7sxo - Revision history

OCA at 04:45, 8 September 2022

OCA — Thu, 08 Sep 2022 04:45:16 GMT

←Older revision		Revision as of 04:45, 8 September 2022
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-	====	+	==Yeast Lon (PIM1) with endogenous substrate==
-	<StructureSection load='7sxo' size='340' side='right'caption='[[7sxo]]' scene=''>	+	<StructureSection load='7sxo' size='340' side='right'caption='[[7sxo]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7sxo]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7SXO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7SXO FirstGlance]. <br>
-	</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=7sxo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7sxo OCA], [https://pdbe.org/7sxo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7sxo RCSB], [https://www.ebi.ac.uk/pdbsum/7sxo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7sxo ProSAT]</span></td></tr>	+	</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=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=7sxo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7sxo OCA], [https://pdbe.org/7sxo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7sxo RCSB], [https://www.ebi.ac.uk/pdbsum/7sxo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7sxo ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/LONM_YEAST LONM_YEAST]] ATP-dependent serine protease that mediates the selective degradation of misfolded, unassembled or oxidatively damaged polypeptides as well as certain short-lived regulatory proteins in the mitochondrial matrix. May also have a chaperone function in the assembly of inner membrane protein complexes. Participates in the regulation of mitochondrial gene expression and in the maintenance of the integrity of the mitochondrial genome. Binds to mitochondrial DNA in a site-specific manner (PubMed:15870080, PubMed:16428434, PubMed:8146662, PubMed:8276800, PubMed:8354406, PubMed:8810243, PubMed:9405361, PubMed:9724747). Endogenous substrates include ABF2, ACO2, ILV1, ILV2, LSC1, LYS4, MGM101 and several oxidized proteins. The 2 nucleic acid-binding proteins ABF2 and MGM101 are protected from degradation by PIM1 when they are bound to DNA (PubMed:16428434, PubMed:20150421, PubMed:28377575).[HAMAP-Rule:MF_03120]<ref>PMID:15870080</ref> <ref>PMID:16428434</ref> <ref>PMID:20150421</ref> <ref>PMID:28377575</ref> <ref>PMID:8146662</ref> <ref>PMID:8276800</ref> <ref>PMID:8354406</ref> <ref>PMID:8810243</ref> <ref>PMID:9405361</ref> <ref>PMID:9724747</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Lon protease is a conserved ATP-dependent serine protease composed of an AAA+ domain that mechanically unfolds substrates and a serine protease domain that degrades these unfolded substrates. In yeast, dysregulation of Lon protease (PIM1) attenuates lifespan and leads to gross mitochondrial morphological perturbations. Although structures of the bacterial and human Lon protease reveal a hexameric assembly, yeast PIM1 was speculated to form a heptameric assembly and is uniquely characterized by a approximately 50-residue insertion between the ATPase and protease domains. To further understand the yeast-specific properties of PIM1, we determined a high-resolution cryo-electron microscopy structure of PIM1 in a substrate-translocating state. Here, we reveal that PIM1 forms a hexamer, conserved with that of bacterial and human Lon proteases, wherein the ATPase domains form a canonical closed spiral that enables pore loop residues to translocate substrates to the protease chamber. In the substrate-translocating state, PIM1 protease domains form a planar protease chamber in an active conformation and are uniquely characterized by a approximately 15-residue C-terminal extension. These additional C-terminal residues form an alpha-helix located along the base of the protease domain. Finally, we did not observe density for the yeast-specific insertion between the ATPase and protease domains, likely due to high conformational flexibility. Biochemical studies to investigate the insertion using constructs that truncated or replaced the insertion with a glycine-serine linker suggest that the yeast-specific insertion is dispensable for PIM1's enzymatic function. Altogether, our structural and biochemical studies highlight unique components of PIM1 machinery and demonstrate evolutionary conservation of Lon protease function.
		+
		+	Cryo-EM structure of hexameric yeast Lon protease (PIM1) highlights the importance of conserved structural elements.,Yang J, Song AS, Wiseman RL, Lander GC J Biol Chem. 2022 Mar;298(3):101694. doi: 10.1016/j.jbc.2022.101694. Epub 2022, Feb 7. PMID:35143841<ref>PMID:35143841</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7sxo" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Saccharomyces cerevisiae S288C]]
		+	[[Category: Lander GC]]
		+	[[Category: Song AS]]
		+	[[Category: Wiseman RL]]
		+	[[Category: Yang J]]

OCA at 10:00, 12 January 2022

OCA — Wed, 12 Jan 2022 10:00:05 GMT

←Older revision		Revision as of 10:00, 12 January 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7sxo ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7sxo' size='340' side='right'caption='[[7sxo]]' scene=''>
-	~~Authors~~: ~~Yang, J~~.~~, Song, A~~.S.~~, Wiseman, R~~.L.~~, Lander, G~~.C.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~: ~~Yeast Lon (PIM1) with endogenous substrate~~	+	</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=7sxo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7sxo OCA], [https://pdbe.org/7sxo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7sxo RCSB], [https://www.ebi.ac.uk/pdbsum/7sxo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7sxo ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[~~[Category~~: ~~Yang~~, J]]	+	__TOC__
-	[~~[Category~~: ~~Wiseman, R~~.L]]	+	</StructureSection>
-	[[Category: ~~Song, A.S~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Lander, G.C~~]]	+	[[Category: Z-disk]]

OCA at 09:17, 5 January 2022

OCA — Wed, 05 Jan 2022 09:17:27 GMT

←Older revision		Revision as of 09:17, 5 January 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7sxo is ON HOLD	+	The entry 7sxo is ON HOLD until Paper Publication

	Authors: Yang, J., Song, A.S., Wiseman, R.L., Lander, G.C.		Authors: Yang, J., Song, A.S., Wiseman, R.L., Lander, G.C.
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	Description: Yeast Lon (PIM1) with endogenous substrate		Description: Yeast Lon (PIM1) with endogenous substrate
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Song, A.S]]
-	[[Category: Lander, G.C]]
	[[Category: Yang, J]]		[[Category: Yang, J]]
	[[Category: Wiseman, R.L]]		[[Category: Wiseman, R.L]]
		+	[[Category: Song, A.S]]
		+	[[Category: Lander, G.C]]

OCA: Protected "7sxo" [edit=sysop:move=sysop]

OCA — Wed, 01 Dec 2021 05:14:42 GMT

Protected "7sxo" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:14, 1 December 2021

OCA: New page: '''Unreleased structure''' The entry 7sxo is ON HOLD Authors: Yang, J., Song, A.S., Wiseman, R.L., Lander, G.C. Description: Yeast Lon (PIM1) with endogenous substrate [[Category: Unre...

OCA — Wed, 01 Dec 2021 05:14:41 GMT

New page: '''Unreleased structure''' The entry 7sxo is ON HOLD Authors: Yang, J., Song, A.S., Wiseman, R.L., Lander, G.C. Description: Yeast Lon (PIM1) with endogenous substrate [[Category: Unre...

New page

'''Unreleased structure'''

The entry 7sxo is ON HOLD

Authors: Yang, J., Song, A.S., Wiseman, R.L., Lander, G.C.

Description: Yeast Lon (PIM1) with endogenous substrate
[[Category: Unreleased Structures]]
[[Category: Song, A.S]]
[[Category: Lander, G.C]]
[[Category: Yang, J]]
[[Category: Wiseman, R.L]]