7sxo

From Proteopedia

(Difference between revisions)

Revision as of 04:45, 8 September 2022

Yeast Lon (PIM1) with endogenous substrate

Structural highlights

7sxo is a 7 chain structure with sequence from Escherichia coli and Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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]^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10]

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^[11]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Ondrovicova G, Liu T, Singh K, Tian B, Li H, Gakh O, Perecko D, Janata J, Granot Z, Orly J, Kutejova E, Suzuki CK. Cleavage site selection within a folded substrate by the ATP-dependent lon protease. J Biol Chem. 2005 Jul 1;280(26):25103-10. Epub 2005 May 3. PMID:15870080 doi:http://dx.doi.org/10.1074/jbc.M502796200
↑ Major T, von Janowsky B, Ruppert T, Mogk A, Voos W. Proteomic analysis of mitochondrial protein turnover: identification of novel substrate proteins of the matrix protease pim1. Mol Cell Biol. 2006 Feb;26(3):762-76. doi: 10.1128/MCB.26.3.762-776.2006. PMID:16428434 doi:http://dx.doi.org/10.1128/MCB.26.3.762-776.2006
↑ Bayot A, Gareil M, Rogowska-Wrzesinska A, Roepstorff P, Friguet B, Bulteau AL. Identification of novel oxidized protein substrates and physiological partners of the mitochondrial ATP-dependent Lon-like protease Pim1. J Biol Chem. 2010 Apr 9;285(15):11445-57. doi: 10.1074/jbc.M109.065425. Epub 2010, Feb 11. PMID:20150421 doi:http://dx.doi.org/10.1074/jbc.M109.065425
↑ Kunova N, Ondrovicova G, Bauer JA, Bellova J, Ambro L, Martinakova L, Kotrasova V, Kutejova E, Pevala V. The role of Lon-mediated proteolysis in the dynamics of mitochondrial nucleic acid-protein complexes. Sci Rep. 2017 Apr 4;7(1):631. doi: 10.1038/s41598-017-00632-8. PMID:28377575 doi:http://dx.doi.org/10.1038/s41598-017-00632-8
↑ Suzuki CK, Suda K, Wang N, Schatz G. Requirement for the yeast gene LON in intramitochondrial proteolysis and maintenance of respiration. Science. 1994 Apr 8;264(5156):273-6. doi: 10.1126/science.8146662. PMID:8146662 doi:http://dx.doi.org/10.1126/science.8146662
↑ Van Dyck L, Pearce DA, Sherman F. PIM1 encodes a mitochondrial ATP-dependent protease that is required for mitochondrial function in the yeast Saccharomyces cerevisiae. J Biol Chem. 1994 Jan 7;269(1):238-42. PMID:8276800
↑ Kutejova E, Durcova G, Surovkova E, Kuzela S. Yeast mitochondrial ATP-dependent protease: purification and comparison with the homologous rat enzyme and the bacterial ATP-dependent protease La. FEBS Lett. 1993 Aug 23;329(1-2):47-50. doi: 10.1016/0014-5793(93)80190-6. PMID:8354406 doi:http://dx.doi.org/10.1016/0014-5793(93)80190-6
↑ Rep M, van Dijl JM, Suda K, Schatz G, Grivell LA, Suzuki CK. Promotion of mitochondrial membrane complex assembly by a proteolytically inactive yeast Lon. Science. 1996 Oct 4;274(5284):103-6. doi: 10.1126/science.274.5284.103. PMID:8810243 doi:http://dx.doi.org/10.1126/science.274.5284.103
↑ Wagner I, van Dyck L, Savel'ev AS, Neupert W, Langer T. Autocatalytic processing of the ATP-dependent PIM1 protease: crucial function of a pro-region for sorting to mitochondria. EMBO J. 1997 Dec 15;16(24):7317-25. doi: 10.1093/emboj/16.24.7317. PMID:9405361 doi:http://dx.doi.org/10.1093/emboj/16.24.7317
↑ van Dijl JM, Kutejova E, Suda K, Perecko D, Schatz G, Suzuki CK. The ATPase and protease domains of yeast mitochondrial Lon: roles in proteolysis and respiration-dependent growth. Proc Natl Acad Sci U S A. 1998 Sep 1;95(18):10584-9. doi:, 10.1073/pnas.95.18.10584. PMID:9724747 doi:http://dx.doi.org/10.1073/pnas.95.18.10584
↑ Yang J, Song AS, Wiseman RL, Lander GC. Cryo-EM structure of hexameric yeast Lon protease (PIM1) highlights the importance of conserved structural elements. J Biol Chem. 2022 Mar;298(3):101694. doi: 10.1016/j.jbc.2022.101694. Epub 2022, Feb 7. PMID:35143841 doi:http://dx.doi.org/10.1016/j.jbc.2022.101694

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/7sxo"

@@ Line 1: / Line 1: @@
-====
+==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]] 3.30&Aring;' scene=''>
 == 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>
+== 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&reg;/PubMed&reg;, 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__
 </StructureSection>
+[[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Z-disk]]
+[[Category: Saccharomyces cerevisiae S288C]]
+[[Category: Lander GC]]
+[[Category: Song AS]]
+[[Category: Wiseman RL]]
+[[Category: Yang J]]

7sxo

From Proteopedia

Revision as of 04:45, 8 September 2022

Yeast Lon (PIM1) with endogenous substrate

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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