9C8P
High-resolution structure of cytochrome c peroxidase from yeast at ambient temperature and 3.0 kbar
Summary for 9C8P
| Entry DOI | 10.2210/pdb9c8p/pdb |
| Related | 9C8L 9C8M 9C8O |
| Descriptor | Cytochrome c peroxidase, mitochondrial, PROTOPORPHYRIN IX CONTAINING FE (3 entities in total) |
| Functional Keywords | electron transfer, hydrogen peroxide, high-pressure, diamond anvil cell, peroxidase, cytochrome, heme, oxidoreductase |
| Biological source | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) |
| Total number of polymer chains | 1 |
| Total formula weight | 34386.09 |
| Authors | Zawistowski, R.K.,Crane, B.R. (deposition date: 2024-06-12, release date: 2024-10-16, Last modification date: 2024-10-23) |
| Primary citation | Zawistowski, R.K.,Crane, B.R. Differential Responses in the Core, Active Site and Peripheral Regions of Cytochrome c Peroxidase to Extreme Pressure and Temperature. J.Mol.Biol., 436:168799-168799, 2024 Cited by PubMed Abstract: In consideration of life in extreme environments, the effects of hydrostatic pressure on proteins at the atomic level have drawn substantial interest. Large deviations of temperature and pressure from ambient conditions can shift the free energy landscape of proteins to reveal otherwise lowly populated structural states and even promote unfolding. We report the crystal structure of the heme-containing peroxidase, cytochrome c peroxidase (CcP) at 1.5 and 3.0 kbar and make comparisons to structures determined at 1.0 bar and cryo-temperatures (100 K). Pressure produces anisotropic changes in CcP, but compressibility plateaus after 1.5 kbar. CcP responds to pressure with volume declines at the periphery of the protein where B-factors are relatively high but maintains nearly intransient core structure, hydrogen bonding interactions and active site channels. Changes in active-site solvation and heme ligation reveal pressure sensitivity to protein-ligand interactions and a potential docking site for the substrate peroxide. Compression at the surface affects neither alternate side-chain conformers nor B-factors. Thus, packing in the core, which resembles a crystalline solid, limits motion and protects the active site, whereas looser packing at the surface preserves side-chain dynamics. These data demonstrate that conformational dynamics and packing densities are not fully correlated in proteins and that encapsulation of cofactors by the polypeptide can provide a precisely structured environment resistant to change across a wide range of physical conditions. PubMed: 39332669DOI: 10.1016/j.jmb.2024.168799 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.31 Å) |
Structure validation
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