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2wgm

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Revision as of 21:38, 5 August 2016

Complete ion-coordination structure in the rotor ring of Na-dependent F-ATP synthase

Structural highlights

2wgm is a 44 chain structure with sequence from Ilyobacter tartaricus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	1yce
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[ATPL_ILYTA] F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane sodium channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to sodium translocation.[HAMAP-Rule:MF_01396] Key component of the F(0) channel; it plays a direct role in translocation across the membrane. A homomeric c-ring of 11 subunits forms the central stalk rotor element with the F(1) delta and epsilon subunits.[HAMAP-Rule:MF_01396]

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 PubMed

The membrane-embedded rotors of Na(+)-dependent F-ATP synthases comprise 11 c-subunits that form a ring, with 11 Na(+) binding sites in between adjacent subunits. Following an updated crystallographic analysis of the c-ring from Ilyobacter tartaricus, we report the complete ion-coordination structure of the Na(+) sites. In addition to the four residues previously identified, there exists a fifth ligand, namely, a buried structural water molecule. This water is itself coordinated by Thr67, which, sequence analysis reveals, is the only residue involved in binding that distinguishes Na(+) synthases from H(+)-ATP synthases known to date. Molecular dynamics simulations and free-energy calculations of the c-ring in a lipid membrane lend clear support to the notion that this fifth ligand is a water molecule, and illustrate its influence on the selectivity of the binding sites. Given the evolutionary ascendancy of sodium over proton bioenergetics, this structure uncovers an ancient strategy for selective ion coupling in ATP synthases.

Complete ion-coordination structure in the rotor ring of Na+-dependent F-ATP synthases.,Meier T, Krah A, Bond PJ, Pogoryelov D, Diederichs K, Faraldo-Gomez JD J Mol Biol. 2009 Aug 14;391(2):498-507. Epub 2009 Jun 3. PMID:19500592^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Meier T, Krah A, Bond PJ, Pogoryelov D, Diederichs K, Faraldo-Gomez JD. Complete ion-coordination structure in the rotor ring of Na+-dependent F-ATP synthases. J Mol Biol. 2009 Aug 14;391(2):498-507. Epub 2009 Jun 3. PMID:19500592 doi:10.1016/j.jmb.2009.05.082

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2wgm"

@@ Line 1: / Line 1: @@
 ==Complete ion-coordination structure in the rotor ring of Na-dependent F-ATP synthase==
 <StructureSection load='2wgm' size='340' side='right' caption='[[2wgm]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
@@ Line 5: / Line 6: @@
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F09:NONAN-1-OL'>F09</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1yce|1yce]]</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2wgm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wgm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2wgm RCSB], [http://www.ebi.ac.uk/pdbsum/2wgm PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2wgm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wgm OCA], [http://pdbe.org/2wgm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2wgm RCSB], [http://www.ebi.ac.uk/pdbsum/2wgm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2wgm ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 17: / Line 18: @@
     <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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2wgm ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2wgm" style="background-color:#fffaf0;"></div>
 ==See Also==

2wgm

From Proteopedia

Revision as of 21:38, 5 August 2016

Complete ion-coordination structure in the rotor ring of Na-dependent F-ATP synthase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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