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TitleStructures of myxobacterial phytochrome revealed by cryo-EM using the Spotiton technique and with x-ray crystallography.
Journal, issue, pagesStruct Dyn, Vol. 12, Issue 3, Page 034701, Year 2025
Publish dateMay 1, 2025
AuthorsPrabin Karki / David Menendez / William Budell / Shishir Dangi / Carolina Hernandez / Joshua Mendez / Srinivasan Muniyappan / Shibom Basu / Peter Schwander / Tek N Malla / Emina A Stojković / Marius Schmidt /
PubMed AbstractPhytochromes 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 ...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.
External linksStruct Dyn / PubMed:40322674 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.1 - 6.0 Å
Structure data

EMDB-70119: Pr/Pr homodimer of Stigmatella aurantiaca bacteriophytochrome 2
Method: EM (single particle) / Resolution: 6.0 Å

PDB-9naa:
Unusual structure of a bacteriophytochrome fragment derived from full length SaBphP2
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

Chemicals

ChemComp-EL5:
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

ChemComp-HOH:
WATER

Source
  • stigmatella aurantiaca (bacteria)
KeywordsSIGNALING PROTEIN / phytochrome / myxobacteria / biliverdin

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