Crystal structure and functional characterization of a light-driven chloride pump having an NTQ motif

Kim, Kuglae; Kwon, Soon Kyeong; Jun, Sung Hoon; Seok, Jeong Ho; Kim, Ho-Young; Lee, Weontae; Kim, Jihyun F.; Cho, Hyun Soo

doi:10.1038/ncomms12677

Cited by 58 publications

(105 citation statements)

References 36 publications

(63 reference statements)

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“…5C, lower panel). These motions were reported to be important for maintaining the function and stability of ClR in previous studies (42) and are similar to the related motion in the function of bR (34). As a result, the structural orientation of the C-D loop, a part of helix E, and C-terminal helix moved toward the exterior of a protein, whereas helix G moved in the opposite direction (Fig.…”

Section: Non-cryogenic Structure Of Clr Derived From Xfelsupporting

confidence: 82%

“…3, A and B). ClR was previously thought to have unique hydrogen bond networks with two water molecules distinct from other chloride pumps such as HR, which have three well-resolved water molecules mediating the hydrogen bond network between Cl Ϫ -I-PSB and Asp 239 -Arg 108 (in HR from Halobacterium salinarum) (42). However, the ClR structure derived from XFEL confirms that it also has three well-resolved water molecules, W507, W508, and W614, and forms similar hydrogen bonding networks between Cl Ϫ -I-PSB and Asp 231 -Arg 95 , like other chloride pumps (Fig.…”

Section: Non-cryogenic Structure Of Clr Derived From Xfelmentioning

confidence: 99%

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Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency

Yun

Park

et al. 2019

Journal of Biological Chemistry

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Section: Non-cryogenic Structure Of Clr Derived From Xfelsupporting

confidence: 82%

Section: Non-cryogenic Structure Of Clr Derived From Xfelmentioning

confidence: 99%

Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency

Yun

Park

et al. 2019

Journal of Biological Chemistry

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“…2A and SI Appendix, Fig. S1), which is conserved among H + -pumping microbial rhodopsins (7,19,20) and is also found in the Cl − pump Nonlabens marinus rhodopsin 3 (NM-R3) (21,22). The hydrated cavity on the intracellular side contains Gln123 of the NDQ motif, as well as Asn61, which plays a role in the ion selectivity (7,23).…”

Section: Significancementioning

confidence: 97%

Energetics and dynamics of a light-driven sodium-pumping rhodopsin

Suomivuori

Gámiz‐Hernández

Sundholm

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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The conversion of light energy into ion gradients across biological membranes is one of the most fundamental reactions in primary biological energy transduction. Recently, the structure of the first light-activated Na + pump, Krokinobacter eikastus rhodopsin 2 (KR2), was resolved at atomic resolution [Kato HE, et al. (2015) Nature 521: [48][49][50][51][52][53]. To elucidate its molecular mechanism for Na + pumping, we perform here extensive classical and quantum molecular dynamics (MD) simulations of transient photocycle states. Our simulations show how the dynamics of key residues regulate water and ion access between the bulk and the buried light-triggered retinal site. We identify putative Na + binding sites and show how protonation and conformational changes gate the ion through these sites toward the extracellular side. We further show by correlated ab initio quantum chemical calculations that the obtained putative photocycle intermediates are in close agreement with experimental transient optical spectroscopic data. The combined results of the ion translocation and gating mechanisms in KR2 may provide a basis for the rational design of novel light-driven ion pumps with optogenetic applications.bacterial ion pumps | bioenergetics | QM/MM | optogenetics | retinal P rimary biological energy conversion is based on the efficient capture and conversion of light and chemical energy into ion gradients across biological membranes (1, 2). The established gradients are used to thermodynamically drive energy-requiring processes, such as active transport and synthesis of adenosine triphosphate (ATP) (3, 4). The rhodopsin family of proteins catalyzes such reactions by harnessing the energy from retinal photoisomerization and deprotonation reactions, followed by conformational changes that further trigger the pumping of ions across the membrane (5). All previously known ion-pumping rhodopsins function either as inward chloride or outward proton pumps, but the structure of the first Na + pumping rhodopsin, Krokinobacter eikastus rhodopsin 2 (KR2) (6), was recently resolved (7,8). In the absence of Na + ions, KR2 functions as an outward proton pump, similarly to bacteriorhodopsin (bR), but under physiological conditions, KR2 pumps Na + out of the cell (6, 9).KR2 shares the heptahelical transmembrane (7TM) structure common to all microbial rhodopsins (Fig. 1A) (5,7,8). In contrast to bR, however, where a highly conserved Asp-Thr-Asp (DTD) motif is used to pump protons, KR2 employs a unique NDQ motif comprising residues Asn112, Asp116, and Gln123 (6). In bR, Asp85 and Asp96 function as proton acceptors and donors for the protonated Schiff base (PSB), respectively, whereas in KR2, Asn112 and Gln123 occupy these positions, and Asp116 replaces Thr89. In analogy to bR, it has been suggested that Gln123 aids in capturing ions from the solvent and that Asn112 might be part of a Na + binding site (6,10).Similarly to other microbial rhodopsins, four photocycle intermediates have been spectroscopically identified in KR2 (Fig. 1B) (6)...

