Crystal Structure of the Light-Driven Chloride Pump Halorhodopsin from Natronomonas pharaonis

Kouyama, Tsutomu; Kanada, Sachie; Takeguchi, Yuu; Narusawa, Akihiro; Murakami, Midori; Ihara, Kenji

doi:10.1016/j.jmb.2009.11.061

Cited by 130 publications

(195 citation statements)

References 64 publications

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“…The r.m.s.d. values between the NM-R3 structure and the two HR structures, HR from Halobacterium salinarum (hHR, PDB code 1E12, 20.6% sequence identity) and HR from Natronomonas pharaonis (nHR, PDB code 3A7K, 19.9% sequence identity), were 4.1 and 3.9 Å, respectively (13,14). Although the structures of the TM regions and the active sites, as well as the positions of the protonated Schiff bases, were similar between NM-R3 and bacteriorhodopsin or HRs, the loop and short N-and C-terminal helix regions adopt quite different structures.…”

Section: Resultsmentioning

confidence: 99%

“…Construction of Plasmids-A codon-optimized NM-R3 gene, originating from the marine flavobacterium N. marinus strain 5), K. eikastus light-driven sodium pump rhodopsin 2 (KR2) (PDB code 3X3B) (15), hHR (PDB code 1E12) (13), nHR (PDB code 3A7K) (14), and bacteriorhodopsin from Halobacterium salinarum R1 (BR) (PDB code 1C3W) (31) were used for comparison. The numbers shown in the right or upper column represent the positions of amino acid residues.…”

Section: Methodsmentioning

confidence: 99%

“…In the bacteriorhodopsin (DTD motif), Asp-85 and Asp-96 work as the H ϩ acceptor and donor, respectively, and these carboxyl groups play key roles in H ϩ translocation (11,12). In HR, Thr and Ser (corresponding to Asp-85 and Thr-89 in bacteriorhodopsin, respectively) interact with Cl Ϫ (13,14). In addition, recent studies showed that Asp-116 of KR2 (corresponding to Thr-89 in bacteriorhodopsin) works as an H ϩ acceptor, and the protonation of Asp-116 is a critical step for Na ϩ translocation (10,15 residues located at positions 85, 89, and 96 (bacteriorhodopsin numbering) play crucial roles in differentiating the specificity of the ion pumping activity.…”

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confidence: 99%

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Structural Mechanism for Light-driven Transport by a New Type of Chloride Ion Pump, Nonlabens marinus Rhodopsin-3

Hosaka

Yoshizawa

Nakajima

et al. 2016

Journal of Biological Chemistry

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The light-driven inward chloride ion-pumping rhodopsin Nonlabens marinus rhodopsin-3 (NM-R3), from a marine flavobacterium, belongs to a phylogenetic lineage distinct from the halorhodopsins known as archaeal inward chloride ion-pumping rhodopsins. NM-R3 and halorhodopsin have distinct motif sequences that are important for chloride ion binding and transport. In this study, we present the crystal structure of a new type of light-driven chloride ion pump, NM-R3, at 1.58 Å resolution. The structure revealed the chloride ion translocation pathway and showed that a single chloride ion resides near the Schiff base. The overall structure, chloride ion-binding site, and translocation pathway of NM-R3 are different from those of halorhodopsin. Unexpectedly, this NM-R3 structure is similar to the crystal structure of the light-driven outward sodium ion pump, Krokinobacter eikastus rhodopsin 2. Structural and mutational analyses of NM-R3 revealed that most of the important amino acid residues for chloride ion pumping exist in the ion influx region, located on the extracellular side of NM-R3. In contrast, on the opposite side, the cytoplasmic regions of K. eikastus rhodopsin 2 were reportedly important for sodium ion pumping. These results provide new insight into ion selection mechanisms in ion pumping rhodopsins, in which the ion influx regions of both the inward and outward pumps are important for their ion selectivities.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

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Structural Mechanism for Light-driven Transport by a New Type of Chloride Ion Pump, Nonlabens marinus Rhodopsin-3

Hosaka

Yoshizawa

Nakajima

et al. 2016

Journal of Biological Chemistry

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“…In our models, Lys-257 results in the correct position to be covalently bound to the retinal forming a Schiff base, which is in line with current evidence. The aromatic residues surrounding the retinal are Trp-124, Phe-178, Tyr-184, Trp-223, Phe-226, and Phe-230 (supplemental Table S2), showing a high degree of homology with the corresponding residues in HR (29). The proton donor and acceptors for the retinal Schiff base were reported to be Arg-134, Glu-123, and Asp-253, respectively (16).…”

Section: Chr2mentioning

confidence: 99%

“…Inner Chamber System and Ion Selectivity Filter in ChR2-Internal water-filled cavities have been described in BR and microbial rhodopsins (33), and a system of inner chambers determines the ion pathway in ion-conducting rhodopsin (29).…”

Section: Chr2mentioning

confidence: 99%

Bioinformatic and Mutational Analysis of Channelrhodopsin-2 Protein Cation-conducting Pathway

Plazzo

Franceschi

Broi

et al. 2012

Journal of Biological Chemistry

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Background: ChR2 is a light-gated ion channel allowing fast non-invasive control of cell membrane potential. Results: We combined bioinformatic modeling and electrophysiology to infer structure/function details on ChR2. Conclusion: We show a complete structural model of the channel, describe the ion-conducting pathway and identify key residues involved in ionic permeability and in photoactivation. Significance: These results expand our knowledge on the structural determinants of ChR2.

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Crystal structure of the O intermediate of the Leu93→Ala mutant of bacteriorhodopsin

et al. 2012

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The lifetime of the O intermediate of bacteriorhodopsin (BR) is extended by a factor of ∼250 in the Leu93-to-Ala mutant (BR_L93A). To clarify the structural changes occurring in the last stage of the proton pumping cycle of BR, we crystallized BR_L93A into a hexagonal P622 crystal. Diffraction data from the unphotolyzed state showed that the deletion of three carbon atoms from Leu93 is compensated by the insertion of four water molecules in the cytoplasmic vicinity of retinal. This insertion of water is suggested to be responsible for the blue-shifted λ(max) (540 nm) of the mutant. A long-lived substate of O with a red-shifted λ(max) (~565 nm) was trapped when the crystal of BR_L93A was flash-cooled after illumination with green light. This substate (O(slow)) bears considerable similarity to the M intermediate of native BR; that is, it commonly shows deformation of helix C and the FG loop, downward orientation of the side chain of Arg82, and disruption of the Glu194/Glu204 pair. In O(slow), however, the main chain of Lys216 is less distorted and retinal takes on the 13-cis/15-syn configuration. Another significant difference is seen in the pH dependence of the structure of the proton release group, the pK(a) value of which is suggested to be much lower in O(slow) than in M.

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Crystal Structure of the Light-Driven Chloride Pump Halorhodopsin from Natronomonas pharaonis

Cited by 130 publications

References 64 publications

Structural Mechanism for Light-driven Transport by a New Type of Chloride Ion Pump, Nonlabens marinus Rhodopsin-3

Structural Mechanism for Light-driven Transport by a New Type of Chloride Ion Pump, Nonlabens marinus Rhodopsin-3

Bioinformatic and Mutational Analysis of Channelrhodopsin-2 Protein Cation-conducting Pathway

Crystal structure of the O intermediate of the Leu93→Ala mutant of bacteriorhodopsin

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