TY - JOUR
T1 - Structural Dynamics and Catalytic Mechanism of ATP13A2 (PARK9) from Simulations
AU - Mateeva, Teodora
AU - Rosta, Edina
AU - Klaehn, Marco
N1 - Funding Information:
We are grateful to Dr Tamás Földes for numerous discussions. We would also like to thank Dr Attila Csikász-Nagy for initial discussions. E.R. acknowledges funding from the ERC (Project 757850 BioNet). T.M. acknowledges funding from the Agency for Science, Technology and Research (A*STAR) Singapore Research Attachment Programme (ARAP) and King’s College London’s Centre for doctoral studies. We acknowledge the use of the research computing facility at King’s College London, Rosalind ( https://rosalind.kcl.ac.uk ).
Publisher Copyright:
© 2021 American Chemical Society
PY - 2021/11/4
Y1 - 2021/11/4
N2 - 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 modeled 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 Mg
2+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 Mg
2+cations. The calculated barrier heights in both cases are found to be ∼12.5 and 7.5 kcal mol
-1, respectively. We elucidated details of the catalytically competent ATP conformation and the binding mode of the second Mg
2+cofactor. We also examined the role of the conserved Arg686 and Lys859 catalytic residues. We observed that by significantly lowering the barrier height of the ATP cleavage reaction, Arg686 had major effect on the reaction. The removal of Arg686 increased the barrier height for the ATP cleavage by more than 5.0 kcal mol
-1while 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 the ATP13A2 cargo binds.
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 modeled 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 Mg
2+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 Mg
2+cations. The calculated barrier heights in both cases are found to be ∼12.5 and 7.5 kcal mol
-1, respectively. We elucidated details of the catalytically competent ATP conformation and the binding mode of the second Mg
2+cofactor. We also examined the role of the conserved Arg686 and Lys859 catalytic residues. We observed that by significantly lowering the barrier height of the ATP cleavage reaction, Arg686 had major effect on the reaction. The removal of Arg686 increased the barrier height for the ATP cleavage by more than 5.0 kcal mol
-1while 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 the ATP13A2 cargo binds.
UR - http://www.scopus.com/inward/record.url?scp=85118713541&partnerID=8YFLogxK
U2 - 10.1021/acs.jpcb.1c05337
DO - 10.1021/acs.jpcb.1c05337
M3 - Article
SN - 1520-6106
VL - 125
SP - 11835
EP - 11847
JO - JOURNAL OF PHYSICAL CHEMISTRY B
JF - JOURNAL OF PHYSICAL CHEMISTRY B
IS - 43
ER -