6afw: Difference between revisions
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New page: '''Unreleased structure''' The entry 6afw is ON HOLD Authors: Tsai, J.-Y., Li, K.-M., Sun, Y.-J. Description: Proton pyrophosphatase-T228D mutant Category: Unreleased Structures [[... |
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The | ==Proton pyrophosphatase-T228D mutant== | ||
<StructureSection load='6afw' size='340' side='right'caption='[[6afw]], [[Resolution|resolution]] 2.19Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6afw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vigna_radiata_var._radiata Vigna radiata var. radiata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AFW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6AFW 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]] 2.185Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PG:2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL'>1PG</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=6afw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6afw OCA], [https://pdbe.org/6afw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6afw RCSB], [https://www.ebi.ac.uk/pdbsum/6afw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6afw ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/AVP_VIGRR AVP_VIGRR] Proton-translocating inorganic pyrophosphatase that contributes to the transtonoplast (from cytosol to vacuole lumen) H(+)-electrochemical potential difference. It establishes a proton gradient of similar and often greater magnitude than the H(+)-ATPase on the same membrane.<ref>PMID:10477275</ref> <ref>PMID:22456709</ref> <ref>PMID:2555340</ref> <ref>PMID:9489011</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Membrane-embedded pyrophosphatase (M-PPase) hydrolyzes pyrophosphate to drive ion (H(+) and/or Na(+)) translocation. We determined crystal structures and functions of Vigna radiata M-PPase (VrH(+)-PPase), the VrH(+)-PPase-2Pi complex and mutants at hydrophobic gate (residue L555) and exit channel (residues T228 and E225). Ion pore diameters along the translocation pathway of three VrH(+)-PPases complexes (Pi-, 2Pi- and imidodiphosphate-bound states) present a unique wave-like profile, with different pore diameters at the hydrophobic gate and exit channel, indicating that the ligands induced pore size alterations. The 2Pi-bound state with the largest pore diameter might mimic the hydrophobic gate open. In mutant structures, ordered waters detected at the hydrophobic gate among VrH(+)-PPase imply the possibility of solvation, and numerous waters at the exit channel might signify an open channel. A salt-bridge, E225-R562 is at the way out of the exit channel of VrH(+)-PPase; E225A mutant makes the interaction eliminated and reveals a decreased pumping ability. E225-R562 might act as a latch to regulate proton release. A water wire from the ion gate (R-D-K-E) through the hydrophobic gate and into the exit channel may reflect the path of proton transfer. | |||
Roles of the Hydrophobic Gate and Exit Channel in Vigna radiata Pyrophosphatase Ion Translocation.,Tsai JY, Tang KZ, Li KM, Hsu BL, Chiang YW, Goldman A, Sun YJ J Mol Biol. 2019 Apr 5;431(8):1619-1632. doi: 10.1016/j.jmb.2019.03.009. Epub, 2019 Mar 13. PMID:30878480<ref>PMID:30878480</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 6afw" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
[[Category: | ==See Also== | ||
*[[Inorganic pyrophosphatase 3D structures|Inorganic pyrophosphatase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Vigna radiata var. radiata]] | |||
[[Category: Li K-M]] | |||
[[Category: Sun Y-J]] | |||
[[Category: Tsai J-Y]] | |||