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“…In E. coli , the RbsD protein existed as a decamer consisting of two pentameric rings and contacted subunits by means of 10 Lys2–Cl − –Lys2 salt linkages , the Lys site is specific (forming salt linkages with chloride ion among subunits ), and seems to be important to the force acting to stabilize urea‐unfolded oligomeric intermediates. In this paper, we mainly studied the effects of Lys2 mutation in the structures of E. coli RbsD protein.…”

Section: Discussionmentioning

confidence: 99%

The role of Lys2–Cl⁻–Lys2 salt linkages in oligomeric intermediates of RbsD protein in Escherichia coli

Zheng

et al. 2019

J Basic Microbiol

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As a homo-oligomeric protein, the disassembly of Escherichia coli RbsD decamer produces a urea-unfolded oligomeric intermediate structure, as the dissociation speed of the protein is lower than that of the unfolding process. There are five Lys2-Cl − -Lys2 salt linkages to connect these subunits. To explore the role of the salt linkages in these oligomeric intermediates, the Lys2Ala mutated in the N-terminal of E. coli RbsD protein subunit was designed. It was found that the RbsD mutation protein (RbsD:K2A) loses its minor larger oligomers, which exist in RbsD, and displays other several oligomeric states (less than decamers), meanwhile the state of the oligomers depends on the protein concentration. It was also found that compared with RbsD, the crosslinking capability of the subunits of RbsD:K2A is weaker, while the crosslinking rate of dimers is higher, RbsD:K2A needs to substantially adjust its conformation to meet the space requirements when combined with D-ribose. On the basis of these results, we suggest that Lys2-Cl − -Lys2 salt linkages in E. coli RbsD protein play an important role in stabilizing the intermediate products of oligomers and maintaining interaction between the intermediate products of oligomers, which may shed light on the study of these oligomeric proteins. K E Y W O R D SEscherichia coli, oligomeric structure, RbsD protein, site-directed mutation Abbreviations: RbsD:K2A, RbsD mutation protein; FPLC, fast protein liquid chromatography; MS, mass spectrometry.

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Crystal structure and functional characterization of a light-driven chloride pump having an NTQ motif

Cited by 58 publications

References 36 publications

Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency

Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency

Energetics and dynamics of a light-driven sodium-pumping rhodopsin

The role of Lys2–Cl⁻–Lys2 salt linkages in oligomeric intermediates of RbsD protein in Escherichia coli

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Crystal structure and functional characterization of a light-driven chloride pump having an NTQ motif

Cited by 58 publications

References 36 publications

Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency

Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency

Energetics and dynamics of a light-driven sodium-pumping rhodopsin

The role of Lys2–Cl−–Lys2 salt linkages in oligomeric intermediates of RbsD protein in Escherichia coli

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The role of Lys2–Cl⁻–Lys2 salt linkages in oligomeric intermediates of RbsD protein in Escherichia coli