2v6v: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:2v6v.jpg|left|200px]]<br /><applet load="2v6v" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="2v6v, resolution 1.50&Aring;" />
-'''THE STRUCTURE OF THE BEM1P PX DOMAIN'''<br />
-==Overview==
+==The structure of the Bem1p PX domain==
-Phox homology (PX) domains, which have been identified in a variety of, proteins involved in cell signaling and membrane trafficking, have been, shown to interact with phosphoinositides (PIs) with different affinities, and specificities. To elucidate the structural origin of diverse PI, specificity of PX domains, we determined the crystal structure of the PX, domain from Bem1p, which has been reported to bind, phosphatidylinositol-4-phosphate (PtdIns4P). We also measured the membrane, binding properties of the PX domain and its mutants by surface plasmon, resonance and monolayer techniques and calculated the electrostatic, potentials for the PX domain in the absence and presence of bound, PtdIns4P. The Bem1p PX domain contains a signature PI-binding site, optimized for PtdIns4P binding and also harbors a cationic membrane, binding surface. The membrane binding of Bem1p PX domain is initiated by, nonspecific electrostatic interactions between the cationic membrane, binding surface of the domain and anionic membrane surfaces, which is, followed by the membrane penetration of hydrophobic residues. Unlike other, PX domains, the Bem1p PX domain has significant intrinsic membrane, penetration activity in the absence of PtdIns4P ligand, suggesting that, the membrane penetration can occur before specific PtdIns4P and last after, the removal of PtdIns4P. Taken together, this structural and functional, study of the PtdIns4P-binding Bem1p PX domain provides new insight into, the diverse PI specificities and membrane binding mechanisms of PX, domains.
+<StructureSection load='2v6v' size='340' side='right'caption='[[2v6v]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2v6v]] 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=2V6V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V6V 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]] 1.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=2v6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v6v OCA], [https://pdbe.org/2v6v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v6v RCSB], [https://www.ebi.ac.uk/pdbsum/2v6v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v6v ProSAT]</span></td></tr>
+</table>
+== 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/v6/2v6v_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2v6v ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Phox homology (PX) domains, which have been identified in a variety of proteins involved in cell signaling and membrane trafficking, have been shown to interact with phosphoinositides (PIs) with different affinities and specificities. To elucidate the structural origin of the diverse PI specificity of PX domains, we determined the crystal structure of the PX domain from Bem1p that has been reported to bind phosphatidylinositol 4-phosphate (PtdIns(4)P). We also measured the membrane binding properties of the PX domain and its mutants by surface plasmon resonance and monolayer techniques and calculated the electrostatic potentials for the PX domain in the absence and presence of bound PtdIns(4)P. The Bem1p PX domain contains a signature PI-binding site optimized for PtdIns(4)P binding and also harbors basic and hydrophobic residues on the membrane-binding surface. The membrane binding of the Bem1p PX domain is initiated by nonspecific electrostatic interactions between the cationic membrane-binding surface of the domain and anionic membrane surfaces, followed by the membrane penetration of hydrophobic residues. Unlike other PX domains, the Bem1p PX domain has high intrinsic membrane penetrating activity in the absence of PtdIns(4)P, suggesting that the partial membrane penetration may occur before specific PtdIns(4)P binding and last after the removal of PtdIns(4)P under certain conditions. This structural and functional study of the PtdIns(4)P-binding Bem1p PX domain provides new insight into the diverse PI specificities and membrane-binding mechanisms of PX domains.
-==About this Structure==
+Structural and membrane binding analysis of the Phox homology domain of Bem1p: basis of phosphatidylinositol 4-phosphate specificity.,Stahelin RV, Karathanassis D, Murray D, Williams RL, Cho W J Biol Chem. 2007 Aug 31;282(35):25737-47. Epub 2007 Jun 20. PMID:17581820<ref>PMID:17581820</ref>
-V6V is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with DTT as [http://en.wikipedia.org/wiki/ligand ligand]. Known structural/functional Site: <scene name='pdbsite=AC1:Dtt Binding Site For Chain A'>AC1</scene>. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2V6V OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Structural and membrane binding analysis of the PX domain of Bem1p: Basis of phosphatidylinositol-4-phosphate specificity., Stahelin RV, Karathanassis D, Murray D, Williams RL, Cho W, J Biol Chem. 2007 Jun 20;. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17581820 17581820]
+</div>
+<div class="pdbe-citations 2v6v" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Single protein]]
+[[Category: Cho W]]
-[[Category: Cho, W.]]
+[[Category: Karathanassis D]]
-[[Category: Karathanassis, D.]]
+[[Category: Murray D]]
-[[Category: Murray, D.]]
+[[Category: Stahelin RV]]
-[[Category: Stahelin, R.V.]]
+[[Category: Williams RL]]
-[[Category: Williams, R.L.]]
-[[Category: DTT]]
-[[Category: 3-kinase]]
-[[Category: cell polarity]]
-[[Category: cytoskeleton]]
-[[Category: homotypic fusion]]
-[[Category: phosphoinositide]]
-[[Category: phosphorylation]]
-[[Category: pi3p]]
-[[Category: px domain]]
-[[Category: regulator]]
-[[Category: sh3 domain]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Dec 18 20:30:02 2007''