2qp9: Difference between revisions

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-[[Image:2qp9.jpg|left|200px]]<br /><applet load="2qp9" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2qp9, resolution 2.90&Aring;" />
-'''Crystal Structure of S.cerevisiae Vps4'''<br />
-==Overview==
+==Crystal Structure of S.cerevisiae Vps4==
-The multivesicular body (MVB) pathway functions in multiple cellular, processes including cell surface receptor down-regulation and viral, budding from host cells. An important step in the MVB pathway is the, correct sorting of cargo molecules, which requires the assembly and, disassembly of endosomal sorting complexes required for transport (ESCRTs), on the endosomal membrane. Disassembly of the ESCRTs is catalyzed by, ATPase associated with various cellular activities (AAA) protein Vps4., Vps4 contains a single AAA domain and undergoes ATP-dependent quaternary, structural change to disassemble the ESCRTs. Structural and biochemical, analyses of the Vps4 ATPase reaction cycle are reported here. Crystal, structures of Saccharomyces cerevisiae Vps4 in both the nucleotide-free, form and the ADP-bound form provide the first structural view illustrating, how nucleotide binding might induce conformational changes within Vps4, that lead to oligomerization and binding to its substrate ESCRT-III, subunits. In contrast to previous models, characterization of the Vps4, structure now supports a model where the ground state of Vps4 in the, ATPase reaction cycle is predominantly a monomer and the activated state, is a dodecamer. Comparison with a previously reported human VPS4B, structure suggests that Vps4 functions in the MVB pathway via a highly, conserved mechanism supported by similar protein-protein interactions, during its ATPase reaction cycle.
+<StructureSection load='2qp9' size='340' side='right'caption='[[2qp9]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2qp9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QP9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QP9 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=2qp9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qp9 OCA], [https://pdbe.org/2qp9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qp9 RCSB], [https://www.ebi.ac.uk/pdbsum/2qp9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qp9 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/VPS4_YEAST VPS4_YEAST] Involved in the transport of biosynthetic membrane proteins from the prevacuolar/endosomal compartment to the vacuole. Required for multivesicular body (MVB) protein sorting. Catalyzes the ATP-dependent dissociation of class E VPS proteins from endosomal membranes, such as the disassembly of the ESCRT-III complex.<ref>PMID:11329380</ref> <ref>PMID:9155008</ref> <ref>PMID:9606181</ref>
+== 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/qp/2qp9_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/main_output.php?pdb_ID=2qp9 ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-QP9 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with <scene name='pdbligand=CD:'>CD</scene> and <scene name='pdbligand=SO4:'>SO4</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Known structural/functional Sites: <scene name='pdbsite=AC1:Cd Binding Site For Residue X 601'>AC1</scene>, <scene name='pdbsite=AC2:Cd Binding Site For Residue X 603'>AC2</scene> and <scene name='pdbsite=AC3:So4 Binding Site For Residue X 701'>AC3</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QP9 OCA].
+*[[Vacuolar protein sorting-associated protein 3D structures|Vacuolar protein sorting-associated protein 3D structures]]
+== References ==
-==Reference==
+<references/>
-Structural characterization of the ATPase reaction cycle of endosomal AAA protein Vps4., Xiao J, Xia H, Yoshino-Koh K, Zhou J, Xu Z, J Mol Biol. 2007 Nov 30;374(3):655-70. Epub 2007 Sep 29. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17949747 17949747]
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Single protein]]
+[[Category: Xiao J]]
-[[Category: Xiao, J.]]
+[[Category: Xu Z]]
-[[Category: Xu, Z.]]
-[[Category: CD]]
-[[Category: SO4]]
-[[Category: atp-binding]]
-[[Category: atpase domain]]
-[[Category: beta domain]]
-[[Category: c-terminal helix]]
-[[Category: endosome]]
-[[Category: nucleotide-binding]]
-[[Category: protein transport]]
-[[Category: transport]]
-[[Category: vacuole]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jan 31 10:59:19 2008''