6ki8: Difference between revisions
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==Pyrophosphatase mutant K149R from Acinetobacter baumannii== | |||
<StructureSection load='6ki8' size='340' side='right'caption='[[6ki8]], [[Resolution|resolution]] 1.79Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6ki8]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KI8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KI8 FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DPO:DIPHOSPHATE'>DPO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=6ki8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ki8 OCA], [http://pdbe.org/6ki8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ki8 RCSB], [http://www.ebi.ac.uk/pdbsum/6ki8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ki8 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[[http://www.uniprot.org/uniprot/N9S5K0_9GAMM N9S5K0_9GAMM]] Catalyzes the hydrolysis of inorganic pyrophosphate (PPi) forming two phosphate ions.[HAMAP-Rule:MF_00209] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
All living things have pyrophosphatases that hydrolyze pyrophosphate and release energy. This energetically favorable reaction drives many energetically unfavorable reactions. An accepted catalytic model of pyrophosphatase shows that a water molecule activated by two divalent cations (M1 and M2) within the catalytic center can attack pyrophosphate in an SN2 mechanism and thus hydrolyze the molecule. However, our co-crystal structure of Acinetobacter baumannii pyrophosphatase with pyrophosphate shows that a water molecule from the solvent may, in fact, be the actual catalytic water. In the co-crystal structure of the wild-type pyrophosphatase with pyrophosphate, the electron density of the catalytic centers of each monomer are different from one another. This indicates that pyrophosphates in the catalytic center are dynamic. Our mass spectroscopy results have identified a highly conserved lysine residue (Lys30) in the catalytic center that is phosphorylated, indicating that the enzyme could form a phosphoryl enzyme intermediate during hydrolysis. Mutation of Lys30 to Arg abolished the activity of the enzyme. In the structure of the apo wild type enzyme, we observed that a Na(+) ion is coordinated by residues within a loop proximal to the catalytic center. Therefore, we mutated three key residues within the loop (K143R, P147G, and K149R) and determined Na(+) and K(+)-induced inhibition on their activities. Compared to the wild type enzyme, P147G is most sensitive to these cations, whereas K143R was inactive and K149R showed no change in activity. These data indicate that monovalent cations could play a role in down-regulating pyrophosphatase activity in vivo. Overall, our results reveal new aspects of pyrophosphatase catalysis and could assist in the design of specific inhibitors of Acinetobacter baumannii growth. | |||
Crystal Structures of Pyrophosphatase from Acinetobacter baumannii: Snapshots of Pyrophosphate Binding and Identification of a Phosphorylated Enzyme Intermediate.,Si Y, Wang X, Yang G, Yang T, Li Y, Ayala GJ, Li X, Wang H, Su J Int J Mol Sci. 2019 Sep 6;20(18). pii: ijms20184394. doi: 10.3390/ijms20184394. PMID:31500178<ref>PMID:31500178</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 6ki8" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Inorganic diphosphatase]] | |||
[[Category: Large Structures]] | |||
[[Category: Su, J]] | [[Category: Su, J]] | ||
[[Category: Hydrolase]] | |||
[[Category: Mutant k149r]] | |||
[[Category: Pyrophosphatase]] | |||
Revision as of 13:24, 2 October 2019
Pyrophosphatase mutant K149R from Acinetobacter baumanniiPyrophosphatase mutant K149R from Acinetobacter baumannii
Structural highlights
Function[N9S5K0_9GAMM] Catalyzes the hydrolysis of inorganic pyrophosphate (PPi) forming two phosphate ions.[HAMAP-Rule:MF_00209] Publication Abstract from PubMedAll living things have pyrophosphatases that hydrolyze pyrophosphate and release energy. This energetically favorable reaction drives many energetically unfavorable reactions. An accepted catalytic model of pyrophosphatase shows that a water molecule activated by two divalent cations (M1 and M2) within the catalytic center can attack pyrophosphate in an SN2 mechanism and thus hydrolyze the molecule. However, our co-crystal structure of Acinetobacter baumannii pyrophosphatase with pyrophosphate shows that a water molecule from the solvent may, in fact, be the actual catalytic water. In the co-crystal structure of the wild-type pyrophosphatase with pyrophosphate, the electron density of the catalytic centers of each monomer are different from one another. This indicates that pyrophosphates in the catalytic center are dynamic. Our mass spectroscopy results have identified a highly conserved lysine residue (Lys30) in the catalytic center that is phosphorylated, indicating that the enzyme could form a phosphoryl enzyme intermediate during hydrolysis. Mutation of Lys30 to Arg abolished the activity of the enzyme. In the structure of the apo wild type enzyme, we observed that a Na(+) ion is coordinated by residues within a loop proximal to the catalytic center. Therefore, we mutated three key residues within the loop (K143R, P147G, and K149R) and determined Na(+) and K(+)-induced inhibition on their activities. Compared to the wild type enzyme, P147G is most sensitive to these cations, whereas K143R was inactive and K149R showed no change in activity. These data indicate that monovalent cations could play a role in down-regulating pyrophosphatase activity in vivo. Overall, our results reveal new aspects of pyrophosphatase catalysis and could assist in the design of specific inhibitors of Acinetobacter baumannii growth. Crystal Structures of Pyrophosphatase from Acinetobacter baumannii: Snapshots of Pyrophosphate Binding and Identification of a Phosphorylated Enzyme Intermediate.,Si Y, Wang X, Yang G, Yang T, Li Y, Ayala GJ, Li X, Wang H, Su J Int J Mol Sci. 2019 Sep 6;20(18). pii: ijms20184394. doi: 10.3390/ijms20184394. PMID:31500178[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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