Figure 4. Structure analyses of the missense mutation in the calcium binding (cb) epidermal growth factor (EGF)-like7 domain. A: The consensus secondary structure of a prototypical cbEGF-like domain. Calcium binding in the NH₂-terminal region of the wild-type domain is mediated by the consensus sequence (D/N) -X- (D/N) (E/Q) Xm (D/N) Xn (Y/F; m and n are variables), and highly conserved amino acids are identified by their single-letter amino acid code. The letter C in the schematic represents the highly conserved cysteine of cbEGF-like domain, and the lines between cysteine represent disulfide bridges. The mutation p.Y754C located at the region between the last two cysteines of the domain, which could probably interfere with the disulfide bond formation between the two cysteines. B: The 3D structure of the wild cbEGF-like7–8 domains, which are created based on the Protein Data Bank (PDB) template 1EMN (47% sequence identity) by PyMOL 1.1r1. The blue represents the unaffected tyrosine. C: The potential conformation change of the mutation. The red represents the substitute cysteine, where the double β-sheet transformed to a loop-region. D and E: The 3D structure of domains in B and C, respectively. The yellow lines represent disulfide bonds, and the blue represents the unaffected tyrosine. The purple displays the residues within the distance of 4Å with tyrosine⁷⁵⁴, and double β-sheet between obligatory glycine⁷⁵³ and aspartic⁷⁶⁵. The red represents the substitute cysteine, which absents the benzene ring. The yellow dashed line represents the potential disulfide bond formation between the introduced cysteine⁷⁵⁴ and cysteine⁷⁵⁰, which would probably disrupt the disulfide bond between cysteine⁷⁵⁰ and cysteine⁷⁶³. The white displays the residues within the distance of 4Å with cysteine⁷⁵⁴; compared with the purple wild type, β-turn, which forms the calcium binding pocket of cbEGF-like8, is farther in distance with cysteine⁷⁵⁴. F and G: A zoom-in change of D and E, respectively. H and I: The surface of the wild and mutant cbEGF-like7–8 domains, respectively. The colors correspond to that of figure D and E. The surface area of the mutant region is smaller than that of the wild. In summary, the conformation of the mutant domain is likely to be strongly altered, to include neighboring domain as well.