6po3 - Revision history

OCA at 09:26, 20 March 2024

OCA — Wed, 20 Mar 2024 09:26:38 GMT

←Older revision		Revision as of 09:26, 20 March 2024
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	<StructureSection load='6po3' size='340' side='right'caption='[[6po3]], [[Resolution\|resolution]] 4.28Å' scene=''>		<StructureSection load='6po3' size='340' side='right'caption='[[6po3]], [[Resolution\|resolution]] 4.28Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6po3]] is a 14 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PO3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6PO3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6po3]] is a 14 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=6PO3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PO3 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene~~>, ~~<scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 4.28Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~UNK~~:~~UNKNOWN~~'>~~UNK~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=6po3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6po3 OCA], [https://pdbe.org/6po3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6po3 RCSB], [https://www.ebi.ac.uk/pdbsum/6po3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6po3 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=6po3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6po3 OCA], [~~http~~://pdbe.org/6po3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6po3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6po3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6po3 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~A0A1Q9L861_ECOLX A0A1Q9L861_ECOLX]~~] ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP.[HAMAP-Rule:MF_00175][SAAS:SAAS01076750] [[http://www.uniprot.org/uniprot/S1IIE7_ECOLX S1IIE7_ECOLX]] 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.[HAMAP-Rule:MF_00444][RuleBase:RU000550][SAAS:SAAS00674840]	+	[https://www.uniprot.org/uniprot/CLPX_ECOLI CLPX_ECOLI] ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. It may bind to the lambda O substrate protein and present it to the ClpP protease in a form that can be recognized and readily hydrolyzed by ClpP. Can perform chaperone functions in the absence of ClpP.[HAMAP-Rule:MF_00175]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	ClpXP is an ATP-dependent protease in which the ClpX AAA+ motor binds, unfolds, and translocates specific protein substrates into the degradation chamber of ClpP. We present cryo-EM studies of the E. coli enzyme that show how asymmetric hexameric rings of ClpX bind symmetric heptameric rings of ClpP and interact with protein substrates. Subunits in the ClpX hexamer assume a spiral conformation and interact with two-residue segments of substrate in the axial channel, as observed for other AAA+ proteases and protein-remodeling machines. Strictly sequential models of ATP hydrolysis and a power stroke that moves two residues of the substrate per translocation step have been inferred from these structural features for other AAA+ unfoldases, but biochemical and single-molecule biophysical studies indicate that ClpXP operates by a probabilistic mechanism in which five to eight residues are translocated for each ATP hydrolyzed. We propose structure-based models that could account for the functional results.	+
-		+
-	Structures of the ATP-fueled ClpXP proteolytic machine bound to protein substrate.,Fei X, Bell TA, Jenni S, Stinson BM, Baker TA, Harrison SC, Sauer RT Elife. 2020 Feb 28;9. pii: 52774. doi: 10.7554/eLife.52774. PMID:32108573<ref>PMID:32108573</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6po3" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Endopeptidase Clp~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fei, X]]	+	[[Category: Fei X]]
-	[[Category: Harrison~~, S C~~]]	+	[[Category: Harrison SC]]
-	[[Category: Jenni, S]]	+	[[Category: Jenni S]]
-	[[Category: Sauer~~, R T]]~~	+	[[Category: Sauer RT]]
-	~~[[Category: Aaa+ protease complex]]~~	+
-	~~[[Category: Chaperone]]~~	+
-	~~[[Category: Protein degradation~~]]	+

OCA at 07:24, 11 March 2020

OCA — Wed, 11 Mar 2020 07:24:12 GMT

←Older revision		Revision as of 07:24, 11 March 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6po3 is ~~ON HOLD~~	+	==ClpX-ClpP complex bound to substrate and ATP-gamma-S, class 3==
		+	<StructureSection load='6po3' size='340' side='right'caption='[[6po3]], [[Resolution\|resolution]] 4.28Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6po3]] is a 14 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PO3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PO3 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></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=6po3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6po3 OCA], [http://pdbe.org/6po3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6po3 RCSB], [http://www.ebi.ac.uk/pdbsum/6po3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6po3 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/A0A1Q9L861_ECOLX A0A1Q9L861_ECOLX]] ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP.[HAMAP-Rule:MF_00175][SAAS:SAAS01076750] [[http://www.uniprot.org/uniprot/S1IIE7_ECOLX S1IIE7_ECOLX]] 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.[HAMAP-Rule:MF_00444][RuleBase:RU000550][SAAS:SAAS00674840]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	ClpXP is an ATP-dependent protease in which the ClpX AAA+ motor binds, unfolds, and translocates specific protein substrates into the degradation chamber of ClpP. We present cryo-EM studies of the E. coli enzyme that show how asymmetric hexameric rings of ClpX bind symmetric heptameric rings of ClpP and interact with protein substrates. Subunits in the ClpX hexamer assume a spiral conformation and interact with two-residue segments of substrate in the axial channel, as observed for other AAA+ proteases and protein-remodeling machines. Strictly sequential models of ATP hydrolysis and a power stroke that moves two residues of the substrate per translocation step have been inferred from these structural features for other AAA+ unfoldases, but biochemical and single-molecule biophysical studies indicate that ClpXP operates by a probabilistic mechanism in which five to eight residues are translocated for each ATP hydrolyzed. We propose structure-based models that could account for the functional results.

-	~~Authors~~:	+	Structures of the ATP-fueled ClpXP proteolytic machine bound to protein substrate.,Fei X, Bell TA, Jenni S, Stinson BM, Baker TA, Harrison SC, Sauer RT Elife. 2020 Feb 28;9. pii: 52774. doi: 10.7554/eLife.52774. PMID:32108573<ref>PMID:32108573</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6po3" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Endopeptidase Clp]]
		+	[[Category: Large Structures]]
		+	[[Category: Fei, X]]
		+	[[Category: Harrison, S C]]
		+	[[Category: Jenni, S]]
		+	[[Category: Sauer, R T]]
		+	[[Category: Aaa+ protease complex]]
		+	[[Category: Chaperone]]
		+	[[Category: Protein degradation]]

OCA at 02:37, 13 February 2020

OCA — Thu, 13 Feb 2020 02:37:00 GMT

←Older revision		Revision as of 02:37, 13 February 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6po3 is ON HOLD ~~until Paper Publication~~	+	The entry 6po3 is ON HOLD

	Authors:		Authors:

OCA at 09:01, 17 July 2019

OCA — Wed, 17 Jul 2019 09:01:11 GMT

←Older revision		Revision as of 09:01, 17 July 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6po3 is ON HOLD	+	The entry 6po3 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6po3" [edit=sysop:move=sysop]

OCA — Wed, 10 Jul 2019 04:19:48 GMT

Protected "6po3" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:19, 10 July 2019

OCA: New page: '''Unreleased structure''' The entry 6po3 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 10 Jul 2019 04:19:47 GMT

New page: '''Unreleased structure''' The entry 6po3 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6po3 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]