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| | ==Complete ion-coordination structure in the rotor ring of Na-dependent F-ATP synthase== | | ==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]] 2.35Å' scene=''> | + | <StructureSection load='2wgm' size='340' side='right'caption='[[2wgm]], [[Resolution|resolution]] 2.35Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2wgm]] is a 44 chain structure with sequence from [http://en.wikipedia.org/wiki/Ilyobacter_tartaricus Ilyobacter tartaricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WGM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2WGM FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2wgm]] is a 44 chain structure with sequence from [https://en.wikipedia.org/wiki/Ilyobacter_tartaricus Ilyobacter tartaricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WGM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WGM FirstGlance]. <br> |
| - | </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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.35Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1yce|1yce]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=F09:NONAN-1-OL'>F09</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2wgm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wgm OCA], [https://pdbe.org/2wgm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wgm RCSB], [https://www.ebi.ac.uk/pdbsum/2wgm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wgm ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/ATPL_ILYTA 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] | + | [https://www.uniprot.org/uniprot/ATPL_ILYTA 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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | ==See Also== | | ==See Also== |
| - | *[[ATPase|ATPase]] | + | *[[ATPase 3D structures|ATPase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Ilyobacter tartaricus]] | | [[Category: Ilyobacter tartaricus]] |
| - | [[Category: Diederichs, K]] | + | [[Category: Large Structures]] |
| - | [[Category: Meier, T]] | + | [[Category: Diederichs K]] |
| - | [[Category: Pogoryelov, D]] | + | [[Category: Meier T]] |
| - | [[Category: Atp synthesis]] | + | [[Category: Pogoryelov D]] |
| - | [[Category: C-ring structure]]
| + | |
| - | [[Category: Cell membrane]]
| + | |
| - | [[Category: F1fo-atp synthase rotor]]
| + | |
| - | [[Category: Hydrogen ion transport]]
| + | |
| - | [[Category: Ion coordination and selectivity]]
| + | |
| - | [[Category: Lipid-binding]]
| + | |
| - | [[Category: Membrane protein]]
| + | |
| - | [[Category: Sodium transport]]
| + | |
| - | [[Category: Sodium-motive force]]
| + | |
| - | [[Category: Transmembrane]]
| + | |
| - | [[Category: Transport]]
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| Structural highlights
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.
See Also
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
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