8H28

Crystal structure of the K87V mutant of cytochrome c' from Shewanella benthica DB6705

8H28 の概要

• エントリーDOI: 10.2210/pdb8h28/pdb
• 分子名称: Class II cytochrome c, HEME C (3 entities in total)
• 機能のキーワード: cytochrome c', shewanella benthica, electron transport
• 由来する生物種: Shewanella sp. DB6705
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 29611.38

構造登録者

Fujii, S.,Sakaguchi, R.,Oki, H.,Kawahara, K.,Ohkubo, T.,Fujiyoshi, S.,Sambongi, Y. (登録日: 2022-10-05, 公開日: 2023-10-11, 最終更新日: 2026-03-04)

主引用文献

Fujii, S.,Sakaguchi, R.,Oki, H.,Kawahara, K.,Ohkubo, T.,Fujiyoshi, S.,Sambongi, Y.
Contribution of a surface salt bridge to the protein stability of deep-sea Shewanella benthica cytochrome c'.
J.Struct.Biol., 215:108031-108031, 2023

PubMed Abstract: Two homologous cytochromes c', SBCP and SVCP, from deep-sea Shewanella benthica and Shewanella violacea respectively exhibit only nine surface amino acid substitutions, along with one at the N-terminus. Despite the small sequence difference, SBCP is thermally more stable than SVCP. Here, we examined the thermal stability of SBCP variants, each containing one of the nine substituted residues in SVCP, and found that the SBCP K87V variant was the most destabilized. We then determined the X-ray crystal structure of the SBCP K87V variant at a resolution of 2.1 Å. The variant retains a four-helix bundle structure similar to the wild-type, but notable differences are observed in the hydration structure around the mutation site. Instead of forming of the intrahelical salt bridge between Lys-87 and Asp-91 in the wild-type, a clathrate-like hydration around Val-87 through a hydrogen bond network with the nearby amino acid residues is observed. This network potentially enhances the ordering of surrounding water molecules, leading to an entropic destabilization of the protein. These results suggest that the unfavorable hydrophobic hydration environment around Val-87 and the inability to form the Asp-91-mediated salt bridge contribute to the observed difference in stability between SBCP and SVCP. These findings will be useful in future protein engineering for controlling protein stability through the manipulation of surface intrahelical salt bridges.

PubMed: 37758155
DOI: 10.1016/j.jsb.2023.108031

実験手法

X-RAY DIFFRACTION (2.06 Å)