4ytx: Difference between revisions

Latest revision as of 15:38, 8 November 2023

Crystal structure of Ups1-Mdm35 complex with PA

Structural highlights

4ytx is a 16 chain structure with sequence from Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.2Å
Ligands:	PX2
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MDM35_YEAST Involved in mitochondrial distribution and morphology. Mediates the import of UPS1, UPS2 and UPS3, 3 atypical mitochondrial intermembrane space (IMS) proteins lacking the two major IMS-targeting signals, into the intermembrane space.^[1] ^[2] ^[3]

Publication Abstract from PubMed

Eukaryotic cells are compartmentalized into membrane-bounded organelles whose functions rely on lipid trafficking to achieve membrane-specific compositions of lipids. Here we focused on the Ups1-Mdm35 system, which mediates phosphatidic acid (PA) transfer between the outer and inner mitochondrial membranes, and determined the X-ray structures of Mdm35 and Ups1-Mdm35 with and without PA. The Ups1-Mdm35 complex constitutes a single domain that has a deep pocket and flexible Omega-loop lid. Structure-based mutational analyses revealed that a basic residue at the pocket bottom and the Omega-loop lid are important for PA extraction from the membrane following Ups1 binding. Ups1 binding to the membrane is enhanced by the dissociation of Mdm35. We also show that basic residues around the pocket entrance are important for Ups1 binding to the membrane and PA extraction. These results provide a structural basis for understanding the mechanism of PA transfer between mitochondrial membranes.

Structural and mechanistic insights into phospholipid transfer by Ups1-Mdm35 in mitochondria.,Watanabe Y, Tamura Y, Kawano S, Endo T Nat Commun. 2015 Aug 3;6:7922. doi: 10.1038/ncomms8922. PMID:26235513^[4]

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

References

↑ Dimmer KS, Fritz S, Fuchs F, Messerschmitt M, Weinbach N, Neupert W, Westermann B. Genetic basis of mitochondrial function and morphology in Saccharomyces cerevisiae. Mol Biol Cell. 2002 Mar;13(3):847-53. PMID:11907266 doi:10.1091/mbc.01-12-0588
↑ Tamura Y, Iijima M, Sesaki H. Mdm35p imports Ups proteins into the mitochondrial intermembrane space by functional complex formation. EMBO J. 2010 Sep 1;29(17):2875-87. doi: 10.1038/emboj.2010.149. Epub 2010 Jul 9. PMID:20622808 doi:https://dx.doi.org/10.1038/emboj.2010.149
↑ Potting C, Wilmes C, Engmann T, Osman C, Langer T. Regulation of mitochondrial phospholipids by Ups1/PRELI-like proteins depends on proteolysis and Mdm35. EMBO J. 2010 Sep 1;29(17):2888-98. doi: 10.1038/emboj.2010.169. Epub 2010 Jul 23. PMID:20657548 doi:https://dx.doi.org/10.1038/emboj.2010.169
↑ Watanabe Y, Tamura Y, Kawano S, Endo T. Structural and mechanistic insights into phospholipid transfer by Ups1-Mdm35 in mitochondria. Nat Commun. 2015 Aug 3;6:7922. doi: 10.1038/ncomms8922. PMID:26235513 doi:https://dx.doi.org/10.1038/ncomms8922

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Dimmer KS, Fritz S, Fuchs F, Messerschmitt M, Weinbach N, Neupert W, Westermann B. Genetic basis of mitochondrial function and morphology in Saccharomyces cerevisiae. Mol Biol Cell. 2002 Mar;13(3):847-53. PMID:11907266 doi:10.1091/mbc.01-12-0588

[2] Tamura Y, Iijima M, Sesaki H. Mdm35p imports Ups proteins into the mitochondrial intermembrane space by functional complex formation. EMBO J. 2010 Sep 1;29(17):2875-87. doi: 10.1038/emboj.2010.149. Epub 2010 Jul 9. PMID:20622808 doi:https://dx.doi.org/10.1038/emboj.2010.149

