High-resolution Crystal Structures of Transient Intermediates in the Phytochrome Photocycle

Carrillo, Melissa; Pandey, Suraj; Sanchez, Juan; Noda, Moraima; Poudyal, Ishwor; Aldama, Luis; Malla, Tek Narsingh; Claesson, Elin; Wahlgren, Weixiao Yuan; Feliz, Denisse; Šrajer, V.; Maj, Michał; Castillon, Leticia; Iwata, So; Nango, Eriko; Tanaka, Rie; Tanaka, Tomoyuki; Fangjia, Luo; Tono, Kensuke; Owada, Shigeki; Westenhoff, Sebastian; Stojković, Emina A.; Schmidt, Marius

doi:10.1101/2020.09.16.298463

Cited by 4 publications

(4 citation statements)

References 67 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To follow the bending of FAD in our structures, and avoid model bias, the dihedral angles for all structures, as listed in Table 1, were calculated by adapting previous real space correlation methods established for the analysis of TR-SFX data as it applies to subtle changes in photoreceptor chromophores 36,64,65 . Briefly, an equilibrium ensemble for the FAD redox dependent conformational space was computationally generated based on the Eox/ss, Esemi/ss and Ered/ss datasets, from which minimum and maximum ρC and ρN values (Fig.…”

Section: Refinement Of the Fad Isoalloxazine Moiety And Its Conformat...mentioning

confidence: 99%

Serial crystallography captures dynamic control of sequential electron and proton transfer events in a flavoenzyme

et al. 2022

Self Cite

View full text Add to dashboard Cite

Flavin coenzymes are universally found in biological redox reactions. DNA photolyases with their flavin chromophore (FAD) utilize blue light for DNA repair and photoreduction. The latter process involves two single-electron transfers to FAD with an intermittent protonation step to prime the enzyme active for DNA repair. Here we use time-resolved serial femtosecond X-ray crystallography to describe how light-driven electron transfers trigger subsequent nanosecond-to-microsecond entanglement between FAD and its Asn/Arg-Asp redox sensor triad. We found that this key feature within the photolyase-cryptochrome family regulates FAD re-hybridization and protonation. After first electron transfer, the FAD •isoalloxazine ring twists strongly when the arginine closes in to stabilize the negative charge. Subsequent breakage of the arginine-aspartate salt bridge promotes proton transfer from arginine to FAD •-. Our molecular movies demonstrate how the protein environment of redox cofactors organizes multiple electron/proton transfer events in an ordered fashion, which could be applicable to other redox systems such as photosynthesis.

show abstract

Section: Refinement Of the Fad Isoalloxazine Moiety And Its Conformat...mentioning

confidence: 99%

Serial crystallography captures dynamic control of sequential electron and proton transfer events in a flavoenzyme

et al. 2022

Self Cite

View full text Add to dashboard Cite

show abstract

“…The majority of published phytochrome structures involve homodimers in parallel and antiparallel configurations, captured in the dark-adapted state (Pr for classical and Pfr for bathy phytochromes) (15,(25)(26)(27). A limited number of light-illuminated structures captured in the Pfr state show homodimers but involve modified proteins created by the deletion of the entire enzymatic domain (27), C-terminal fusions to stabilize full-length proteins (24), and/or mutations to slow down dark reversion during crystallization (25).…”

Section: Discussionmentioning

confidence: 99%

“…1C). This drives the phytochrome into the first half of the photocycle (25)(26)(27)(28). The sensory tongue of the PHY domain (Fig.…”

Section: Introductionmentioning

confidence: 99%

Photoreception and signaling in bacterial phytochrome revealed by single-particle cryo-EM

Malla,

Hernandez,

Muniyappan

et al. 2024

Sci. Adv.

View full text Add to dashboard Cite

Phytochromes are red-light photoreceptors discovered in plants with homologs in bacteria and fungi that regulate a variety of physiological responses. They display a reversible photocycle between two distinct states: a red-light–absorbing Pr state and a far-red light–absorbing Pfr state. The photoconversion regulates the activity of an enzymatic domain, usually a histidine kinase (HK). The molecular mechanism that explains how light controls the HK activity is not understood because structures of unmodified bacterial phytochromes with HK activity are missing. Here, we report three cryo–electron microscopy structures of a wild-type bacterial phytochrome with HK activity determined as Pr and Pfr homodimers and as a Pr/Pfr heterodimer with individual subunits in distinct states. We propose that the Pr/Pfr heterodimer is a physiologically relevant signal transduction intermediate. Our results offer insight into the molecular mechanism that controls the enzymatic activity of the HK as part of a bacterial two-component system that perceives and transduces light signals.

show abstract

“…These motions are accompanied by ultrafast backbone and water movements around the bilin, which allow the PHY tongue to alter its conformation and trigger the photoresponse. Further TR-SFX data collected after 5 ns and 33 ms on another bacteriophytochrome from Stigmatella aurantiaca has provided important insights into the displacement of the covalently bound bilin chromophore (121). It was suggested that rearrangement of the water network and amino acid residues in the bilin binding pocket, together with changes at the dimeric interface, aid the propagation of the signal towards the PHY domains.…”

Section: Accepted Articlementioning

confidence: 99%

A guide to time‐resolved structural analysis of light‐activated proteins

et al. 2021

View full text Add to dashboard Cite

Dynamical changes in protein structures are essential for protein function and occur over femtoseconds to seconds timescales. X-ray free electron lasers have facilitated investigations of structural dynamics in proteins with unprecedented temporal and spatial resolution. Lightactivated proteins are attractive targets for time-resolved structural studies, as the reaction chemistry and associated protein structural changes can be triggered by short laser pulses. Proteins with different light-absorbing centres have evolved to detect light and harness photon energy to bring about downstream chemical and biological output responses. Following light-absorption, rapid chemical/small-scale structural changes are typically localised around the chromophore. These localised changes are followed by larger structural changes propagated throughout the photoreceptor/photocatalyst that enable the desired chemical and/or biological output response. Time-resolved serial-femtosecond crystallography (SFX) and solution scattering techniques enable direct visualisation of early chemical change in light-activated proteins on timescales previously inaccessible, whereas scattering gives access to slower timescales associated with more global structural change. Here, we review how advances in time-resolved SFX and solution scattering techniques have uncovered mechanisms of photochemistry and its coupling to output responses. We also provide a prospective on how these time-resolved structural approaches might impact on other photoreceptors/photoenzymes that have not yet been studied by these methods.

show abstract

High-resolution Crystal Structures of Transient Intermediates in the Phytochrome Photocycle

Cited by 4 publications

References 67 publications

Serial crystallography captures dynamic control of sequential electron and proton transfer events in a flavoenzyme

Serial crystallography captures dynamic control of sequential electron and proton transfer events in a flavoenzyme

Photoreception and signaling in bacterial phytochrome revealed by single-particle cryo-EM

A guide to time‐resolved structural analysis of light‐activated proteins

Contact Info

Product

Resources

About