5dn6: Difference between revisions
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The | ==ATP synthase from Paracoccus denitrificans== | ||
<StructureSection load='5dn6' size='340' side='right'caption='[[5dn6]], [[Resolution|resolution]] 3.98Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5dn6]] is a 25 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DN6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DN6 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]] 3.98Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=5dn6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dn6 OCA], [https://pdbe.org/5dn6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dn6 RCSB], [https://www.ebi.ac.uk/pdbsum/5dn6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dn6 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/ATPA_PARDP ATPA_PARDP] Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit. | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The structure of the intact ATP synthase from the alpha-proteobacterium Paracoccus denitrificans, inhibited by its natural regulatory zeta-protein, has been solved by X-ray crystallography at 4.0 A resolution. The zeta-protein is bound via its N-terminal alpha-helix in a catalytic interface in the F1 domain. The bacterial F1 domain is attached to the membrane domain by peripheral and central stalks. The delta-subunit component of the peripheral stalk binds to the N-terminal regions of two alpha-subunits. The stalk extends via two parallel long alpha-helices, one in each of the related b and b' subunits, down a noncatalytic interface of the F1 domain and interacts in an unspecified way with the a-subunit in the membrane domain. The a-subunit lies close to a ring of 12 c-subunits attached to the central stalk in the F1 domain, and, together, the central stalk and c-ring form the enzyme's rotor. Rotation is driven by the transmembrane proton-motive force, by a mechanism where protons pass through the interface between the a-subunit and c-ring via two half-channels in the a-subunit. These half-channels are probably located in a bundle of four alpha-helices in the a-subunit that are tilted at approximately 30 degrees to the plane of the membrane. Conserved polar residues in the two alpha-helices closest to the c-ring probably line the proton inlet path to an essential carboxyl group in the c-subunit in the proton uptake site and a proton exit path from the proton release site. The structure has provided deep insights into the workings of this extraordinary molecular machine. | |||
Structure of ATP synthase from Paracoccus denitrificans determined by X-ray crystallography at 4.0 A resolution.,Morales-Rios E, Montgomery MG, Leslie AG, Walker JE Proc Natl Acad Sci U S A. 2015 Oct 27;112(43):13231-6. doi:, 10.1073/pnas.1517542112. Epub 2015 Oct 12. PMID:26460036<ref>PMID:26460036</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: Leslie | <div class="pdbe-citations 5dn6" style="background-color:#fffaf0;"></div> | ||
[[Category: Montgomery | |||
[[Category: Morales-Rios | ==See Also== | ||
[[Category: Walker | *[[ATPase 3D structures|ATPase 3D structures]] | ||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Paracoccus denitrificans]] | |||
[[Category: Leslie AGW]] | |||
[[Category: Montgomery MG]] | |||
[[Category: Morales-Rios E]] | |||
[[Category: Walker JE]] | |||
Latest revision as of 00:50, 29 June 2023
ATP synthase from Paracoccus denitrificansATP synthase from Paracoccus denitrificans
Structural highlights
FunctionATPA_PARDP Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit. Publication Abstract from PubMedThe structure of the intact ATP synthase from the alpha-proteobacterium Paracoccus denitrificans, inhibited by its natural regulatory zeta-protein, has been solved by X-ray crystallography at 4.0 A resolution. The zeta-protein is bound via its N-terminal alpha-helix in a catalytic interface in the F1 domain. The bacterial F1 domain is attached to the membrane domain by peripheral and central stalks. The delta-subunit component of the peripheral stalk binds to the N-terminal regions of two alpha-subunits. The stalk extends via two parallel long alpha-helices, one in each of the related b and b' subunits, down a noncatalytic interface of the F1 domain and interacts in an unspecified way with the a-subunit in the membrane domain. The a-subunit lies close to a ring of 12 c-subunits attached to the central stalk in the F1 domain, and, together, the central stalk and c-ring form the enzyme's rotor. Rotation is driven by the transmembrane proton-motive force, by a mechanism where protons pass through the interface between the a-subunit and c-ring via two half-channels in the a-subunit. These half-channels are probably located in a bundle of four alpha-helices in the a-subunit that are tilted at approximately 30 degrees to the plane of the membrane. Conserved polar residues in the two alpha-helices closest to the c-ring probably line the proton inlet path to an essential carboxyl group in the c-subunit in the proton uptake site and a proton exit path from the proton release site. The structure has provided deep insights into the workings of this extraordinary molecular machine. Structure of ATP synthase from Paracoccus denitrificans determined by X-ray crystallography at 4.0 A resolution.,Morales-Rios E, Montgomery MG, Leslie AG, Walker JE Proc Natl Acad Sci U S A. 2015 Oct 27;112(43):13231-6. doi:, 10.1073/pnas.1517542112. Epub 2015 Oct 12. PMID:26460036[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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