6FTD

Deinococcus radiodurans BphP PAS-GAF H290T mutant

6FTD の概要

• エントリーDOI: 10.2210/pdb6ftd/pdb
• 分子名称: Bacteriophytochrome, ACETATE ION, (4S)-2-METHYL-2,4-PENTANEDIOL, ... (5 entities in total)
• 機能のキーワード: kinase, photosensor, transferase, phytochrome
• 由来する生物種: Deinococcus radiodurans R1
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 76146.77

構造登録者

Edlund, P.,Takala, H.,Westenhoff, S.,Ihalainen, J.A. (登録日: 2018-02-21, 公開日: 2018-07-18, 最終更新日: 2024-10-23)

主引用文献

Lenngren, N.,Edlund, P.,Takala, H.,Stucki-Buchli, B.,Rumfeldt, J.,Peshev, I.,Hakkanen, H.,Westenhoff, S.,Ihalainen, J.A.
Coordination of the biliverdin D-ring in bacteriophytochromes.
Phys Chem Chem Phys, 20:18216-18225, 2018

PubMed Abstract: Phytochrome proteins translate light into biochemical signals in plants, fungi and microorganisms. Light cues are absorbed by a bilin chromophore, leading to an isomerization and a rotation of the D-ring. This relays the signal to the protein matrix. A set of amino acids, which is conserved across the phytochrome superfamily, holds the chromophore in the binding pocket. However, the functional role of many of these amino acids is not yet understood. Here, we investigate the hydrogen bonding network which surrounds the D-ring of the chromophore in the resting (Pr) state. We use UV/vis spectroscopy, infrared absorption spectroscopy and X-ray crystallography to compare the photosensory domains from Deinococcus radiodurans, the phytochrome 1 from Stigmatella aurantiaca, and a D. radiodurans H290T mutant. In the latter two, an otherwise conserved histidine next to the D-ring is replaced by a threonine. Our infrared absorption data indicate that the carbonyl of the D-ring is more strongly coordinated by hydrogen bonds when the histidine is missing. This is in apparent contrast with the crystal structure of the PAS-GAF domain of phytochrome 1 from S. aurantiaca (pdb code 4RPW), which did not resolve any obvious binding partners for the D-ring carbonyl. We present a new crystal structure of the H290T mutant of the PAS-GAF from D. radiodurans phytochrome. The 1.4 Å-resolution structure reveals additional water molecules, which fill the void created by the mutation. Two of the waters are significantly disordered, suggesting that flexibility might be important for the photoconversion. Finally, we report a spectral analysis which quantitatively explains why the histidine-less phytochromes do not reach equal Pfr-type absorption in the photoequilibrium compared to the Deinococcus radiodurans wild-type protein. The study highlights the importance of water molecules and the hydrogen bonding network around the chromophore for controlling the isomerization reaction and spectral properties of phytochromes.

PubMed: 29938729
DOI: 10.1039/c8cp01696h

実験手法

X-RAY DIFFRACTION (1.4 Å)