3vr6: Difference between revisions
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==Crystal structure of AMP-PNP bound Enterococcus hirae V1-ATPase [bV1]== | ==Crystal structure of AMP-PNP bound Enterococcus hirae V1-ATPase [bV1]== | ||
<StructureSection load='3vr6' size='340' side='right' caption='[[3vr6]], [[Resolution|resolution]] 2.68Å' scene=''> | <StructureSection load='3vr6' size='340' side='right'caption='[[3vr6]], [[Resolution|resolution]] 2.68Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3vr6]] is a 8 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3vr6]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_8043 Atcc 8043]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VR6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VR6 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3vr2|3vr2]], [[3vr3|3vr3]], [[3vr4|3vr4]], [[3vr5|3vr5]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3vr2|3vr2]], [[3vr3|3vr3]], [[3vr4|3vr4]], [[3vr5|3vr5]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ntpA ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ntpA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1354 ATCC 8043]), ntpB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1354 ATCC 8043]), ntpD ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1354 ATCC 8043]), ntpG ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1354 ATCC 8043])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Sodium-transporting_two-sector_ATPase Sodium-transporting two-sector ATPase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.3.15 3.6.3.15] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3vr6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vr6 OCA], [https://pdbe.org/3vr6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vr6 RCSB], [https://www.ebi.ac.uk/pdbsum/3vr6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vr6 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[[ | [[https://www.uniprot.org/uniprot/NTPG_ENTHA NTPG_ENTHA]] Involved in ATP-driven sodium extrusion. [[https://www.uniprot.org/uniprot/NTPA_ENTHA NTPA_ENTHA]] Involved in ATP-driven sodium extrusion. [[https://www.uniprot.org/uniprot/NTPB_ENTHA NTPB_ENTHA]] Involved in ATP-driven sodium extrusion. | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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</div> | </div> | ||
<div class="pdbe-citations 3vr6" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 3vr6" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[ATPase 3D structures|ATPase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Atcc 8043]] | [[Category: Atcc 8043]] | ||
[[Category: Large Structures]] | |||
[[Category: Sodium-transporting two-sector ATPase]] | [[Category: Sodium-transporting two-sector ATPase]] | ||
[[Category: Arai, S]] | [[Category: Arai, S]] | ||
Revision as of 21:59, 27 July 2022
Crystal structure of AMP-PNP bound Enterococcus hirae V1-ATPase [bV1]Crystal structure of AMP-PNP bound Enterococcus hirae V1-ATPase [bV1]
Structural highlights
Function[NTPG_ENTHA] Involved in ATP-driven sodium extrusion. [NTPA_ENTHA] Involved in ATP-driven sodium extrusion. [NTPB_ENTHA] Involved in ATP-driven sodium extrusion. Publication Abstract from PubMedIn various cellular membrane systems, vacuolar ATPases (V-ATPases) function as proton pumps, which are involved in many processes such as bone resorption and cancer metastasis, and these membrane proteins represent attractive drug targets for osteoporosis and cancer. The hydrophilic V(1) portion is known as a rotary motor, in which a central axis DF complex rotates inside a hexagonally arranged catalytic A(3)B(3) complex using ATP hydrolysis energy, but the molecular mechanism is not well defined owing to a lack of high-resolution structural information. We previously reported on the in vitro expression, purification and reconstitution of Enterococcus hirae V(1)-ATPase from the A(3)B(3) and DF complexes. Here we report the asymmetric structures of the nucleotide-free (2.8 A) and nucleotide-bound (3.4 A) A(3)B(3) complex that demonstrate conformational changes induced by nucleotide binding, suggesting a binding order in the right-handed rotational orientation in a cooperative manner. The crystal structures of the nucleotide-free (2.2 A) and nucleotide-bound (2.7 A) V(1)-ATPase are also reported. The more tightly packed nucleotide-binding site seems to be induced by DF binding, and ATP hydrolysis seems to be stimulated by the approach of a conserved arginine residue. To our knowledge, these asymmetric structures represent the first high-resolution view of the rotational mechanism of V(1)-ATPase. Rotation mechanism of Enterococcus hirae V1-ATPase based on asymmetric crystal structures.,Arai S, Saijo S, Suzuki K, Mizutani K, Kakinuma Y, Ishizuka-Katsura Y, Ohsawa N, Terada T, Shirouzu M, Yokoyama S, Iwata S, Yamato I, Murata T Nature. 2013 Jan 31;493(7434):703-7. doi: 10.1038/nature11778. Epub 2013 Jan 13. PMID:23334411[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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