1
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Chiang WT, Chang YK, Hui WH, Chang SW, Liao CY, Chang YC, Chen CJ, Wang WC, Lai CC, Wang CH, Luo SY, Huang YP, Chou SH, Horng TL, Hou MH, Muench SP, Chen RS, Tsai MD, Hu NJ. Structural basis and synergism of ATP and Na + activation in bacterial K + uptake system KtrAB. Nat Commun 2024; 15:3850. [PMID: 38719864 PMCID: PMC11078986 DOI: 10.1038/s41467-024-48057-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 04/17/2024] [Indexed: 05/12/2024] Open
Abstract
The K+ uptake system KtrAB is essential for bacterial survival in low K+ environments. The activity of KtrAB is regulated by nucleotides and Na+. Previous studies proposed a putative gating mechanism of KtrB regulated by KtrA upon binding to ATP or ADP. However, how Na+ activates KtrAB and the Na+ binding site remain unknown. Here we present the cryo-EM structures of ATP- and ADP-bound KtrAB from Bacillus subtilis (BsKtrAB) both solved at 2.8 Å. A cryo-EM density at the intra-dimer interface of ATP-KtrA was identified as Na+, as supported by X-ray crystallography and ICP-MS. Thermostability assays and functional studies demonstrated that Na+ binding stabilizes the ATP-bound BsKtrAB complex and enhances its K+ flux activity. Comparing ATP- and ADP-BsKtrAB structures suggests that BsKtrB Arg417 and Phe91 serve as a channel gate. The synergism of ATP and Na+ in activating BsKtrAB is likely applicable to Na+-activated K+ channels in central nervous system.
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Affiliation(s)
- Wesley Tien Chiang
- Graduate Institute of Biochemistry, National Chung Hsing University, Taichung, 402202, Taiwan
| | - Yao-Kai Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115201, Taiwan
| | - Wei-Han Hui
- Department of Civil Engineering, National Taiwan University, Taipei, 106319, Taiwan
| | - Shu-Wei Chang
- Department of Civil Engineering, National Taiwan University, Taipei, 106319, Taiwan
- Department of Biomedical Engineering, National Taiwan University, Taipei, 10663, Taiwan
| | - Chen-Yi Liao
- Graduate Institute of Biochemistry, National Chung Hsing University, Taichung, 402202, Taiwan
| | - Yi-Chuan Chang
- Graduate Institute of Biochemistry, National Chung Hsing University, Taichung, 402202, Taiwan
| | - Chun-Jung Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, 30092, Taiwan
| | - Wei-Chen Wang
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 402202, Taiwan
| | - Chien-Chen Lai
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 402202, Taiwan
- Graduate Institute of Chinese Medical Science, China Medical University, Taichung, 406040, Taiwan
| | - Chun-Hsiung Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115201, Taiwan
| | - Siou-Ying Luo
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115201, Taiwan
| | - Ya-Ping Huang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115201, Taiwan
| | - Shan-Ho Chou
- Graduate Institute of Biochemistry, National Chung Hsing University, Taichung, 402202, Taiwan
| | - Tzyy-Leng Horng
- Department of Applied Mathematics, Feng Chia University, Taichung, 407102, Taiwan
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402202, Taiwan
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Ren-Shiang Chen
- Department of Life Science, Tunghai University, Taichung, 407224, Taiwan
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115201, Taiwan.
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 106319, Taiwan.
| | - Nien-Jen Hu
- Graduate Institute of Biochemistry, National Chung Hsing University, Taichung, 402202, Taiwan.
- Ph.D Program in Translational Medicine, National Chung Hsing University, Taichung, 402202, Taiwan.
