5TY3

Crystal structure of K72A variant of Human Cytochrome c

Summary for 5TY3

• Entry DOI: 10.2210/pdb5ty3/pdb
• Descriptor: Cytochrome c, HEME C, SULFATE ION, ... (4 entities in total)
• Functional Keywords: human cytochrome c, oxidoreductase, electron transport
• Biological source: Homo sapiens (Human)
• Cellular location: Mitochondrion intermembrane space: P99999
• Total number of polymer chains: 2
• Total formula weight: 24594.09

Authors

Mou, T.C.,Nold, S.M.,Lei, H.,Sprang, S.R.,Bowler, B.E. (deposition date: 2016-11-18, release date: 2017-09-06, Last modification date: 2024-11-06)

Primary citation

Nold, S.M.,Lei, H.,Mou, T.C.,Bowler, B.E.
Effect of a K72A Mutation on the Structure, Stability, Dynamics, and Peroxidase Activity of Human Cytochrome c.
Biochemistry, 56:3358-3368, 2017

PubMed Abstract: We test the hypothesis that Lys72 suppresses the intrinsic peroxidase activity of human cytochrome c, as observed previously for yeast iso-1-cytochrome c [McClelland, L. J., et al. (2014) Proc. Natl. Acad. Sci. U. S. A. 111, 6648-6653]. A 1.25 Å X-ray structure of K72A human cytochrome c shows that the mutation minimally affects structure. Guanidine hydrochloride denaturation demonstrates that the K72A mutation increases global stability by 0.5 kcal/mol. The K72A mutation also increases the apparent pK of the alkaline transition, a measure of the stability of the heme crevice, by 0.5 unit. Consistent with the increase in the apparent pK, the rate of formation of the dominant alkaline conformer decreases, and this conformer is no longer stabilized by proline isomerization. Peroxidase activity measurements show that the K72A mutation increases k by 1.6-4-fold at pH 7-10, an effect larger than that seen for the yeast protein. X-ray structures of wild type and K72A human cytochrome c indicate that direct interactions of Lys72 with the far side of Ω-loop D, which are seen in X-ray structures of horse and yeast cytochrome c and could suppress peroxidase activity, are lacking. Instead, we propose that the stronger effect of the K72A mutation on the peroxidase activity of human versus yeast cytochrome c results from relief of steric interactions between the side chains at positions 72 and 81 (Ile in human vs Ala in yeast), which suppress the dynamics of Ω-loop D necessary for the intrinsic peroxidase activity of cytochrome c.

PubMed: 28598148
DOI: 10.1021/acs.biochem.7b00342

Experimental method

X-RAY DIFFRACTION (1.25 Å)