7MRI

Crystal structure of N63T yeast iso-1-cytochrome c

Summary for 7MRI

• Entry DOI: 10.2210/pdb7mri/pdb
• Descriptor: Cytochrome c isoform 1, HEME C (3 entities in total)
• Functional Keywords: peroxidase activity, electron transport chain, electron transport
• Biological source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
• Total number of polymer chains: 3
• Total formula weight: 37686.51

Authors

Lei, H.,Bowler, B.E.,Evenson, G.E. (deposition date: 2021-05-07, release date: 2022-05-11, Last modification date: 2024-10-30)

Primary citation

Frederick, A.K.,Thompson, S.L.,Vakharia, Z.M.,Cherney, M.M.,Lei, H.,Evenson, G.,Bowler, B.E.
Effect on intrinsic peroxidase activity of substituting coevolved residues from Omega-loop C of human cytochrome c into yeast iso-1-cytochrome c.
J.Inorg.Biochem., 232:111819-111819, 2022

PubMed Abstract: Naturally-occurring variants of human cytochrome c (Cytc) that induce thrombocytopenia IV occur within Ω-loop C (residues 40-57). These variants enhance the peroxidase activity of human Cytc apparently by facilitating access to the heme by destabilizing Ω-loops C and D (residues 70-85). Given the importance of peroxidase activity in the early stages of apoptosis, we identified three sites with the EVmutation algorithm in or near Ω-loop C that coevolve and differ between yeast iso-1-Cytc and human Cytc. We prepared iso-1-Cytc variants with all possible combinations of the S40T, V57I and N63T substitutions to determine if these residues decrease the peroxidase activity of iso-1-Cytc to that of human Cytc producing an effective off state for a peroxidase signaling switch. At pH 6 and above, all variants significantly decreased peroxidase activity. However, the correlation of peroxidase activity with local and global stability, expected if cooperative unfolding of Ω-loops C and D is required for peroxidase activity, was generally poor. The m-values derived from the guanidine hydrochloride dependence of the kinetics of imidazole binding to horse Cytc, which is well-characterized by native-state hydrogen exchange methods, and K72A/K73A/K79A iso-1-Cytc show that local structural fluctuations and not subglobal cooperative unfolding of Ω-loops C and D are sufficient to permit binding of a small molecule like peroxide to the heme. A 2.46 Å structure of N63T iso-1-Cytc identifies a change to a hydrogen bond network linking Ω-loops C and D that could modulate the local fluctuations needed for the intrinsic peroxidase activity of Cytc.

PubMed: 35428021
DOI: 10.1016/j.jinorgbio.2022.111819

Experimental method

X-RAY DIFFRACTION (2.46 Å)