Homology Modeling of Type-P5 ATPases from the Malaria Parasite: Insight into Their Functions and Evolution, and Implications About the Effect and Role of Intrinsically Disordered Protein Structure

Type-P5 ATPases are the least characterized among the P-type ATPases and this is especially true in the case of the malaria parasite. In this study, Spf1, a subtype-P5A ATPase of yeast, and ATP13A2, a subtype-P5B ATPase of humans, were used as templates to extensively characterize the sequences and structural features of haemosporidian type-P5 ATPases. Malaria parasites have both subtype-P5A and subtype-P5B ATPase genes and the structural features of the proteins recapitulate the known structures of subtype-P5A and subtype-P5B ATPases. Detailed structural analysis detected an additional α-helix in the P-domain of subtype-P5A ATPases, which is not found in subtype-P5B ATPases. This feature may be an additional signature to distinguish subtype-P5A and subtype-P5B ATPases, in addition to the previously described differences in the membrane loops of the N-terminal domain, the arm in the P-domain of subtype-P5A, and substrate differences. A notable difference in the type-P5 ATPases from the malaria parasite, as compared to the templates, is the insertion of multiple variable and low-complexity regions that form intrinsically disorganized loops. These loops may form a shroud-like structure that protects the core ATPase structure and/or participates in low-affinity interprotein interactions. Homology modeling did not provide definitive answers about the substrate specificity of the haemosporidian type-P5 ATPases. However, the haemosporidian subtype-P5A ATPase is likely an ER transmembrane dislocase as are the other subtype-P5A ATPases. In contrast, the subtype-P5B ATPases of the malaria parasite are not likely to be polyamine transporters in lysosomes, as have been described in fungi and metazoans. This suggests that subtype-P5B ATPases have undergone lineage-specific divergence in regard to their function(s).