200px]]	+	==The structure of a V6A variant of ClpP.==
		+	<StructureSection load='1yg8' size='340' side='right' caption='[[1yg8]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1yg8]] is a 28 chain structure with 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=1YG8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YG8 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1yg6\|1yg6]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">clpP, lopP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endopeptidase_Clp Endopeptidase Clp], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.92 3.4.21.92] </span></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=1yg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yg8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yg8 RCSB], [http://www.ebi.ac.uk/pdbsum/1yg8 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/yg/1yg8_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 ==
		+	ClpP is a self-compartmentalized proteolytic assembly comprised of two, stacked, heptameric rings that, when associated with its cognate hexameric ATPase (ClpA or ClpX), form the ClpAP and ClpXP ATP-dependent protease, respectively. The symmetry mismatch is an absolute feature of this large energy-dependent protease and also of the proteasome, which shares a similar barrel-shaped architecture, but how it is accommodated within the complex has yet to be understood, despite recent structural investigations, due in part to the conformational lability of the N-termini. We present the structures of Escherichia coli ClpP to 1.9A and an inactive variant that provide some clues for how this might be achieved. In the wild type protein, the highly conserved N-terminal 20 residues can be grouped into two major structural classes. In the first, a loop formed by residues 10-15 protrudes out of the central access channel extending approximately 12-15A from the surface of the oligomer resulting in the closing of the access channel observed in one ring. Similar loops are implied to be exclusively observed in human ClpP and a variant of ClpP from Streptococcus pneumoniae. In the other ring, a second class of loop is visible in the structure of wt ClpP from E. coli that forms closer to residue 16 and faces toward the interior of the molecule creating an open conformation of the access channel. In both classes, residues 18-20 provide a conserved interaction surface. In the inactive variant, a third class of N-terminal conformation is observed, which arises from a conformational change in the position of F17. We have performed a detailed functional analysis on each of the first 20 amino acid residues of ClpP. Residues that extend beyond the plane of the molecule (10-15) have a lesser effect on ATPase interaction than those lining the pore (1-7 and 16-20). Based upon our structure-function analysis, we present a model to explain the widely disparate effects of individual residues on ClpP-ATPase complex formation and also a possible functional reason for this mismatch.

-	~~{{STRUCTURE_1yg8\| PDB=1yg8 \| SCENE= }}~~	+	The asymmetry in the mature amino-terminus of ClpP facilitates a local symmetry match in ClpAP and ClpXP complexes.,Bewley MC, Graziano V, Griffin K, Flanagan JM J Struct Biol. 2006 Feb;153(2):113-28. Epub 2005 Dec 1. PMID:16406682<ref>PMID:16406682</ref>

-	~~===The structure of~~ a ~~V6A variant~~ of ~~ClpP~~.~~===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16406682}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1yg8]] is a 28 chain structure with 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=1YG8 OCA].~~	+

	==See Also==		==See Also==
	*[[Clp Protease\|Clp Protease]]		*[[Clp Protease\|Clp Protease]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:016406682<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Endopeptidase Clp]]		[[Category: Endopeptidase Clp]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]

OCA: Protected "1yg8" [edit=sysop:move=sysop]

OCA — Sat, 20 Oct 2012 08:12:57 GMT

Protected "1yg8" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:12, 20 October 2012

OCA at 08:12, 20 October 2012

OCA — Sat, 20 Oct 2012 08:12:54 GMT

←Older revision		Revision as of 08:12, 20 October 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1yg8.png\|left\|200px]]		[[Image:1yg8.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1yg8", 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_1yg8\| PDB=1yg8 \| SCENE= }}		{{STRUCTURE_1yg8\| PDB=1yg8 \| SCENE= }}

	===The structure of a V6A variant of ClpP.===		===The structure of a V6A variant of ClpP.===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16406682}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16406682 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16406682}}		{{ABSTRACT_PUBMED_16406682}}

	==About this Structure==		==About this Structure==
-	~~1YG8~~ is a 28 ~~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=1YG8 OCA].	+	[[1yg8]] is a 28 chain structure with 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=1YG8 OCA].
		+
		+	==See Also==
		+	*[[Clp Protease\|Clp Protease]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16406682~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016406682</ref><references group="xtra"/>
	[[Category: Endopeptidase Clp]]		[[Category: Endopeptidase Clp]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
Line 33:		Line 24:
	[[Category: Endopeptidase clp]]		[[Category: Endopeptidase clp]]
	[[Category: Heat shock protein f21 5]]		[[Category: Heat shock protein f21 5]]
		+	[[Category: Hydrolase]]
	[[Category: Protease ti]]		[[Category: Protease ti]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 17:18:38 2009''