The crystal structure of the Ca²⁺-ATPase 1 fromListeria monocytogenesreveals a pump primed for dephosphorylation

Abstract

Bacteria regulate intracellular calcium concentrations by exporting calcium from the cell using active transporters. These transporters include homologues of the mammalian sarco/endoplasmic reticulum Ca 2+ -ATPase (SERCA), which has served as a paradigm for the structure and mechanism of P-type ATPase ion transport. Here we present three crystal structures of the Ca 2+ -ATPase 1 from Listeria monocytogenes (LMCA1). Structures with BeF3mimicking a phosphoenzyme state reveal an intermediate between the outward-open E2P and the proton-occluded E2-P* conformations known for SERCA. This suggests that LMCA1 pre-organizes for dephosphorylation already at the E2P state, consistent with the rapid dephosphorylation of this pump and observations from single-molecule studies. Comparison of ion binding sites show that an arginine side-chain occupies the position equivalent to the calcium binding site I in SERCA leaving a single Ca 2+ -binding site in LMCA1, corresponding to SERCA site II. Absence of putative proton pathways suggest a direct mechanism of proton counter transport through the Ca 2+ exchange pathways. In total, the new structures provide insight into the evolutionary divergence and conserved features of an important class of ion transporters. Sara Basse Hansen et al. (2020)

Structure and ion-release mechanism of PIB-4-type ATPases

“…Notably, analogous highly similar BeF3 --and AlF4-stablized structures have recently also been observed for the Ca 2+ -specific P-type ATPase from Listeria monocytogenes (LMCA1) (43) . It was proposed that LMCA1 pre-organizes for dephosphorylation already in a late E2P state (E2P*, stabilized by BeF3 -), in accordance with its rapid dephosphorylation.…”

Structure and ion-release mechanism of PIB-4-type ATPases

“…Surprisingly however, analysis of the two obtained structures suggests that the anticipated significant domain reorientations are absent in sCoaT (Figure 2b Notably, analogous highly similar BeF 3 --and AlF 4 -stablized structures have recently also been observed for the Ca 2+ -specific P-type ATPase from Listeria monocytogenes (LMCA1) (46) . It was proposed that LMCA1 pre-organizes for dephosphorylation Conversely, the M-domains of the two sCoaT structures are overall similar and appear outward-occluded (Figure 2c), as also supported by comparisons with the equivalent structures of SsZntA, again contrasting to the situation observed in P IB-1 -and P IB-2 -ATPases.…”

Fast-forward on P-type ATPases: recent advances on structure and function

“…Within the P2A subfamily members adapt to their specific environment. This is true for LMCA1 which has evolved to be a simple version of SERCA with fast dephosphorylation, reduced ion capacity and no dedicated proton pathways (38,42). Recently, structures of the secretory pathway Ca 2+ /Mn 2+ -ATPase (SPCA1) suggested that flexibility of TM2 and TM6 allows Ca 2+ and Mn 2+ to share the same binding site (43).…”