2eqb

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[[Image:2eqb.jpg|left|200px]]<br /><applet load="2eqb" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2eqb, resolution 2.70&Aring;" />
 
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'''Crystal structure of the Rab GTPase Sec4p, the Sec2p GEF domain, and phosphate complex'''<br />
 
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==Overview==
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==Crystal structure of the Rab GTPase Sec4p, the Sec2p GEF domain, and phosphate complex==
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Vesicular transport during exocytosis is regulated by Rab GTPase (Sec4p in, yeast), which is activated by a guanine nucleotide exchange factor (GEF), called Sec2p. Here, we report the crystal structure of the Sec2p GEF, domain in a complex with the nucleotide-free Sec4p at 2.7 A resolution., Upon complex formation, the Sec2p helices approach each other, flipping, the side chain of Phe-109 toward Leu-104 and Leu-108 of Sec2p. These three, residues provide a hydrophobic platform to attract the side chains of, Phe-49, Ile-53, and Ile-55 in the switch I region as well as Phe-57 and, Trp-74 in the interswitch region of Sec4p. Consequently, the switch I and, II regions are largely deformed, to create a flat hydrophobic interface, that snugly fits the surface of the Sec2p coiled coil. These drastic, conformational changes disrupt the interactions between switch I and the, bound guanine nucleotide, which facilitates the GDP release. Unlike the, recently reported 3.3 A structure of the Sec4p.Sec2p complex, our, structure contains a phosphate ion bound to the P-loop, which may, represent an intermediate state of the nucleotide exchange reaction.
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<StructureSection load='2eqb' size='340' side='right'caption='[[2eqb]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[2eqb]] is a 3 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=2EQB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EQB FirstGlance]. <br>
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2EQB is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with <scene name='pdbligand=PO4:'>PO4</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EQB OCA].
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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==Reference==
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2eqb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eqb OCA], [https://pdbe.org/2eqb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2eqb RCSB], [https://www.ebi.ac.uk/pdbsum/2eqb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2eqb ProSAT]</span></td></tr>
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Crystal structure of the Sec4p{middle dot}Sec2p complex in the nucleotide exchanging intermediate state., Sato Y, Fukai S, Ishitani R, Nureki O, Proc Natl Acad Sci U S A. 2007 May 15;104(20):8305-10. Epub 2007 May 8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17488829 17488829]
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</table>
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[[Category: Protein complex]]
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== Function ==
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[https://www.uniprot.org/uniprot/SEC4_YEAST SEC4_YEAST] Involved in exocytosis. Maybe by regulating the binding and fusion of secretory vesicles with the cell surface. The GTP-bound form of SEC4 may interact with an effector, thereby stimulating its activity and leading to exocytotic fusion. SEC4 may be an upstream activator of the 19.5S SEC8/SEC15 particle. SEC4 probably interacts directly with SEC8; it could serve as the attachment site for the SEC8/SEC15 particle.<ref>PMID:16390997</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/eq/2eqb_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2eqb ConSurf].
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<div style="clear:both"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
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[[Category: Fukai, S.]]
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[[Category: Fukai S]]
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[[Category: Ishitani, R.]]
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[[Category: Ishitani R]]
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[[Category: Nureki, O.]]
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[[Category: Nureki O]]
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[[Category: Sato, Y.]]
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[[Category: Sato Y]]
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[[Category: PO4]]
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[[Category: coiled coil]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 14:57:33 2008''
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Current revision

Crystal structure of the Rab GTPase Sec4p, the Sec2p GEF domain, and phosphate complex

PDB ID 2eqb

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