Solution structure of S. cerevisiae PDCD5-like protein and its promoting role in H(2)O(2)-induced apoptosis in yeast.

Human PDCD5 protein is a novel programmed cell death-promoting molecule. However, the function of Ymr074cP, a S. cerevisiae homologue of hPDCD5, is still unknown. Heteronuclear NMR methods were used to determine the solution structure of the N-terminal 116-residue fragment (N116) of Ymr074cP protein. N116 is shown to be a heterogeneous ensemble of flexibly folded conformations, adopting an extended triple-helix bundle fold that is connected to a mobile but structured alpha-helix in the N-terminus by means of a lengthy highly flexible linker. By the nitroxide spin label, attached to the mutant cysteine residue at position 7 or 11, significant transient interactions were probed between the N-terminal helical portion and the core moiety plus several residues in the C-terminal tail. The topology of the triple-helix bundle is encoded mainly by hydrophobic interactions, and the N-terminal helical structure has a unique electrostatic potential character. A comparison of the solution structures of PDCD5-related proteins indicates that the structure of the triple-helix bundle is significantly conserved during evolution. We are the first to demonstrate that YMR074c overexpression promotes H(2)O(2)-induced apoptosis in yeast, not only in a metacaspase Yca1-dependent manner but also in a Yca1-independent manner and that deletion of the N-terminal helical portion greatly attenuates the apoptosis-promoting activity of this protein.