6G1Y image
Deposition Date 2018-03-22
Release Date 2018-11-28
Last Version Date 2024-02-07
Entry Detail
PDB ID:
6G1Y
Title:
Crystal structure of the photosensory core module (PCM) of a bathy phytochrome from Agrobacterium fabrum in the Pfr state.
Biological Source:
Method Details:
Experimental Method:
Resolution:
2.50 Å
R-Value Free:
0.24
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 21 21 21
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Bacteriophytochrome protein
Gene (Uniprot):Atu2165
Chain IDs:A
Chain Length:507
Number of Molecules:1
Biological Source:Agrobacterium fabrum (strain C58 / ATCC 33970)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Bacteriophytochrome protein
Gene (Uniprot):Atu2165
Chain IDs:B
Chain Length:507
Number of Molecules:1
Biological Source:Agrobacterium fabrum (strain C58 / ATCC 33970)
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
MLZ A LYS modified residue
Ligand Molecules
Primary Citation
Structural snapshot of a bacterial phytochrome in its functional intermediate state.
Nat Commun 9 4912 4912 (2018)
PMID: 30464203 DOI: 10.1038/s41467-018-07392-7

Abstact

Phytochromes are modular photoreceptors of plants, bacteria and fungi that use light as a source of information to regulate fundamental physiological processes. Interconversion between the active and inactive states is accomplished by a photoinduced reaction sequence which couples the sensor with the output module. However, the underlying molecular mechanism is yet not fully understood due to the lack of structural data of functionally relevant intermediate states. Here we report the crystal structure of a Meta-F intermediate state of an Agp2 variant from Agrobacterium fabrum. This intermediate, the identity of which was verified by resonance Raman spectroscopy, was formed by irradiation of the parent Pfr state and displays significant reorientations of almost all amino acids surrounding the chromophore. Structural comparisons allow identifying structural motifs that might serve as conformational switch for initiating the functional secondary structure change that is linked to the (de-)activation of these photoreceptors.

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Primary Citation of related structures