6qxa: Difference between revisions

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~~'''Unreleased structure'''~~

~~The entry~~ 6qxa is ~~ON HOLD~~ ~~until Paper~~ Publication

==Structure of membrane bound pyrophosphatase from Thermotoga maritima in complex with imidodiphosphate and N-[(2-amino-6-benzothiazolyl)methyl]-1H-indole-2-carboxamide (ATC)==

== Structural highlights ==

<table><tr><td colspan='2'>[[6qxa]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QXA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QXA FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2PN:IMIDODIPHOSPHORIC+ACID'>2PN</scene>, <scene name='pdbligand=D1D:(4S,5S)-1,2-DITHIANE-4,5-DIOL'>D1D</scene>, <scene name='pdbligand=GQB:~{N}-[(2-azanyl-3~{H}-1,3-benzothiazol-6-yl)methyl]-1~{H}-indole-2-carboxamide'>GQB</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>

<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6ht3|6ht3]]</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=6qxa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qxa OCA], [http://pdbe.org/6qxa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qxa RCSB], [http://www.ebi.ac.uk/pdbsum/6qxa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qxa ProSAT]</span></td></tr>

</table>

== Function ==

[[http://www.uniprot.org/uniprot/HPPA_THEMA HPPA_THEMA]] Sodium pump that utilizes the energy of pyrophosphate hydrolysis as the driving force for Na(+) movement across the membrane.[HAMAP-Rule:MF_01129]<ref>PMID:11343697</ref> <ref>PMID:17605473</ref> <ref>PMID:22837527</ref>

== Publication Abstract from PubMed ==

Membrane-bound pyrophosphatases (M-PPases), which couple proton/sodium ion transport to pyrophosphate synthesis/hydrolysis, are important in abiotic stress resistance and in the infectivity of protozoan parasites. Here, three M-PPase structures in different catalytic states show that closure of the substrate-binding pocket by helices 5-6 affects helix 13 in the dimer interface and causes helix 12 to move down. This springs a 'molecular mousetrap', repositioning a conserved aspartate and activating the nucleophilic water. Corkscrew motion at helices 6 and 16 rearranges the key ionic gate residues and leads to ion pumping. The pumped ion is above the ion gate in one of the ion-bound structures, but below it in the other. Electrometric measurements show a single-turnover event with a non-hydrolysable inhibitor, supporting our model that ion pumping precedes hydrolysis. We propose a complete catalytic cycle for both proton and sodium-pumping M-PPases, and one that also explains the basis for ion specificity.

~~Authors: Vidilaseris~~, K., Goldman, A.

Membrane pyrophosphatases from Thermotoga maritima and Vigna radiata suggest a conserved coupling mechanism.,Li KM, Wilkinson C, Kellosalo J, Tsai JY, Kajander T, Jeuken LJ, Sun YJ, Goldman A Nat Commun. 2016 Dec 6;7:13596. doi: 10.1038/ncomms13596. PMID:27922000<ref>PMID:27922000</ref>

~~Description: Structure~~ of ~~membrane bound pyrophosphatase from Thermotoga maritima in complex with imidodiphosphate and N~~-[~~(2-amino-6-benzothiazolyl)methyl~~]~~-1H-indole-2-carboxamide (ATC)~~

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: ~~Unreleased Structures~~]]

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Large Structures]]

[[Category: Goldman, A]]

[[Category: Vidilaseris, K]]

[[Category: ~~Goldman, A~~]]

[[Category: Inhibitor]]

[[Category: Membrane protein]]

[[Category: Membrane-bound pyrophosphatase]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 6qxa is ON HOLD  until Paper Publication
+==Structure of membrane bound pyrophosphatase from Thermotoga maritima in complex with imidodiphosphate and N-[(2-amino-6-benzothiazolyl)methyl]-1H-indole-2-carboxamide (ATC)==
+<StructureSection load='6qxa' size='340' side='right'caption='[[6qxa]], [[Resolution|resolution]] 3.41&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6qxa]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QXA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QXA FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2PN:IMIDODIPHOSPHORIC+ACID'>2PN</scene>, <scene name='pdbligand=D1D:(4S,5S)-1,2-DITHIANE-4,5-DIOL'>D1D</scene>, <scene name='pdbligand=GQB:~{N}-[(2-azanyl-3~{H}-1,3-benzothiazol-6-yl)methyl]-1~{H}-indole-2-carboxamide'>GQB</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6ht3|6ht3]]</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=6qxa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qxa OCA], [http://pdbe.org/6qxa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qxa RCSB], [http://www.ebi.ac.uk/pdbsum/6qxa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qxa ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/HPPA_THEMA HPPA_THEMA]] Sodium pump that utilizes the energy of pyrophosphate hydrolysis as the driving force for Na(+) movement across the membrane.[HAMAP-Rule:MF_01129]<ref>PMID:11343697</ref> <ref>PMID:17605473</ref> <ref>PMID:22837527</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Membrane-bound pyrophosphatases (M-PPases), which couple proton/sodium ion transport to pyrophosphate synthesis/hydrolysis, are important in abiotic stress resistance and in the infectivity of protozoan parasites. Here, three M-PPase structures in different catalytic states show that closure of the substrate-binding pocket by helices 5-6 affects helix 13 in the dimer interface and causes helix 12 to move down. This springs a 'molecular mousetrap', repositioning a conserved aspartate and activating the nucleophilic water. Corkscrew motion at helices 6 and 16 rearranges the key ionic gate residues and leads to ion pumping. The pumped ion is above the ion gate in one of the ion-bound structures, but below it in the other. Electrometric measurements show a single-turnover event with a non-hydrolysable inhibitor, supporting our model that ion pumping precedes hydrolysis. We propose a complete catalytic cycle for both proton and sodium-pumping M-PPases, and one that also explains the basis for ion specificity.
-Authors: Vidilaseris, K., Goldman, A.
+Membrane pyrophosphatases from Thermotoga maritima and Vigna radiata suggest a conserved coupling mechanism.,Li KM, Wilkinson C, Kellosalo J, Tsai JY, Kajander T, Jeuken LJ, Sun YJ, Goldman A Nat Commun. 2016 Dec 6;7:13596. doi: 10.1038/ncomms13596. PMID:27922000<ref>PMID:27922000</ref>
-Description: Structure of membrane bound pyrophosphatase from Thermotoga maritima in complex with imidodiphosphate and N-[(2-amino-6-benzothiazolyl)methyl]-1H-indole-2-carboxamide (ATC)
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 6qxa" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Goldman, A]]
 [[Category: Vidilaseris, K]]
-[[Category: Goldman, A]]
+[[Category: Inhibitor]]
+[[Category: Membrane protein]]
+[[Category: Membrane-bound pyrophosphatase]]