2efe: Difference between revisions

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 <StructureSection load='2efe' size='340' side='right'caption='[[2efe]], [[Resolution|resolution]] 2.08&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2efe]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EFE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EFE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2efe]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EFE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EFE FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GNH:AMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNH</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.08&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2fec|2fec]], [[2efd|2efd]], [[2efh|2efh]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GNH:AMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNH</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=2efe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2efe OCA], [https://pdbe.org/2efe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2efe RCSB], [https://www.ebi.ac.uk/pdbsum/2efe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2efe ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/VPS9A_ARATH VPS9A_ARATH]] Functions as guanine nucleotide exchange factor (GEF) for Rab small GTPases. Activates specifically RABF1, RABF2A and RABF2B proteins. Required for early stages of embryogenesis, cytokinesis, embryogenesis, and organ development. Is essential for the establishment or maintenance of the polar localization of the auxin efflux carrier PIN1.<ref>PMID:18055610</ref> <ref>PMID:20833725</ref>  [[https://www.uniprot.org/uniprot/RAF2B_ARATH RAF2B_ARATH]] Endosomal protein that may be involved in endocytosis.<ref>PMID:20833725</ref>
+[https://www.uniprot.org/uniprot/VPS9A_ARATH VPS9A_ARATH] Functions as guanine nucleotide exchange factor (GEF) for Rab small GTPases. Activates specifically RABF1, RABF2A and RABF2B proteins. Required for early stages of embryogenesis, cytokinesis, embryogenesis, and organ development. Is essential for the establishment or maintenance of the polar localization of the auxin efflux carrier PIN1.<ref>PMID:18055610</ref> <ref>PMID:20833725</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
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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=2efe ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Many GTPases regulate intracellular transport and signaling in eukaryotes. Guanine nucleotide exchange factors (GEFs) activate GTPases by catalyzing the exchange of their GDP for GTP. Here we present crystallographic and biochemical studies of a GEF reaction with four crystal structures of Arabidopsis thaliana ARA7, a plant homolog of Rab5 GTPase, in complex with its GEF, VPS9a, in the nucleotide-free and GDP-bound forms, as well as a complex with aminophosphonic acid-guanylate ester and ARA7.VPS9a(D185N) with GDP. Upon complex formation with ARA7, VPS9 wedges into the interswitch region of ARA7, inhibiting the coordination of Mg(2+) and decreasing the stability of GDP binding. The aspartate finger of VPS9a recognizes GDP beta-phosphate directly and pulls the P-loop lysine of ARA7 away from GDP beta-phosphate toward switch II to further destabilize GDP for its release during the transition from the GDP-bound to nucleotide-free intermediates in the nucleotide exchange reaction.
-GDP-bound and nucleotide-free intermediates of the guanine nucleotide exchange in the Rab5.Vps9 system.,Uejima T, Ihara K, Goh T, Ito E, Sunada M, Ueda T, Nakano A, Wakatsuki S J Biol Chem. 2010 Nov 19;285(47):36689-97. Epub 2010 Sep 10. PMID:20833725<ref>PMID:20833725</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2efe" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
 [[Category: Large Structures]]
-[[Category: Ihara, K]]
+[[Category: Ihara K]]
-[[Category: Uejima, T]]
+[[Category: Uejima T]]
-[[Category: Wakatsuki, S]]
+[[Category: Wakatsuki S]]
-[[Category: Gef]]
-[[Category: Gtpase]]
-[[Category: Nucleotide]]
-[[Category: Rab5]]
-[[Category: Transport protein]]
-[[Category: Vps9]]