6T3L

PAS-GAF fragment from Deinococcus radiodurans phytochrome in dark state

Summary for 6T3L

• Entry DOI: 10.2210/pdb6t3l/pdb
• Descriptor: Bacteriophytochrome, 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid (3 entities in total)
• Functional Keywords: kinase, photosensor, transferase, phytochrome
• Biological source: Deinococcus radiodurans
• Total number of polymer chains: 2
• Total formula weight: 75630.25

Authors

Claesson, E.,Takala, H.,Yuan Wahlgren, W.,Pandey, S.,Schmidt, M.,Westenhoff, S. (deposition date: 2019-10-11, release date: 2020-04-08, Last modification date: 2024-11-13)

Primary citation

Claesson, E.,Wahlgren, W.Y.,Takala, H.,Pandey, S.,Castillon, L.,Kuznetsova, V.,Henry, L.,Panman, M.,Carrillo, M.,Kubel, J.,Nanekar, R.,Isaksson, L.,Nimmrich, A.,Cellini, A.,Morozov, D.,Maj, M.,Kurttila, M.,Bosman, R.,Nango, E.,Tanaka, R.,Tanaka, T.,Fangjia, L.,Iwata, S.,Owada, S.,Moffat, K.,Groenhof, G.,A Stojkovic, E.,A Ihalainen, J.,Schmidt, M.,Westenhoff, S.
The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser.
Elife, 9:-, 2020

PubMed Abstract: Phytochrome proteins control the growth, reproduction, and photosynthesis of plants, fungi, and bacteria. Light is detected by a bilin cofactor, but it remains elusive how this leads to activation of the protein through structural changes. We present serial femtosecond X-ray crystallographic data of the chromophore-binding domains of a bacterial phytochrome at delay times of 1 ps and 10 ps after photoexcitation. The data reveal a twist of the D-ring, which leads to partial detachment of the chromophore from the protein. Unexpectedly, the conserved so-called pyrrole water is photodissociated from the chromophore, concomitant with movement of the A-ring and a key signaling aspartate. The changes are wired together by ultrafast backbone and water movements around the chromophore, channeling them into signal transduction towards the output domains. We suggest that the observed collective changes are important for the phytochrome photoresponse, explaining the earliest steps of how plants, fungi and bacteria sense red light.

PubMed: 32228856
DOI: 10.7554/eLife.53514

Experimental method

X-RAY DIFFRACTION (2.07 Å)