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The mollusk shell is a hard tissue consisting of calcium carbonate and organic matrices. The organic matrices are considered to play important roles in shell formation. We have previously identified a prismatic layer-specific protein named Prismalin-14, which consists of 105 amino acid residues and includes four structurally characteristic regions; a repeated sequence of Pro-Ile-Tyr-Arg, a Gly/Tyr-rich region and N- and C-terminal Asp-rich regions. Prismalin-14 showed an inhibitory activity on calcium carbonate precipitation and a calcium-binding ability in vitro. In this study, we prepared some molecular species of recombinant proteins including Prismalin-14 and its truncated proteins in an Escherichia coli expression system to reveal a structure–function relationship of Prismalin-14. The results showed that the Gly/Tyr-rich region was responsible for chitin binding and was identified as a novel chitin-binding sequence. On the other hand, both N- and C-terminal Asp-rich regions are related to inhibitory activity on calcium carbonate precipitation in vitro. Immunohistological observation revealed that Prismalin-14 was localized at the acid-insoluble organic framework including chitin. All these results strongly suggest that Prismalin-14 is a framework protein that mediates chitin and calcium carbonate crystals by using its acidic and chitin-binding regions.