9G8C

Crystal structure of the photosensory core module (PCM) of a cyano-phenylalanine mutant oCNF165 of the bathy phytochrome Agp2 from Agrobacterium fabrum in the Pfr state.

Summary for 9G8C

• Entry DOI: 10.2210/pdb9g8c/pdb
• Related: 6G1Y 6G1Z 6G20 8RJM 8RJN 8RJO 8RJP 8RJQ 8RJR 8RJS 8RJT 8RJU 9G8D
• Descriptor: histidine kinase, HEXAETHYLENE GLYCOL, (4S)-2-METHYL-2,4-PENTANEDIOL, ... (8 entities in total)
• Functional Keywords: fluorescent protein, phytochrome, bacteriophytochrome, pfr-state, ortho-cyano-phenylalanine, stark labels, signaling protein
• Biological source: Agrobacterium fabrum str. C58; More
• Total number of polymer chains: 2
• Total formula weight: 115765.57

Authors

Sauthof, L.,Schmidt, A.,Scheerer, P. (deposition date: 2024-07-23, release date: 2024-11-27, Last modification date: 2024-12-11)

Primary citation

Nguyen, A.D.,Michael, N.,Sauthof, L.,von Sass, J.,Hoang, O.T.,Schmidt, A.,La Greca, M.,Schlesinger, R.,Budisa, N.,Scheerer, P.,Mroginski, M.A.,Kraskov, A.,Hildebrandt, P.
Hydrogen Bonding and Noncovalent Electric Field Effects in the Photoconversion of a Phytochrome.
J.Phys.Chem.B, 128:11644-11657, 2024

PubMed Abstract: A profound understanding of protein structure and mechanism requires dedicated experimental and theoretical tools to elucidate electrostatic and hydrogen bonding interactions in proteins. In this work, we employed an approach to disentangle noncovalent and hydrogen-bonding electric field changes during the reaction cascade of a multidomain protein, i.e., the phytochrome Agp2. The approach exploits the spectroscopic properties of nitrile probes commonly used as reporter groups of the vibrational Stark effect. These probes were introduced into the protein through site-specific incorporation of noncanonical amino acids resulting in four variants with different positions and orientations of the nitrile groups. All substitutions left structures and the reaction mechanism unchanged. Structural models of the dark states (Pfr) were used to evaluate the total electric field at the nitrile label and its transition dipole moment. These quantities served as an internal standard to calculate the respective properties of the photoinduced products (Lumi-F, Meta-F, and Pr) based on the relative intensities of the nitrile stretching bands. In most cases, the spectral analysis revealed two substates with a nitrile in a hydrogen-bonded or hydrophobic environment. Using frequencies and intensities, we managed to extract the noncovalent contribution of the electric field from the individual substates. This analysis resulted in profiles of the noncovalent and hydrogen-bond-related electric fields during the photoinduced reaction cascade of Agp2. These profiles, which vary significantly among the four variants due to the different positions and orientations of the nitrile probes, were discussed in the context of the molecular events along the Pfr → Pr reaction cascade.

PubMed: 39561028
DOI: 10.1021/acs.jpcb.4c06419

Experimental method

X-RAY DIFFRACTION (1.9 Å)