2db4: Difference between revisions
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==Crystal structure of rotor ring with DCCD of the V- ATPase from Enterococcus hirae== | ==Crystal structure of rotor ring with DCCD of the V- ATPase from Enterococcus hirae== | ||
<StructureSection load='2db4' size='340' side='right' caption='[[2db4]], [[Resolution|resolution]] 2.40Å' scene=''> | <StructureSection load='2db4' size='340' side='right'caption='[[2db4]], [[Resolution|resolution]] 2.40Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2db4]] is a 10 chain structure with sequence from [ | <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> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4Å</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> | |||
<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> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/NTPK_ENTHA NTPK_ENTHA] Involved in ATP-driven sodium extrusion. | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/db/2db4_consurf.spt"</scriptWhenChecked> | <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/ | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </jmolCheckbox> | ||
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==See Also== | ==See Also== | ||
*[[ATPase|ATPase | *[[ATPase 3D structures|ATPase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Enterococcus hirae]] | [[Category: Enterococcus hirae]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Kakinuma Y]] | ||
[[Category: | [[Category: Murata T]] | ||
[[Category: | [[Category: Shirouzu M]] | ||
[[Category: | [[Category: Walker JE]] | ||
[[Category: | [[Category: Yamato I]] | ||
[[Category: | [[Category: Yokoyama S]] | ||
Latest revision as of 08:09, 17 October 2024
Crystal structure of rotor ring with DCCD of the V- ATPase from Enterococcus hiraeCrystal structure of rotor ring with DCCD of the V- ATPase from Enterococcus hirae
Structural highlights
FunctionNTPK_ENTHA Involved in ATP-driven sodium extrusion. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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