6afs: Difference between revisions
No edit summary |
No edit summary |
||
| (2 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
==Proton pyrophosphatase - two phosphates-bound== | |||
<StructureSection load='6afs' size='340' side='right'caption='[[6afs]], [[Resolution|resolution]] 2.30Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6afs]] 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=6AFS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6AFS 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]] 2.299Å</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=6afs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6afs OCA], [https://pdbe.org/6afs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6afs RCSB], [https://www.ebi.ac.uk/pdbsum/6afs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6afs 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 6afs" 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]] | |||
Latest revision as of 12:29, 22 November 2023
Proton pyrophosphatase - two phosphates-boundProton pyrophosphatase - two phosphates-bound
Structural highlights
FunctionAVP_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.[1] [2] [3] [4] Publication Abstract from PubMedMembrane-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[5] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||