9NAA

Unusual structure of a bacteriophytochrome fragment derived from full length SaBphP2

Summary for 9NAA

• Entry DOI: 10.2210/pdb9naa/pdb
• Descriptor: histidine kinase, 3-[(2Z)-2-({3-(2-carboxyethyl)-5-[(E)-(4-ethenyl-3-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-2-yl}methylidene)-5-{(Z)-[(3E,4S)-3-ethylidene-4-methyl-5-oxopyrrolidin-2-ylidene]methyl}-4-methyl-2H-pyrrol-3-yl]propanoic acid (3 entities in total)
• Functional Keywords: phytochrome, myxobacteria, biliverdin, signaling protein
• Biological source: Stigmatella aurantiaca
• Total number of polymer chains: 2
• Total formula weight: 66116.39

Authors

Schmidt, M.,Prabin, K. (deposition date: 2025-02-11, release date: 2025-05-14)

Primary citation

Karki, P.,Menendez, D.,Budell, W.,Dangi, S.,Hernandez, C.,Mendez, J.,Muniyappan, S.,Basu, S.,Schwander, P.,Malla, T.N.,Stojkovic, E.A.,Schmidt, M.
Structures of myxobacterial phytochrome revealed by cryo-EM using the Spotiton technique and with x-ray crystallography.
Struct Dyn., 12:034701-034701, 2025

PubMed Abstract: Phytochromes are red-light photoreceptors first identified in plants, with homologs found in bacteria and fungi, that regulate a variety of critical physiological processes. They undergo a reversible photocycle between two distinct states: a red-light-absorbing Pr form and a far-red light-absorbing Pfr form. This Pr/Pfr photoconversion controls the activity of a C-terminal enzymatic domain, typically a histidine kinase (HK). However, the molecular mechanisms underlying light-induced regulation of HK activity in bacteria remain poorly understood, as only a few structures of unmodified bacterial phytochromes with HK activity are known. Recently, cryo-EM structures of a wild-type bacterial phytochrome with HK activity are solved that reveal homodimers in both the Pr and Pfr states, as well as a heterodimer with individual monomers in distinct Pr and Pfr states. Cryo-EM structures of a truncated version of the same phytochrome-lacking the HK domain-also show a homodimer in the Pfr state and a Pr/Pfr heterodimer. Here, we describe in detail how structural information is obtained from cryo-EM data on a full-length intact bacteriophytochrome, and how the cryo-EM structure can contribute to the understanding of the function of the phytochrome. In addition, we compare the cryo-EM structure to an unusual x-ray structure that is obtained from a fragmented full-length phytochrome crystallized in the Pr-state.

PubMed: 40322674
DOI: 10.1063/4.0000301

Experimental method

X-RAY DIFFRACTION (2.1 Å)