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Development of the signal in sensory rhodopsin and its transfer to the cognate transducer

Abstract

The microbial phototaxis receptor sensory rhodopsin II (NpSRII, also named phoborhodopsin) mediates the photophobic response of the haloarchaeon Natronomonas pharaonis1,2 by modulating the swimming behaviour of the bacterium3. After excitation by blue-green light NpSRII triggers, by means of a tightly bound transducer protein (NpHtrII), a signal transduction chain homologous with the two-component system of eubacterial chemotaxis4. Two molecules of NpSRII and two molecules of NpHtrII form a 2:2 complex in membranes as shown by electron paramagnetic resonance5 and X-ray structure analysis6. Here we present X-ray structures of the photocycle intermediates K and late M (M2) explaining the evolution of the signal in the receptor after retinal isomerization and the transfer of the signal to the transducer in the complex. The formation of late M has been correlated with the formation of the signalling state2,7. The observed structural rearrangements allow us to propose the following mechanism for the light-induced activation of the signalling complex. On excitation by light, retinal isomerization leads in the K state to a rearrangement of a water cluster that partly disconnects two helices of the receptor. In the transition to late M the changes in the hydrogen bond network proceed further. Thus, in late M state an altered tertiary structure establishes the signalling state of the receptor. The transducer responds to the activation of the receptor by a clockwise rotation of about 15° of helix TM2 and a displacement of this helix by 0.9 Å at the cytoplasmic surface.

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Figure 1: Crystal structure of the complex and its spectroscopic characterization.
Figure 2: Structural changes in the extracellular vicinity of the retinal Schiff base.
Figure 3: Interhelical interactions.
Figure 4: Overall views of helices F, G, TM1 and TM2 in ground and late M states.

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Acknowledgements

We thank K.-E. Jaeger and H. Gieren for their help in expressing NpSRII; G. Kachalova, J. Granzin and J. Heberle for scientific discussions; B. Gehrmann for administrative assistance; the staff of beamlines ID14-1 and ID13, in particular E. Mitchell; and the staff of beamline X13 at DESY, in particular W. R. Rypniewski. This study was supported by the Deutsche Forschungsgemeinschaft, the Max-Planck-Gesellschaft, the Alexander von Humboldt Foundation and the Helmholtz Association of National Research Centres.

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Correspondence to Martin Engelhard or Georg Büldt.

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The coordinates for these structures have been deposited in the Protein Data Bank under accession codes 2F93 and 2F95. Reprints and permissions information is available at npg.nature.com/reprintsandpermissions. The authors declare no competing financial interests.

Supplementary information

Supplementary Figure 1

Stereo views of details of interhelical interactions. Changes in helical structure and interactions between ground state and late M-state. (PDF 719 kb)

Supplementary Figure 2

Double distance matrix for Cα atoms of the complex between late M-state and ground state. Double distances (in Å) between two Cα atoms in the structure of the complex are calculated by subtracting the distances between these Cα atoms in the structure of the ground state from those in late M-state. (PDF 788 kb)

Supplementary Figure 3

Significance of structural changes. The significance of structural changes between ground and late M-state is investigated refining data sets of 9 different crystals. Distances between Cα atoms of two models (ground and late M-state) of each refinement are calculated. (PDF 172 kb)

Supplementary Methods

Characterization of M-state. The amount of M1 and M2 in crystals of NpSRII/NpHtrII at 100 K was determined by flash-photolysis experiments at 25°C and characteristic cooling rates. (PDF 42 kb)

Supplementary Table 1

X-ray crystallographic data. Data collection and refinement statistics (Molecular replacement) (PDF 52 kb)

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Moukhametzianov, R., Klare, J., Efremov, R. et al. Development of the signal in sensory rhodopsin and its transfer to the cognate transducer. Nature 440, 115–119 (2006). https://doi.org/10.1038/nature04520

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