Linking Biochemical and Structural States of SERCA: Achievements, Challenges, and New Opportunities

Abstract

Sarcoendoplasmic reticulum calcium ATPase (SERCA), a member of the P-type ATPase family of ion and lipid pumps, is responsible for the active transport of Ca²⁺ from the cytoplasm into the sarcoplasmic reticulum lumen of muscle cells, into the endoplasmic reticulum (ER) of non-muscle cells. X-ray crystallography has proven to be an invaluable tool in understanding the structural changes of SERCA, and more than 70 SERCA crystal structures representing major biochemical states (defined by bound ligand) have been deposited in the Protein Data Bank. Consequently, SERCA is one of the best characterized components of the calcium transport machinery in the cell. Emerging approaches in the field, including spectroscopy and molecular simulation, now help integrate and interpret this rich structural information to understand the conformational transitions of SERCA that occur during activation, inhibition, and regulation. In this review, we provide an overview of the crystal structures of SERCA, focusing on identifying metrics that facilitate structure-based categorization of major steps along the catalytic cycle. We examine the integration of crystallographic data with different biophysical approaches and computational methods to link biochemical and structural states of SERCA that are populated in the cell. Finally, we discuss the challenges and new opportunities in the field, including structural elucidation of functionally important and novel regulatory complexes of SERCA, understanding the structural basis of functional divergence among homologous SERCA regulators, and bridging the gap between basic and translational research directed toward therapeutic modulation of SERCA.

Keywords: P-type ATPase; SERCA; X-ray crystallography; biophysical methods; calcium; inhibition; molecular simulation; regulation.

Figure A1

Sequence of SERCA1a from rabbit (Oryctolagus cuniculus) showing the location of all major domains.

Figure A2

Root-mean-square deviation (RMSD) matrix calculated for the (A) Cytosolic domains and (B) TM domain of SERCA1a (70 structures), SERCA2a (2 structures), and SERCA2b (2 structures). RMSD-based clustering shows the presence of six major structural clusters, C1 through C6.

Figure A3

Rotation angle (R) calculated for (A) P-A domains and displacement distance (T) for (B) A-N, (C) P-N, and (D) P-A domains. A total of 74 SERCA1a structures were compared, using 2c9m as reference.

Figure A4

Interhelical angle of selected SERCA TM helix pairs.

Figure 1

(A) Three-dimensional structure of the cytosolic N (green), A (red), and P (blue) domains and transmembrane helices (TM, yellow) of sarcoendoplasmic reticulum calcium ATPase (SERCA). (B) Close-up view of calcium binding sites I and II of SERCA showing two Ca²⁺ ions (green) and the interactions stabilizing their position in these sites. (C) Schematic representation of the Post-Albers pumping cycle of SERCA.

Figure 2

(A) Backbone root-mean-square deviation (RMSD) matrix of SERCA1a and SERCA2a/b structures and state information of the six clusters found. (B) Depiction of the superimposed SERCA structures comprising the six major clusters. SERCA1a structures 1kju and 4nab were excluded from the analysis because they were obtained at low resolution, or because they were missing large regions/domains in the reported structure. Short loops and missing side chains were built to perform the backbone alignment (see methods). Clustering analysis was performed using a cut-off RMSD value of 0.23 nm.

Figure 3

Displacement distances and rotation angles of the (A) N domain, (B) P domain, and (C) A domain recovered from the transformation matrix calculation for the 74 SERCA structures using 2c9m (E1-2Ca state) as reference. The displacement (D) and rotation (R) movements of each of the domains are represented below each plot, coloring in purple and orange the initial and final positions. (D) Distribution of the six clusters based on the rotation of the A and P domains. (E) Distance between the center of geometry (COG) of A and N domains (top), A and P domains (middle), and N and P domains (bottom) for each cluster. (F) Fluorescence resonance energy transfer (FRET) and Met1-Asn510 distance comparison performed by Raguimova et al. [47] to analyze the population distribution of SERCA in response to dynamic changes in intracellular calcium. The figure in the middle represents the distance between the Met1 and Asn510 residues, the table and the graph contain the experimental and theoretical data generated by Raguimova et al. E1-2Ca state (C1) distance values were not considered for the linear regression. All plots are colored using the cluster analysis in Figure 2 as reference (C1, purple; C2, blue; C3, green; C4, yellow; C5, orange; C6, red).

Figure 4

(A) Cytosolic view of the transmembrane domain with labeled TM helices. (B) Topological distribution of proline, glycine, aromatic, and charged residues. (C) Average helicity fraction of the TM helices in the six clusters. Distribution of the (D) bending and (E) TM tilt angles of the ten TM helices. (F) Angle between the helices of most representative TM helix pairs. Box and whisker plots are colored using the cluster analysis in Figure 2 as reference (C1, purple; C2, blue; C3, green; C4, yellow; C5, orange; C6, red).

Figure 5

Summary of the binding sites located in the cytosolic and TM domains of SERCA. We show the cytosolic and transmembrane regions of SERCA bound to ions, lipids, small molecules, regulatory peptides, inorganic coordination entity, and water molecules in the six clusters described in this review. In all panels, the TM domain is shown from the cytosolic space in the membrane bilayer normal direction. Water molecules are shown as small red spheres.

Figure 6

Chemical structures of small molecules cited in the text and schematic representation of their binding sites (BS) in the (A) cytosolic domain and (B) TM domain of SERCA.