2bcg
From Proteopedia
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| - | {{Seed}} | ||
| - | [[Image:2bcg.png|left|200px]] | ||
| - | < | + | ==Structure of doubly prenylated Ypt1:GDI complex== |
| - | + | <StructureSection load='2bcg' size='340' side='right'caption='[[2bcg]], [[Resolution|resolution]] 1.48Å' scene=''> | |
| - | You may | + | == Structural highlights == |
| - | + | <table><tr><td colspan='2'>[[2bcg]] is a 2 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=2BCG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BCG 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]] 1.48Å</td></tr> | |
| - | - | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=GER:GERAN-8-YL+GERAN'>GER</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=2bcg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bcg OCA], [https://pdbe.org/2bcg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bcg RCSB], [https://www.ebi.ac.uk/pdbsum/2bcg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bcg ProSAT]</span></td></tr> | |
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/GDI1_YEAST GDI1_YEAST] Regulates the GDP/GTP exchange reaction of SEC4 by inhibiting the dissociation of GDP from it, and the subsequent binding of GTP to SEC4. Plays an essential role in the yeast secretory pathway.<ref>PMID:8157010</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/bc/2bcg_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=2bcg ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | In eukaryotic cells Rab/Ypt GTPases represent a family of key membrane traffic controllers that associate with their targeted membranes via C-terminally conjugated geranylgeranyl groups. GDP dissociation inhibitor (GDI) is a general and essential regulator of Rab recycling that extracts prenylated Rab proteins from membranes at the end of their cycle of activity and facilitates their delivery to the donor membranes. Here, we present the structure of a complex between GDI and a doubly prenylated Rab protein. We show that one geranylgeranyl residue is deeply buried in a hydrophobic pocket formed by domain II of GDI, whereas the other lipid is more exposed to solvent and is skewed across several atoms of the first moiety. Based on structural information and biophysical measurements, we propose mechanistic and thermodynamic models for GDI and Rab escort protein-mediated interaction of RabGTPase with intracellular membranes. | ||
| - | + | Structure of doubly prenylated Ypt1:GDI complex and the mechanism of GDI-mediated Rab recycling.,Pylypenko O, Rak A, Durek T, Kushnir S, Dursina BE, Thomae NH, Constantinescu AT, Brunsveld L, Watzke A, Waldmann H, Goody RS, Alexandrov K EMBO J. 2006 Jan 11;25(1):13-23. Epub 2006 Jan 5. PMID:16395334<ref>PMID:16395334</ref> | |
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 2bcg" style="background-color:#fffaf0;"></div> | ||
| - | + | ==See Also== | |
| - | + | *[[GTP-binding protein 3D structures|GTP-binding protein 3D structures]] | |
| - | + | == References == | |
| - | + | <references/> | |
| - | + | __TOC__ | |
| - | + | </StructureSection> | |
| - | == | + | [[Category: Large Structures]] |
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| - | == | + | |
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[[Category: Saccharomyces cerevisiae]] | [[Category: Saccharomyces cerevisiae]] | ||
| - | [[Category: Alexandrov | + | [[Category: Alexandrov K]] |
| - | [[Category: Pylypenko | + | [[Category: Pylypenko O]] |
| - | [[Category: Rak | + | [[Category: Rak A]] |
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Current revision
Structure of doubly prenylated Ypt1:GDI complex
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