6MT2 image
Entry Detail
PDB ID:
6MT2
Keywords:
Title:
Crystal structure of Inorganic Pyrophosphatase from Medicago truncatula (I23 crystal form)
Biological Source:
PDB Version:
Deposition Date:
2018-10-18
Release Date:
2019-08-14
Method Details:
Experimental Method:
Resolution:
2.89 Å
R-Value Free:
0.19
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
I 2 3
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Soluble inorganic pyrophosphatase
Chain IDs:A, B, C, D
Chain Length:214
Number of Molecules:4
Biological Source:Medicago truncatula
Primary Citation
Crystal structures of plant inorganic pyrophosphatase, an enzyme with a moonlighting autoproteolytic activity.
Biochem.J. 476 2297 2319 (2019)
PMID: 31371393 DOI: 10.1042/BCJ20190427

Abstact

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 (AtPPA1) and Medicago truncatula (MtPPA1) were cloned into a bacterial expression vector and the proteins were produced in Escherichia coli cells and crystallized. In terms of their subunit fold, AtPPA1 and MtPPA1 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 with the fungal counterparts, which are dimeric. Unexpectedly, the crystallized AtPPA1 and MtPPA1 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 cleavage of a mitochondrial targeting peptide would change our perception of this signaling process.

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