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| - | [[Image:3bw6.jpg|left|200px]] | |
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| - | <!--
| + | ==Crystal structure of the longin domain of yeast Ykt6== |
| - | The line below this paragraph, containing "STRUCTURE_3bw6", creates the "Structure Box" on the page.
| + | <StructureSection load='3bw6' size='340' side='right'caption='[[3bw6]], [[Resolution|resolution]] 2.50Å' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet)
| + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <table><tr><td colspan='2'>[[3bw6]] 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=3BW6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BW6 FirstGlance]. <br> |
| - | or leave the SCENE parameter empty for the default display.
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5Å</td></tr> |
| - | -->
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | {{STRUCTURE_3bw6| PDB=3bw6 | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3bw6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bw6 OCA], [https://pdbe.org/3bw6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bw6 RCSB], [https://www.ebi.ac.uk/pdbsum/3bw6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bw6 ProSAT]</span></td></tr> |
| - | | + | </table> |
| - | '''Crystal structure of the longin domain of yeast Ykt6'''
| + | == Function == |
| - | | + | [https://www.uniprot.org/uniprot/YKT6_YEAST YKT6_YEAST] |
| - | | + | == Evolutionary Conservation == |
| - | ==Overview== | + | [[Image:Consurf_key_small.gif|200px|right]] |
| - | The evolutionarily conserved soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins are involved in the fusion of vesicles with their target membranes. While most SNAREs are permanently anchored to membranes by their transmembrane domains, the vesicle-associated SNARE Ykt6 has been found both in soluble and in membrane-bound pools. The R-SNARE Ykt6 is thought to mediate interactions between various Q-SNAREs by a reversible membrane-targeting cycle. Membrane attachment of Ykt6 is achieved by its C-terminal prenylation and palmitoylation motif succeeding the SNARE motif. In this study, we have analyzed full-length farnesylated Ykt6 from yeast and humans by biochemical and structural means. In vitro farnesylation of the C-terminal CAAX box of recombinant full-length Ykt6 resulted in stabilization of the native protein and a more compactly folded structure, as shown by size exclusion chromatography and limited proteolysis. Circular dichroism spectroscopy indicated a specific increase in the helical content of the farnesylated Ykt6 compared to the nonlipidated form or the single-longin domain, which correlated with a marked increase in stability as observed by heat denaturation experiments. Although highly soluble, farnesylated Ykt6 is capable of lipid membrane binding independent of the membrane charge, as shown by surface plasmon resonance. The crystal structure of the N-terminal longin domain of yeast Ykt6 (1-140) was determined at 2.5 A resolution. As similarly found in a previous NMR structure, the Ykt6 longin domain contains a hydrophobic patch at its surface that may accommodate the lipid moiety. In the crystal structure, this hydrophobic surface is buried in a crystallographic homomeric dimer interface. Together, these observations support a previously suggested closed conformation of cytosolic Ykt6, where the C-terminal farnesyl moiety folds onto a hydrophobic groove in the N-terminal longin domain.
| + | Check<jmol> |
| - | | + | <jmolCheckbox> |
| - | ==About this Structure== | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bw/3bw6_consurf.spt"</scriptWhenChecked> |
| - | 3BW6 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BW6 OCA].
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| - | | + | <text>to colour the structure by Evolutionary Conservation</text> |
| - | ==Reference== | + | </jmolCheckbox> |
| - | Farnesylation of the SNARE protein Ykt6 increases its stability and helical folding., Pylypenko O, Schonichen A, Ludwig D, Ungermann C, Goody RS, Rak A, Geyer M, J Mol Biol. 2008 Apr 11;377(5):1334-45. Epub 2008 Feb 13. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18329045 18329045]
| + | </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=3bw6 ConSurf]. |
| | + | <div style="clear:both"></div> |
| | + | __TOC__ |
| | + | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | [[Category: Saccharomyces cerevisiae]] | | [[Category: Saccharomyces cerevisiae]] |
| - | [[Category: Single protein]]
| + | [[Category: Geyer M]] |
| - | [[Category: Geyer, M.]] | + | [[Category: Goody RS]] |
| - | [[Category: Goody, R S.]] | + | [[Category: Ludwig D]] |
| - | [[Category: Ludwig, D.]] | + | [[Category: Pylypenko O]] |
| - | [[Category: Pylypenko, O.]] | + | [[Category: Rak A]] |
| - | [[Category: Rak, A.]] | + | [[Category: Schonichen A]] |
| - | [[Category: Schonichen, A.]] | + | [[Category: Ungermann C]] |
| - | [[Category: Ungermann, C.]] | + | |
| - | [[Category: Coiled coil]]
| + | |
| - | [[Category: Farnesylation]]
| + | |
| - | [[Category: Lipoprotein]]
| + | |
| - | [[Category: Membrane]]
| + | |
| - | [[Category: Phosphoprotein]]
| + | |
| - | [[Category: Prenylation]]
| + | |
| - | [[Category: Snare]]
| + | |
| - | [[Category: Transferase]]
| + | |
| - | [[Category: Vacuole fusion]]
| + | |
| - | [[Category: Ykt6p]]
| + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 21:09:31 2008''
| + | |
