2db4: Difference between revisions

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-[[Image:2db4.png|left|200px]]
-<!--
+==Crystal structure of rotor ring with DCCD of the V- ATPase from Enterococcus hirae==
-The line below this paragraph, containing "STRUCTURE_2db4", creates the "Structure Box" on the page.
+<StructureSection load='2db4' size='340' side='right'caption='[[2db4]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2db4]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterococcus_hirae Enterococcus hirae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DB4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DB4 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DCW:DICYCLOHEXYLUREA'>DCW</scene>, <scene name='pdbligand=LHG:1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE'>LHG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=UMQ:UNDECYL-MALTOSIDE'>UMQ</scene></td></tr>
-{{STRUCTURE_2db4|  PDB=2db4  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2db4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2db4 OCA], [https://pdbe.org/2db4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2db4 RCSB], [https://www.ebi.ac.uk/pdbsum/2db4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2db4 ProSAT], [https://www.topsan.org/Proteins/RSGI/2db4 TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NTPK_ENTHA NTPK_ENTHA] Involved in ATP-driven sodium extrusion.
+== 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/db/2db4_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=2db4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The prokaryotic V-ATPase of Enterococcus hirae, closely related to the eukaryotic enzymes, provides a unique opportunity to study the ion-translocation mechanism because it transports Na(+), which can be detected by radioisotope ( ) experiments and X-ray crystallography. In this study, we demonstrated that the binding affinity of the rotor ring (K ring) for decreased approximately 30-fold by reaction with N,N(')-dicyclohexylcarbodiimide (DCCD), and determined the crystal structures of Na(+)-bound and Na(+)-unbound K rings modified with DCCD at 2.4- and 3.1-A resolutions, respectively. Overall these structures were similar, indicating that there is no global conformational change associated with release of Na(+) from the DCCD-K ring. A conserved glutamate residue (E139) within all 10 ion-binding pockets of the K ring was neutralized by modification with DCCD, and formed an "open" conformation by losing hydrogen bonds with the Y68 and T64 side chains, resulting in low affinity for Na(+). This open conformation is likely to be comparable to that of neutralized E139 forming a salt bridge with the conserved arginine of the stator during the ion-translocation process. Based on these findings, we proposed the ion-translocation model that the binding affinity for Na(+) decreases due to the neutralization of E139, thus releasing bound Na(+), and that the structures of Na(+)-bound and Na(+)-unbound DCCD-K rings are corresponding to intermediate states before and after release of Na(+) during rotational catalysis of V-ATPase, respectively.
-===Crystal structure of rotor ring with DCCD of the V- ATPase from Enterococcus hirae===
+Structure of the rotor ring modified with N,N'-dicyclohexylcarbodiimide of the Na+-transporting vacuolar ATPase.,Mizutani K, Yamamoto M, Suzuki K, Yamato I, Kakinuma Y, Shirouzu M, Walker JE, Yokoyama S, Iwata S, Murata T Proc Natl Acad Sci U S A. 2011 Aug 3. PMID:21813759<ref>PMID:21813759</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-==About this Structure==
+</div>
-[[2db4]] is a 10 chain structure of [[ATPase]] with sequence from [http://en.wikipedia.org/wiki/Enterococcus_hirae Enterococcus hirae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DB4 OCA].
+<div class="pdbe-citations 2db4" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[ATPase]]
+*[[ATPase 3D structures|ATPase 3D structures]]
-[[Category: Enterococcus hirae]]
+== References ==
-[[Category: Kakinuma, Y.]]
+<references/>
-[[Category: Murata, T.]]
+__TOC__
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+</StructureSection>
-[[Category: Shirouzu, M.]]
-[[Category: Walker, J E.]]
-[[Category: Yamato, I.]]
-[[Category: Yokoyama, S.]]
-[[Category: Dccd]]
 [[Category: Enterococcus hirae]]
-[[Category: Hydrolase]]
+[[Category: Large Structures]]
-[[Category: National project on protein structural and functional analyse]]
+[[Category: Kakinuma Y]]
-[[Category: Nppsfa]]
+[[Category: Murata T]]
-[[Category: Ntpk]]
+[[Category: Shirouzu M]]
-[[Category: Proteolipid]]
+[[Category: Walker JE]]
-[[Category: Riken structural genomics/proteomics initiative]]
+[[Category: Yamato I]]
-[[Category: Rsgi]]
+[[Category: Yokoyama S]]
-[[Category: Structural genomic]]
-[[Category: V-atpase]]