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==Crystal structure of Inorganic Pyrophosphatase PPA1 from Arabidopsis thaliana== | ==Crystal structure of Inorganic Pyrophosphatase PPA1 from Arabidopsis thaliana== | ||
<StructureSection load='5ls0' size='340' side='right' caption='[[5ls0]], [[Resolution|resolution]] 1.83Å' scene=''> | <StructureSection load='5ls0' size='340' side='right'caption='[[5ls0]], [[Resolution|resolution]] 1.83Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5ls0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LS0 OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[5ls0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LS0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LS0 FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.83Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=5ls0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ls0 OCA], [https://pdbe.org/5ls0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ls0 RCSB], [https://www.ebi.ac.uk/pdbsum/5ls0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ls0 ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/IPYR1_ARATH IPYR1_ARATH] Catalyzes the irreversible hydrolysis of pyrophosphate (PPi) to phosphate. The MgPPi(2-) complex binds to the enzyme only after a free Mg(2+) ion has bound (Ref.9). No activity with glycerol-3-phosphate, glucose-6-phosphate, p-nitrophenylphosphate, ADP, NADP(+), NAD(+),NADH, NADPH or phosphoribosyl pyrophosphate as substrates (Ref.9). Controls the equilibrium of gluconeogenic reactions in the heterotrophic growth phase of early seedling establishment. Determinates the rate of cytosolic glycolysis, providing carbon for seed storage lipid accumulation (PubMed:22566496).<ref>PMID:22566496</ref> [REFERENCE:9] | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
Inorganic | Inorganic pyrophosphatases (PPases, EC 3.6.1.1), which hydrolyze inorganic pyrophosphate to phosphate in the presence of divalent metal cations, play a key role in maintaining phosphorus homeostasis in cells. DNA coding inorganic pyrophosphatases from Arabidopsis thaliana ( At PPA1) and Medicago truncatula ( Mt PPA1) were cloned into a bacterial expression vector and the proteins were produced in Escherichia coli cells and crystallized. In terms of their subunit fold, At PPA1 and Mt PPA1 are reminiscent of other members of Family I soluble pyrophosphatases from bacteria and yeast. Like their bacterial orthologs, both plant PPases form hexamers, as confirmed in solution by multi-angle light scattering and size-exclusion chromatography. This is in contrast to the fungal counterparts, which are dimeric. Unexpectedly, the crystallized At PPA1 and Mt PPA1 proteins lack ~30 amino acid residues at their N-termini, as independently confirmed by chemical sequencing. In vitro , self-cleavage of the recombinant proteins is observed after prolonged storage or during crystallization. The cleaved fragment corresponds to a putative signal peptide of mitochondrial targeting, with a predicted cleavage site at Val31-Ala32. Site-directed mutagenesis shows that mutations of the key active site Asp residues dramatically reduce the cleavage rate, which suggests a moonlighting proteolytic activity. Moreover, the discovery of autoproteolytic (rather than mitochondrion-mediated) cleavage of a mitochondrial-targeting peptide would change our perception of this signaling process. | ||
Crystal structures of plant inorganic pyrophosphatase, an enzyme with a moonlighting autoproteolytic activity.,Grzechowiak M, Ruszkowski M, Sliwiak J, Szpotkowski K, Sikorski M, Jaskolski M Biochem J. 2019 Aug 1. pii: BCJ20190427. doi: 10.1042/BCJ20190427. PMID:31371393<ref>PMID:31371393</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 5ls0" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 5ls0" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Inorganic pyrophosphatase 3D structures|Inorganic pyrophosphatase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Arabidopsis thaliana]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Grzechowiak M]] | ||
[[Category: | [[Category: Jaskolski M]] | ||
[[Category: | [[Category: Sikorski M]] | ||
Latest revision as of 21:44, 18 October 2023
Crystal structure of Inorganic Pyrophosphatase PPA1 from Arabidopsis thalianaCrystal structure of Inorganic Pyrophosphatase PPA1 from Arabidopsis thaliana
Structural highlights
FunctionIPYR1_ARATH Catalyzes the irreversible hydrolysis of pyrophosphate (PPi) to phosphate. The MgPPi(2-) complex binds to the enzyme only after a free Mg(2+) ion has bound (Ref.9). No activity with glycerol-3-phosphate, glucose-6-phosphate, p-nitrophenylphosphate, ADP, NADP(+), NAD(+),NADH, NADPH or phosphoribosyl pyrophosphate as substrates (Ref.9). Controls the equilibrium of gluconeogenic reactions in the heterotrophic growth phase of early seedling establishment. Determinates the rate of cytosolic glycolysis, providing carbon for seed storage lipid accumulation (PubMed:22566496).[1] [REFERENCE:9] Publication Abstract from PubMedInorganic pyrophosphatases (PPases, EC 3.6.1.1), which hydrolyze inorganic pyrophosphate to phosphate in the presence of divalent metal cations, play a key role in maintaining phosphorus homeostasis in cells. DNA coding inorganic pyrophosphatases from Arabidopsis thaliana ( At PPA1) and Medicago truncatula ( Mt PPA1) were cloned into a bacterial expression vector and the proteins were produced in Escherichia coli cells and crystallized. In terms of their subunit fold, At PPA1 and Mt PPA1 are reminiscent of other members of Family I soluble pyrophosphatases from bacteria and yeast. Like their bacterial orthologs, both plant PPases form hexamers, as confirmed in solution by multi-angle light scattering and size-exclusion chromatography. This is in contrast to the fungal counterparts, which are dimeric. Unexpectedly, the crystallized At PPA1 and Mt PPA1 proteins lack ~30 amino acid residues at their N-termini, as independently confirmed by chemical sequencing. In vitro , self-cleavage of the recombinant proteins is observed after prolonged storage or during crystallization. The cleaved fragment corresponds to a putative signal peptide of mitochondrial targeting, with a predicted cleavage site at Val31-Ala32. Site-directed mutagenesis shows that mutations of the key active site Asp residues dramatically reduce the cleavage rate, which suggests a moonlighting proteolytic activity. Moreover, the discovery of autoproteolytic (rather than mitochondrion-mediated) cleavage of a mitochondrial-targeting peptide would change our perception of this signaling process. Crystal structures of plant inorganic pyrophosphatase, an enzyme with a moonlighting autoproteolytic activity.,Grzechowiak M, Ruszkowski M, Sliwiak J, Szpotkowski K, Sikorski M, Jaskolski M Biochem J. 2019 Aug 1. pii: BCJ20190427. doi: 10.1042/BCJ20190427. PMID:31371393[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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