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Updated: Jun 15, 2025
Visualization of ATP Synthase Dimers in Mitochondria by Electron Cryo-tomography
Published on: September 14, 2014
The crystal structure of yeast mitochondrial type pyrophosphatase provides a model to study pathological mutations in
Ekaterina Y Bezpalaya1, Ilya O Matyuta2, Natalia N Vorobyeva3
1Lomonosov Moscow State University, Chemistry Department, 119991, Moscow, Russia.
Abstract:
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.
Insights
Mitochondrial inorganic pyrophosphatase (PPA2) mutations cause severe health issues. This study reveals the yeast PPA2 structure, offering insights into human PPA2 mutations and related pathologies.
Area of Science:
- Biochemistry
- Structural Biology
- Molecular Biology
Background:
- Mutations in the human PPA2 gene lead to mitochondrial dysfunction, impacting the heart and brain, and causing early mortality.
- The 3D structure and detailed biochemical characteristics of PPA2, particularly the mitochondrial isoform, remain largely uncharacterized compared to its cytosolic counterpart.
Purpose of the Study:
- To determine the crystal structure of yeast Ogataea parapolymorpha PPA2 (OpPPA2).
- To biochemically characterize OpPPA2 and investigate the structural basis of PPA2-associated pathologies.
- To provide insights into the functional implications of pathogenic mutations in human PPA2.
Main Methods:
- X-ray crystallography was used to determine the 3D structure of OpPPA2.
- Biochemical assays were performed to characterize the enzyme's activity.
- Structural analysis was conducted to compare OpPPA2 with other pyrophosphatases and analyze conserved residues.
Main Results:
- The crystal structure of OpPPA2 was determined, revealing a dimeric structure with a fold characteristic of eukaryotic Family I pyrophosphatases.
- Cofactor Mg2+ ion coordination in OpPPA2 is similar to other Family I pyrophosphatases.
- Analysis of conserved residues, including a comparison with the pathogenic human variant Met94Val (OpPPA2 Met52Val), suggests mechanisms for mutation-induced dysfunction.
Conclusions:
- The determined structure of OpPPA2 provides a structural framework for understanding Family I pyrophosphatases.
- Structural insights into conserved residues offer potential explanations for the pathogenicity of human PPA2 mutations.
- This study represents a significant step towards elucidating the structural basis of PPA2-related diseases.
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