Substrate-induced conformational changes in sarcoplasmic reticulum Ca2+-ATPase probed by surface modification using diethylpyrocarbonate with mass spectrometry

► Use of DEPC modification and mass spectrometry to identify 15 residues from SERCA. ► The effects of Ca2+, ATP, and MgF4 at these residues have been addressed. ► The reactivity of many residues was consistent with the crystal surface structures. ► Similar structural changes occur both in the membranous and crystalline states. ► 4 Residues near the interface of 3 cytoplasmic domains suggest larger changes. We have identified 15 residues from the surface of sarcoplasmic reticulum Ca2+-pump ATPase, by mass spectrometry using diethylpyrocarbonate modification. The reactivity of 9 residues remained high under all the conditions. The reactivity of Lys-515 at the nucleotide site was severely inhibited by ATP, whereas that of Lys-158 in the A-domain decreased by one-half and increased by five-fold in the presence of Ca2+ and MgF4, respectively. These are well explained by solvent accessibility, pKa and nearby hydrophobicity of the reactive atom on the basis of the atomic structure. However, the reactivity of 4 residues near the interface among A-, N- and P-domain suggested larger conformational changes of these domains in membrane upon binding of Ca2+ (Lys-436), ATP (Lys-158) and MgF4 (His-5, -190, Lys-436).