The crystal structure of yeast mitochondrial type pyrophosphatase provides a model to study pathological mutations in its human ortholog

• Published in: Biochemical and biophysical research communications 2024-12, Vol.738, p.150563, Article 150563
• Main Authors: Bezpalaya, Ekaterina Y., Matyuta, Ilya O., Vorobyeva, Natalia N., Kurilova, Svetlana A., Oreshkov, Sergey D., Minyaev, Mikhail E., Boyko, Konstantin M., Rodina, Elena V.
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Crystal structure; Crystallography, X-Ray; Humans; Inorganic pyrophosphatase; Inorganic Pyrophosphatase - chemistry; Inorganic Pyrophosphatase - genetics; Inorganic Pyrophosphatase - metabolism; Mitochondria - enzymology; Mitochondria - genetics; Mitochondrial enzyme; Models, Molecular; Mutation; Ogataea parapolymorpha; Pathogenic mutation; Protein Conformation; Pyrophosphatases - chemistry; Pyrophosphatases - genetics; Pyrophosphatases - metabolism; Saccharomycetales - enzymology; Saccharomycetales - genetics
• ISSN: 0006-291X; 1090-2104; 1090-2104
• DOI: 10.1016/j.bbrc.2024.150563

Mutations in human ppa2 gene encoding mitochondrial inorganic pyrophosphatase (PPA2) result in the mitochondria malfunction in heart and brain and lead to early death. In comparison with its cytosolic counterpart, PPA2 of any species is a poorly characterized enzyme with a previously unknown 3D structure. We report here the crystal structure of PPA2 from yeast Ogataea parapolymorpha (OpPPA2), as well as its biochemical characterization. OpPPA2 is a dimer, demonstrating the fold typical for other eukaryotic Family I pyrophosphatases, including the human cytosolic enzyme. Cofactor Mg2+ ions found in OpPPA2 structure have similar coordination to most known Family I pyrophosphatases. Most of the residues associated with the pathological mutations in human PPA2 are conserved in OpPPA2, and their structural context suggests possible explanations for the effects of the mutations on the human enzyme. In this work, the mutant variant of OpPPA2, Met52Val, corresponding to the natural pathogenic variant Met94Val of human PPA2, is characterized. The obtained structural and biochemical data provide a step to understanding the structural basis of PPA2-associated pathologies. [Display omitted] •The structure of mitochondrial type inorganic pyrophosphatase OpPPA2 is presented.•Met52Val in OpPPA2 is analogous to pathogenic variant Met94Val of a human ortholog.•Met52Val mutation impairs catalytic properties of OpPPA2 but not its stability.•Presented data provide a step to understanding PPA2-associated pathologies.