[3] Potting C, Wilmes C, Engmann T, Osman C, Langer T. Regulation of mitochondrial phospholipids by Ups1/PRELI-like proteins depends on proteolysis and Mdm35. EMBO J. 2010 Sep 1;29(17):2888-98. doi: 10.1038/emboj.2010.169. Epub 2010 Jul 23. PMID:20657548 doi:https://dx.doi.org/10.1038/emboj.2010.169

[4] Watanabe Y, Tamura Y, Kawano S, Endo T. Structural and mechanistic insights into phospholipid transfer by Ups1-Mdm35 in mitochondria. Nat Commun. 2015 Aug 3;6:7922. doi: 10.1038/ncomms8922. PMID:26235513 doi:https://dx.doi.org/10.1038/ncomms8922

[1]

[2]

[3]

[4]

@@ Line 1: / Line 1: @@
 ==Crystal structure of Ups1-Mdm35 complex with PA==
-<StructureSection load='4ytx' size='340' side='right' caption='[[4ytx]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
+<StructureSection load='4ytx' size='340' side='right'caption='[[4ytx]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4ytx]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YTX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YTX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4ytx]] is a 16 chain structure with sequence from [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=4YTX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YTX FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PX2:1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE'>PX2</scene></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]] 3.2&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ytv|4ytv]], [[4ytw|4ytw]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PX2:1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE'>PX2</scene></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=4ytx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ytx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ytx RCSB], [http://www.ebi.ac.uk/pdbsum/4ytx PDBsum]</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=4ytx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ytx OCA], [https://pdbe.org/4ytx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ytx RCSB], [https://www.ebi.ac.uk/pdbsum/4ytx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ytx ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/MDM35_YEAST MDM35_YEAST]] Involved in mitochondrial distribution and morphology. Mediates the import of UPS1, UPS2 and UPS3, 3 atypical mitochondrial intermembrane space (IMS) proteins lacking the two major IMS-targeting signals, into the intermembrane space.<ref>PMID:11907266</ref> <ref>PMID:20622808</ref> <ref>PMID:20657548</ref>  [[http://www.uniprot.org/uniprot/UPS1_YEAST UPS1_YEAST]] Required for maintenance of normal mitochondrial morphology as well as PCP1-dependent processing of MGM1. With UPS2, controls the level of cardiolipin in mitochondria. Cardiolipin is a unique phospholipid with four fatty acid chains and is present mainly in the mitochondrial inner membrane where it stabilizes the electron transport chain supercomplex between complexes III and IV through direct interaction of their subunits.<ref>PMID:16754953</ref> <ref>PMID:19221197</ref> <ref>PMID:19506038</ref> <ref>PMID:20622808</ref>
+[https://www.uniprot.org/uniprot/MDM35_YEAST MDM35_YEAST] Involved in mitochondrial distribution and morphology. Mediates the import of UPS1, UPS2 and UPS3, 3 atypical mitochondrial intermembrane space (IMS) proteins lacking the two major IMS-targeting signals, into the intermembrane space.<ref>PMID:11907266</ref> <ref>PMID:20622808</ref> <ref>PMID:20657548</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 17: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4ytx" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Endo, T]]
+[[Category: Large Structures]]
-[[Category: Kawano, S]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Tamura, Y]]
+[[Category: Endo T]]
-[[Category: Watanabe, Y]]
+[[Category: Kawano S]]
-[[Category: Lipid transport]]
+[[Category: Tamura Y]]
-[[Category: Mitochondria]]
+[[Category: Watanabe Y]]
-[[Category: Phosphatidic acid]]
-[[Category: Phospholipid transfer]]

4ytx: Difference between revisions

Latest revision as of 15:38, 8 November 2023

Crystal structure of Ups1-Mdm35 complex with PA

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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