Ground state structure of D75N mutant of sensory rhodopsin II in complex with its cognate transducer

Abstract

International audienceThe complex of sensory rhodopsin II (NpSRII) with its cognate transducer (NpHtrII) mediates negative phototaxis in halobacteria Natronomonas pharaonis. Upon light activation NpSRII triggers, by means of NpHtrII, a signal transduction chain homologous to the two component system in eubacterial chemotaxis. Here we report on the crystal structure of the ground state of the mutant NpSRII-D75N/NpHtrII complex in the space group I212121. Mutations of this aspartic acid in light-driven proton pumps dramatically modify or/and inhibit protein functions. However, in vivo studies show that the similar D75N mutation retains functionality of the NpSRII/NpHtrII complex. The structure provides the molecular basis for the explanation of the unexpected observation that the wild and the mutant complexes display identical physiological response on light excitation

Sensory Rhodopsin I and Sensory Rhodopsin II Form Trimers of Dimers in Complex with their Cognate Transducers

“…The third normal mode largely overlaps with the PC1 of PCA analysis. This motional mode is of special interest as it closely resembles the transition between the “U”‐ and “V”‐shaped conformations of the Np SRII: Np HtrII complex, which was previously argued to represent a functionally relevant global conformational change accompanying the activation process . Indeed, the histogram of the trajectory projection on the PC1 as well as the histograms of the intermonomer SRII‐SRII angle (between helices F) and distance (between the COMs of the cytoplasmic segment of helix F in both monomers) distributions are clearly bimodal indicating the presence of two conformations.…”

Sensory Rhodopsin I and Sensory Rhodopsin II Form Trimers of Dimers in Complex with their Cognate Transducers

“…The third normal mode largely overlaps with the PC1 of PCA analysis. This motional mode is of special interest as it closely resembles the transition between the “U”‐ and “V”‐shaped conformations of the Np SRII: Np HtrII complex, which was previously argued to represent a functionally relevant global conformational change accompanying the activation process . Indeed, the histogram of the trajectory projection on the PC1 as well as the histograms of the intermonomer SRII‐SRII angle (between helices F) and distance (between the COMs of the cytoplasmic segment of helix F in both monomers) distributions are clearly bimodal indicating the presence of two conformations.…”

Signaling and Adaptation Modulate the Dynamics of the Photosensoric Complex of Natronomonas pharaonis

“…This shift caused a tilt of the whole dimer and corresponds to the minimum of the free energy for the isolated inter-HAMP region [ 51 ]. Second, both sensory rhodopsins underwent a motion in the transmembrane region resembling the U-V shape transition observed in recent X-ray structures [ 12 ]. This rearrangement preserves most contacts between Np SRII and Np HtrII and could provide a route for receptor cross-talk in the dense membrane lattice which might be physiologically relevant.…”

A Large and Phylogenetically Diverse Class of Type 1 Opsins Lacking a Canonical Retinal Binding Site

“…Conversely, residues involved in sensory signaling are conserved in one or both ORP clades. Y51 and R72, which together form a water-mediated hydrogen-bond complex important in propagation of signal to the linked signal transducer [ 31 ], are highly conserved in group B, but not group A ORPs. Y199, which forms a hydrogen bond with the signal transducer in Natronomonas pharaonis SRII [ 32 ], is universally conserved across the ORP clade.…”

Sensory Rhodopsin I and Sensory Rhodopsin II Form Trimers of Dimers in Complex with their Cognate Transducers

“…The third normal mode largely overlaps with the PC1 of PCA analysis. This motional mode is of special interest as it closely resembles the transition between the “U”‐ and “V”‐shaped conformations of the Np SRII: Np HtrII complex, which was previously argued to represent a functionally relevant global conformational change accompanying the activation process . Indeed, the histogram of the trajectory projection on the PC1 as well as the histograms of the intermonomer SRII‐SRII angle (between helices F) and distance (between the COMs of the cytoplasmic segment of helix F in both monomers) distributions are clearly bimodal indicating the presence of two conformations.…”

Signaling and Adaptation Modulate the Dynamics of the Photosensoric Complex of Natronomonas pharaonis

“…This shift caused a tilt of the whole dimer and corresponds to the minimum of the free energy for the isolated inter-HAMP region [ 51 ]. Second, both sensory rhodopsins underwent a motion in the transmembrane region resembling the U-V shape transition observed in recent X-ray structures [ 12 ]. This rearrangement preserves most contacts between Np SRII and Np HtrII and could provide a route for receptor cross-talk in the dense membrane lattice which might be physiologically relevant.…”

A Large and Phylogenetically Diverse Class of Type 1 Opsins Lacking a Canonical Retinal Binding Site

“…Conversely, residues involved in sensory signaling are conserved in one or both ORP clades. Y51 and R72, which together form a water-mediated hydrogen-bond complex important in propagation of signal to the linked signal transducer [ 31 ], are highly conserved in group B, but not group A ORPs. Y199, which forms a hydrogen bond with the signal transducer in Natronomonas pharaonis SRII [ 32 ], is universally conserved across the ORP clade.…”

Sensory Rhodopsin I and Sensory Rhodopsin II Form Trimers of Dimers in Complex with their Cognate Transducers

“…The third normal mode largely overlaps with the PC1 of PCA analysis. This motional mode is of special interest as it closely resembles the transition between the “U”‐ and “V”‐shaped conformations of the Np SRII: Np HtrII complex, which was previously argued to represent a functionally relevant global conformational change accompanying the activation process . Indeed, the histogram of the trajectory projection on the PC1 as well as the histograms of the intermonomer SRII‐SRII angle (between helices F) and distance (between the COMs of the cytoplasmic segment of helix F in both monomers) distributions are clearly bimodal indicating the presence of two conformations.…”

Signaling and Adaptation Modulate the Dynamics of the Photosensoric Complex of Natronomonas pharaonis

“…This shift caused a tilt of the whole dimer and corresponds to the minimum of the free energy for the isolated inter-HAMP region [ 51 ]. Second, both sensory rhodopsins underwent a motion in the transmembrane region resembling the U-V shape transition observed in recent X-ray structures [ 12 ]. This rearrangement preserves most contacts between Np SRII and Np HtrII and could provide a route for receptor cross-talk in the dense membrane lattice which might be physiologically relevant.…”

A Large and Phylogenetically Diverse Class of Type 1 Opsins Lacking a Canonical Retinal Binding Site

“…Conversely, residues involved in sensory signaling are conserved in one or both ORP clades. Y51 and R72, which together form a water-mediated hydrogen-bond complex important in propagation of signal to the linked signal transducer [ 31 ], are highly conserved in group B, but not group A ORPs. Y199, which forms a hydrogen bond with the signal transducer in Natronomonas pharaonis SRII [ 32 ], is universally conserved across the ORP clade.…”