Structure of a sarcoplasmic calcium-binding protein from Nereis diversicolor refined at 2·0 Å resolution

Abstract

The crystal structure of a sarcoplasmic Ca 2+-binding protein (SCP) from the sandworm Nereis diversicolor has been determined and refined at 2·0 Å resolution using restrained least-squares techniques. The two molecules in the crystallographic asymmetric unit, which are related by a non-crystallographic 2-fold axis, were refined independently. The refined model includes all 174 residues and three calcium ions for each molecule, as well as 213 water molecules. The root-mean-square difference in co-ordinates for backbone atoms and calcium ions of the two molecules is 0·51 Å. The final crystallographic R-factor, based on 18,959 reflections in the range 2·0 A ̊ ≤ d ≤ 7·0 A ̊ , with intensities exceeding 2·0 σ, is 0·182. Bond lengths and bond angles in the molecules have root-mean-square deviations from ideal values of 0·013 Å and 2·2 °, respectively. SCP has four distinct domains with the typical helix-loop-helix (EF-hand) Ca 2+-binding motif, although the second Ca 2+-binding domain is not functional due to amino acid changes in the loop. The structure shows several unique features compared to other Ca 2+-binding proteins with four EF-hand domains. The overall structure is highly compact and globular with a predominant hydrophobic core, unlike the extended dumbbell-shaped structure of calmodulin or troponin C. A hydrophobic tail at the COOH terminus adds to the structural stability by packing against a hydrophobic pocket created by the folding of the NH 2 and COOH-terminal Ca 2+-binding domain pairs. The first and second domains show different helix-packing arrangements from any previously described for Ca 2+-binding proteins.