6ll7: Difference between revisions

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OCA

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-'''Unreleased structure'''
-The entry 6ll7 is ON HOLD
+==Type II inorganic pyrophosphatase (PPase) from the psychrophilic bacterium Shewanella sp. AS-11, Mn-activated form==
+<StructureSection load='6ll7' size='340' side='right'caption='[[6ll7]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6ll7]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_sp._AS-11 Shewanella sp. AS-11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LL7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LL7 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]] 2.2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=6ll7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ll7 OCA], [https://pdbe.org/6ll7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ll7 RCSB], [https://www.ebi.ac.uk/pdbsum/6ll7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ll7 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/L8AXY8_9GAMM L8AXY8_9GAMM]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Inorganic pyrophosphatase (PPase) catalyses the hydrolysis reaction of inorganic pyrophosphate to phosphates. Our previous studies showed that manganese (Mn) activated PPase from the psychrophilic bacterium Shewanella sp. AS-11 (Mn-Sh-PPase) has a characteristic temperature dependence of the activity with an optimum at 5 degrees C. Here we report the X-ray crystallography and electron paramagnetic resonance (EPR) spectroscopy structural analyses of Sh-PPase in the absence and presence of substrate analogues. We successfully determined the crystal structure of Mn-Sh-PPase without substrate and Mg-activated Sh-PPase (Mg-Sh-PPase) complexed with substrate analogue (imidodiphosphate; PNP). Crystallographic studies revealed a bridged water placed at a distance from the di-Mn centre in Mn-Sh-PPase without substrate. The water came closer to the metal centre when PNP bound. EPR analysis of Mn-Sh-PPase without substrate revealed considerably weak exchange coupling, whose magnitude was increased by binding of substrate analogues. The data indicate that the bridged molecule has weak bonds with the di-Mn centre, which suggests a 'loose' structure, whereas it comes closer to di-Mn centre by substrate binding, which suggests a 'well-tuned' structure for catalysis. Thus, we propose that Sh-PPase can rearrange the active site and that the 'loose' structure plays an important role in the cold adaptation mechanism.
-Authors:
+X-ray Crystallography and Electron Paramagnetic Resonance Spectroscopy Reveal Active Site Rearrangement of Cold-Adapted Inorganic Pyrophosphatase.,Horitani M, Kusubayashi K, Oshima K, Yato A, Sugimoto H, Watanabe K Sci Rep. 2020 Mar 9;10(1):4368. doi: 10.1038/s41598-020-61217-6. PMID:32152422<ref>PMID:32152422</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 6ll7" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Inorganic pyrophosphatase 3D structures|Inorganic pyrophosphatase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Shewanella sp. AS-11]]
+[[Category: Horitani M]]
+[[Category: Kusubayashi K]]
+[[Category: Oshima K]]
+[[Category: Sugimoto H]]
+[[Category: Watanabe K]]
+[[Category: Yato A]]