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| - | [[Image:3bw6.jpg|left|200px]] | |
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| - | {{Structure
| + | ==Crystal structure of the longin domain of yeast Ykt6== |
| - | |PDB= 3bw6 |SIZE=350|CAPTION= <scene name='initialview01'>3bw6</scene>, resolution 2.5Å
| + | <StructureSection load='3bw6' size='340' side='right'caption='[[3bw6]], [[Resolution|resolution]] 2.50Å' scene=''> |
| - | |SITE= <scene name='pdbsite=AC1:So4+Binding+Site+For+Residue+A+4000'>AC1</scene>
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
| + | <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> |
| - | |ACTIVITY=
| + | </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> |
| - | |GENE= YKT6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])
| + | <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> |
| - | |DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam00957 Synaptobrevin], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=COG5143 SNC1]</span>
| + | <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> |
| - | |RELATEDENTRY= | + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3bw6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bw6 OCA], [http://www.ebi.ac.uk/pdbsum/3bw6 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3bw6 RCSB]</span>
| + | == Function == |
| - | }}
| + | [https://www.uniprot.org/uniprot/YKT6_YEAST YKT6_YEAST] |
| - | | + | == Evolutionary Conservation == |
| - | '''Crystal structure of the longin domain of yeast Ykt6'''
| + | [[Image:Consurf_key_small.gif|200px|right]] |
| - | | + | Check<jmol> |
| - | | + | <jmolCheckbox> |
| - | ==Overview== | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bw/3bw6_consurf.spt"</scriptWhenChecked> |
| - | 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.
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| - | | + | <text>to colour the structure by Evolutionary Conservation</text> |
| - | ==About this Structure== | + | </jmolCheckbox> |
| - | 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].
| + | </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> |
| - | ==Reference==
| + | __TOC__ |
| - | 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]
| + | </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 Wed Apr 2 11:59:41 2008''
| + | |
