6afv - Revision history

OCA at 09:29, 22 November 2023

2023-11-22T09:29:54Z

←Older revision		Revision as of 09:29, 22 November 2023
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	<StructureSection load='6afv' size='340' side='right'caption='[[6afv]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='6afv' size='340' side='right'caption='[[6afv]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6afv]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Mung_bean Mung bean~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AFV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6AFV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6afv]] 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=6AFV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6AFV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.701Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1] </span></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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6afv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6afv OCA], [~~http~~://pdbe.org/6afv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6afv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6afv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6afv ProSAT]</span></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=6afv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6afv OCA], [https://pdbe.org/6afv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6afv RCSB], [https://www.ebi.ac.uk/pdbsum/6afv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6afv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://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>	+	[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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6afv" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6afv" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Inorganic pyrophosphatase 3D structures\|Inorganic pyrophosphatase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Inorganic diphosphatase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Mung bean~~]]	+	[[Category: Vigna radiata var. radiata]]
-	[[Category: Li, K M]]	+	[[Category: Li K-M]]
-	[[Category: Sun, Y J]]	+	[[Category: Sun Y-J]]
-	[[Category: Tsai, J Y]]	+	[[Category: Tsai J-Y]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Proton pumping]]~~	+
-	~~[[Category: Vigna radiata~~]]	+

OCA at 07:45, 24 April 2019

2019-04-24T07:45:35Z

←Older revision		Revision as of 07:45, 24 April 2019
Line 3:		Line 3:
	<StructureSection load='6afv' size='340' side='right'caption='[[6afv]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='6afv' size='340' side='right'caption='[[6afv]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6afv]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AFV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AFV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6afv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mung_bean Mung bean]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AFV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AFV FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1] </span></td></tr>
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	[[Category: Inorganic diphosphatase]]		[[Category: Inorganic diphosphatase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Mung bean]]
	[[Category: Li, K M]]		[[Category: Li, K M]]
	[[Category: Sun, Y J]]		[[Category: Sun, Y J]]

OCA at 07:07, 10 April 2019

2019-04-10T07:07:18Z

←Older revision		Revision as of 07:07, 10 April 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6afv is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Proton pyrophosphatase-L555K mutant==
		+	<StructureSection load='6afv' size='340' side='right'caption='[[6afv]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6afv]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AFV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AFV FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1] </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=6afv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6afv OCA], [http://pdbe.org/6afv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6afv RCSB], [http://www.ebi.ac.uk/pdbsum/6afv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6afv ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://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.

-	~~Authors:~~ Tsai, ~~J.-Y.~~, Li, ~~K.-M.~~, ~~Sun~~, Y.-J.	+	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>

-	~~Description: Proton pyrophosphatase~~-~~L555K mutant~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Sun, Y.-J]]	+	<div class="pdbe-citations 6afv" style="background-color:#fffaf0;"></div>
-	[[Category: Tsai, J.-Y]]	+	== References ==
-	[[Category: ~~Li, K.-M~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Inorganic diphosphatase]]
		+	[[Category: Large Structures]]
		+	[[Category: Li, K M]]
		+	[[Category: Sun, Y J]]
		+	[[Category: Tsai, J Y]]
		+	[[Category: Hydrolase]]
		+	[[Category: Membrane protein]]
		+	[[Category: Proton pumping]]
		+	[[Category: Vigna radiata]]

OCA at 04:52, 21 February 2019

2019-02-21T04:52:54Z

←Older revision		Revision as of 04:52, 21 February 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6afv is ON HOLD	+	The entry 6afv is ON HOLD until Paper Publication

	Authors: Tsai, J.-Y., Li, K.-M., Sun, Y.-J.		Authors: Tsai, J.-Y., Li, K.-M., Sun, Y.-J.

OCA: Protected "6afv" [edit=sysop:move=sysop]

2018-08-15T14:41:55Z

Protected "6afv" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:41, 15 August 2018

OCA: New page: '''Unreleased structure''' The entry 6afv is ON HOLD Authors: Tsai, J.-Y., Li, K.-M., Sun, Y.-J. Description: Proton pyrophosphatase-L555K mutant Category: Unreleased Structures [[...

2018-08-15T14:41:53Z

New page: '''Unreleased structure''' The entry 6afv is ON HOLD Authors: Tsai, J.-Y., Li, K.-M., Sun, Y.-J. Description: Proton pyrophosphatase-L555K mutant Category: Unreleased Structures [[...

New page

'''Unreleased structure'''

The entry 6afv is ON HOLD

Authors: Tsai, J.-Y., Li, K.-M., Sun, Y.-J.

Description: Proton pyrophosphatase-L555K mutant
[[Category: Unreleased Structures]]
[[Category: Sun, Y.-J]]
[[Category: Tsai, J.-Y]]
[[Category: Li, K.-M]]