9C8P

High-resolution structure of cytochrome c peroxidase from yeast at ambient temperature and 3.0 kbar

9C8P の概要

• エントリーDOI: 10.2210/pdb9c8p/pdb
• 関連するPDBエントリー: 9C8L 9C8M 9C8O
• 分子名称: Cytochrome c peroxidase, mitochondrial, PROTOPORPHYRIN IX CONTAINING FE (3 entities in total)
• 機能のキーワード: electron transfer, hydrogen peroxide, high-pressure, diamond anvil cell, peroxidase, cytochrome, heme, oxidoreductase
• 由来する生物種: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 34386.09

構造登録者

Zawistowski, R.K.,Crane, B.R. (登録日: 2024-06-12, 公開日: 2024-10-16, 最終更新日: 2024-10-23)

主引用文献

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

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: 39332669
DOI: 10.1016/j.jmb.2024.168799

実験手法

X-RAY DIFFRACTION (2.31 Å)