Spectroscopic and biochemical characterization of heme binding to yeast Dap1p and mouse PGRMC1p

Yeast damage-associated response protein (Dap1p) and mouse progesterone receptor membrane component-1 protein (mPGRMC1p) belong to a highly conserved class of putative membrane-associated progesterone binding proteins (MAPR), with Dap1p and inner zone antigen (IZA), the rat homologue of mPGRMC1p, recently being reported to bind heme. While primary structure analysis reveals similarities to the cytochrome b(5) motif, neither of the two axial histidines responsible for ligation to the heme is present in any of the MAPR proteins. In this paper, EPR, MCD, CD, UV-vis, and general biochemical methods have been used to characterize the nature of heme binding in both Dap1p and a His-tagged, membrane anchor-truncated mPGRMC1p. As isolated, Dap1p is a tetramer which can be converted to a dimer upon addition of 150 mM salt. The heme is noncovalently attached, with a maximal, in vitro, heme loading of approximately 30%, for both proteins. CD and fluorescence spectroscopies indicate a well-ordered structure, suggesting the low level of heme loading is probably not due to improperly folded protein. EPR confirmed a five-coordinate, high-spin, ferric resting state for both proteins, indicating one axial amino acid ligand, in contrast to the six-coordinate, low-spin, ferric state of cytochrome b(5). The MCD spectrum confirmed this conclusion for Dap1p and indicated the axial ligand is most likely a tyrosine and not a histidine, or a cysteine; however, an aspartic acid residue could not be conclusively ruled out. Potential axial ligands, which are conserved in all MAPRs, were mutated (Y78F, D118A, and Y138F) and purified to homogeneity. The Y78F and D118A mutants were found to bind heme; however, Y138F did not. This result is consistent with the MCD data and indicates that Tyr138 is most likely the axial ligand to the heme in Dap1p.