6ll8: Difference between revisions
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==Type II inorganic pyrophosphatase (PPase) from the psychrophilic bacterium Shewanella sp. AS-11, Mg-PNP form== | |||
<StructureSection load='6ll8' size='340' side='right'caption='[[6ll8]], [[Resolution|resolution]] 1.30Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6ll8]] is a 2 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=6LL8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LL8 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]] 1.3Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2PN:IMIDODIPHOSPHORIC+ACID'>2PN</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=F:FLUORIDE+ION'>F</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=6ll8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ll8 OCA], [https://pdbe.org/6ll8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ll8 RCSB], [https://www.ebi.ac.uk/pdbsum/6ll8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ll8 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. | |||
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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 6ll8" 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]] | |||