Structure of a Sarcoplasmic Calcium-binding Protein from Amphioxus Refined at 2·4 Å Resolution

Abstract

The three-dimensional structure of a sarcoplasmic Ca2+-binding protein from the protochordate amphioxus has been determined at 2·4 Å resolution using multiple-isomorphous-replacement techniques. The refined model includes all 185 residues, three calcium ions, and one water molecule. The final crystallographic R-factor is 0·199. Bond lengths and bond angles in the molecules have root-mean-square deviations from ideal values of 0·015 Å and 2·8°, respectively. The overall structure is highly compact and globular with a predominantly hydrophobic core, unlike the extended dumbbell-shaped structures of calmodulin or troponin C. These are four distinct domains with the typical helix-loop-helix Ca2+-binding motif (EF hand). The conformation of the pair of EF hands in the N-terminal half of the protein is unusual due to the presence of an aspartate residue in the twelfth position of the first Ca2+-binding loop, rather than the usual glutamate. The C-terminal half of the molecule contains one Ca2+-binding domain with a novel helix-loop-helix conformation and one Ca2+-binding domain that is no longer functional because of amino acid changes. The overall structure is quite similar to a sarcoplasmic Ca2+-binding protein from sandworm, although there is only about 12% amino acid sequence identity between them. The similarity of the structures of these two proteins suggests that all sarcoplasmic Ca2+-binding proteins will have the same general conformation, even thought there is very little conservation of primary structure among the proteins from various species.