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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]] | |||
Latest revision as of 14:03, 22 November 2023
Type II inorganic pyrophosphatase (PPase) from the psychrophilic bacterium Shewanella sp. AS-11, Mg-PNP formType II inorganic pyrophosphatase (PPase) from the psychrophilic bacterium Shewanella sp. AS-11, Mg-PNP form
Structural highlights
FunctionPublication Abstract from PubMedInorganic 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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