PT  - JOURNAL ARTICLE
AU  - Teodora Mateeva
AU  - Marco Klähn
AU  - Edina Rosta
TI  - Structural Dynamics and Catalytic Mechanism of ATP13A2 (PARK9) from Simulations
AID  - 10.1101/2021.06.01.446648
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.06.01.446648
4099  - http://biorxiv.org/content/early/2021/07/19/2021.06.01.446648.short
4100  - http://biorxiv.org/content/early/2021/07/19/2021.06.01.446648.full
AB  - ATP13A2 is a gene encoding a protein of the P5B subfamily of ATPases and is a PARK gene. Molecular defects of the gene are mainly associated with variations of Parkinson’s Disease (PD). Despite the established importance of the protein in regulating neuronal integrity, the three-dimensional structure of the protein currently remains unresolved crystallographically. We have modelled the structure and reactivity of the full-length protein in its E1-ATP state. Using Molecular Dynamics (MD), Quantum cluster and Quantum Mechanical/Molecular mechanical (QM/MM) methods, we aimed at describing the main catalytic reaction, leading to the phosphorylation of Asp513. Our MD simulations suggest that two positively charged Mg2+ cations are present at the active site during the catalytic reaction, stabilizing a specific triphosphate binding mode. Using QM/MM calculations, we subsequently calculated the reaction profiles for the phosphoryl transfer step in the presence of one and two Mg2+ cations. The calculated barrier heights in both cases are found to be ∼12.5 and 7.0 kcal mol-1, respectively. We elucidated details of the catalytically competent ATP conformation and the binding mode of the second Mg2+ cofactor. We also examined the role of the conserved Arg686 and Lys859 catalytic residues. We observed that by lowering significantly the barrier height of the ATP cleavage reaction, Arg686 had significant effect on the reaction. The removal of Arg686 increased the barrier height for the ATP cleavage by more than 5.0 kcal mol-1 while the removal of key electrostatic interactions created by Lys859 to the γ-phosphate and Asp513 destabilizes the reactant state. When missense mutations occur in close proximity to an active site residue, they can interfere with the barrier height of the reaction, which can halt the normal enzymatic rate of the protein. We also found large binding pockets in the full-length structure, including a transmembrane domain pocket, which is likely where ATP13A2 cargo binds.Competing Interest StatementThe authors have declared no competing interest.