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| | <StructureSection load='5knb' size='340' side='right'caption='[[5knb]], [[Resolution|resolution]] 3.25Å' scene=''> | | <StructureSection load='5knb' size='340' side='right'caption='[[5knb]], [[Resolution|resolution]] 3.25Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5knb]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Entha Entha]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KNB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KNB FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5knb]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterococcus_hirae_ATCC_9790 Enterococcus hirae ATCC 9790]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KNB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KNB FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 3.251Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5knc|5knc]], [[5knd|5knd]]</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ntpA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=768486 ENTHA]), ntpB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=768486 ENTHA]), ntpD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=768486 ENTHA]), ntpG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=768486 ENTHA])</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=5knb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5knb OCA], [https://pdbe.org/5knb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5knb RCSB], [https://www.ebi.ac.uk/pdbsum/5knb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5knb ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sodium-transporting_two-sector_ATPase Sodium-transporting two-sector ATPase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5knb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5knb OCA], [http://pdbe.org/5knb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5knb RCSB], [http://www.ebi.ac.uk/pdbsum/5knb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5knb ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/NTPG_ENTHA NTPG_ENTHA]] Involved in ATP-driven sodium extrusion. [[http://www.uniprot.org/uniprot/NTPA_ENTHA NTPA_ENTHA]] Involved in ATP-driven sodium extrusion. [[http://www.uniprot.org/uniprot/NTPD_ENTHA NTPD_ENTHA]] Involved in ATP-driven sodium extrusion.<ref>PMID:8157629</ref> [[http://www.uniprot.org/uniprot/NTPB_ENTHA NTPB_ENTHA]] Involved in ATP-driven sodium extrusion. | + | [https://www.uniprot.org/uniprot/NTPA_ENTHA NTPA_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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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Entha]] | + | [[Category: Enterococcus hirae ATCC 9790]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Sodium-transporting two-sector ATPase]]
| + | [[Category: Imai FL]] |
| - | [[Category: Imai, F L]] | + | [[Category: Ishizuka-Katsura Y]] |
| - | [[Category: Ishizuka-Katsura, Y]] | + | [[Category: Kakinuma Y]] |
| - | [[Category: Kakinuma, Y]] | + | [[Category: Maruyama S]] |
| - | [[Category: Maruyama, S]] | + | [[Category: Mizutani K]] |
| - | [[Category: Mizutani, K]] | + | [[Category: Muneyuki E]] |
| - | [[Category: Muneyuki, E]] | + | [[Category: Murata T]] |
| - | [[Category: Murata, T]] | + | [[Category: Shimono K]] |
| - | [[Category: Shimono, K]] | + | [[Category: Shirouzu M]] |
| - | [[Category: Shirouzu, M]] | + | [[Category: Suzuki K]] |
| - | [[Category: Suzuki, K]] | + | [[Category: Yamato I]] |
| - | [[Category: Yamato, I]] | + | [[Category: Yokoyama S]] |
| - | [[Category: Yokoyama, S]] | + | |
| - | [[Category: Atp binding]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: P-loop]]
| + | |
| Structural highlights
Function
NTPA_ENTHA Involved in ATP-driven sodium extrusion.
Publication Abstract from PubMed
V1-ATPases are highly conserved ATP-driven rotary molecular motors found in various membrane systems. We recently reported the crystal structures for the Enterococcus hirae A3B3DF (V1) complex, corresponding to the catalytic dwell state waiting for ATP hydrolysis. Here we present the crystal structures for two other dwell states obtained by soaking nucleotide-free V1 crystals in ADP. In the presence of 20 muM ADP, two ADP molecules bind to two of three binding sites and cooperatively induce conformational changes of the third site to an ATP-binding mode, corresponding to the ATP-binding dwell. In the presence of 2 mM ADP, all nucleotide-binding sites are occupied by ADP to induce conformational changes corresponding to the ADP-release dwell. Based on these and previous findings, we propose a V1-ATPase rotational mechanism model.
Crystal structures of the ATP-binding and ADP-release dwells of the V1 rotary motor.,Suzuki K, Mizutani K, Maruyama S, Shimono K, Imai FL, Muneyuki E, Kakinuma Y, Ishizuka-Katsura Y, Shirouzu M, Yokoyama S, Yamato I, Murata T Nat Commun. 2016 Oct 27;7:13235. doi: 10.1038/ncomms13235. PMID:27807367[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Suzuki K, Mizutani K, Maruyama S, Shimono K, Imai FL, Muneyuki E, Kakinuma Y, Ishizuka-Katsura Y, Shirouzu M, Yokoyama S, Yamato I, Murata T. Crystal structures of the ATP-binding and ADP-release dwells of the V1 rotary motor. Nat Commun. 2016 Oct 27;7:13235. doi: 10.1038/ncomms13235. PMID:27807367 doi:http://dx.doi.org/10.1038/ncomms13235
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