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2
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Fan C, Flood E, Sukomon N, Agarwal S, Allen TW, Nimigean CM. Calcium-gated potassium channel blockade via membrane-facing fenestrations. Nat Chem Biol 2024; 20:52-61. [PMID: 37653172 PMCID: PMC10847966 DOI: 10.1038/s41589-023-01406-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/18/2023] [Indexed: 09/02/2023]
Abstract
Quaternary ammonium blockers were previously shown to bind in the pore to block both open and closed conformations of large-conductance calcium-activated potassium (BK and MthK) channels. Because blocker entry was assumed through the intracellular entryway (bundle crossing), closed-pore access suggested that the gate was not at the bundle crossing. Structures of closed MthK, a Methanobacterium thermoautotrophicum homolog of BK channels, revealed a tightly constricted intracellular gate, leading us to investigate the membrane-facing fenestrations as alternative pathways for blocker access directly from the membrane. Atomistic free energy simulations showed that intracellular blockers indeed access the pore through the fenestrations, and a mutant channel with narrower fenestrations displayed no closed-state TPeA block at concentrations that blocked the wild-type channel. Apo BK channels display similar fenestrations, suggesting that blockers may use them as access paths into closed channels. Thus, membrane fenestrations represent a non-canonical pathway for selective targeting of specific channel conformations, opening novel ways to selectively drug BK channels.
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Affiliation(s)
- Chen Fan
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Emelie Flood
- School of Science, RMIT University, Melbourne, Victoria, Australia
- Schrödinger, Inc., New York, NY, USA
| | - Nattakan Sukomon
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - Shubhangi Agarwal
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - Toby W Allen
- School of Science, RMIT University, Melbourne, Victoria, Australia.
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA.
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
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3
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Kopec W, Thomson AS, de Groot BL, Rothberg BS. Interactions between selectivity filter and pore helix control filter gating in the MthK channel. J Gen Physiol 2023; 155:e202213166. [PMID: 37318452 PMCID: PMC10274084 DOI: 10.1085/jgp.202213166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 01/13/2023] [Accepted: 05/31/2023] [Indexed: 06/16/2023] Open
Abstract
K+ channel activity can be limited by C-type inactivation, which is likely initiated in part by dissociation of K+ ions from the selectivity filter and modulated by the side chains that surround it. While crystallographic and computational studies have linked inactivation to a "collapsed" selectivity filter conformation in the KcsA channel, the structural basis for selectivity filter gating in other K+ channels is less clear. Here, we combined electrophysiological recordings with molecular dynamics simulations, to study selectivity filter gating in the model potassium channel MthK and its V55E mutant (analogous to KcsA E71) in the pore-helix. We found that MthK V55E has a lower open probability than the WT channel, due to decreased stability of the open state, as well as a lower unitary conductance. Simulations account for both of these variables on the atomistic scale, showing that ion permeation in V55E is altered by two distinct orientations of the E55 side chain. In the "vertical" orientation, in which E55 forms a hydrogen bond with D64 (as in KcsA WT channels), the filter displays reduced conductance compared to MthK WT. In contrast, in the "horizontal" orientation, K+ conductance is closer to that of MthK WT; although selectivity filter stability is lowered, resulting in more frequent inactivation. Surprisingly, inactivation in MthK WT and V55E is associated with a widening of the selectivity filter, unlike what is observed for KcsA and reminisces recent structures of inactivated channels, suggesting a conserved inactivation pathway across the potassium channel family.
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Affiliation(s)
- Wojciech Kopec
- Computational Biomolecular Dynamics Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Andrew S. Thomson
- Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Bert L. de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Brad S. Rothberg
- Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
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4
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Zhao X, Xu J, Dai Z, Guo J, Xu H, Zhao J, Song YY, Gao Z. Target-Modulated Hydrophobic Precipitation in Photocatalytic Nanochannels for Sensitive Detection of Alpha Fetoprotein. Anal Chem 2022; 94:11282-11289. [PMID: 35921648 DOI: 10.1021/acs.analchem.2c01937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
It is important to detect cancer biomarkers at an early stage of tumor development for the effective diagnosis and treatment of cancer. As a well-known probe for detecting superoxide (·O2-) radicals, nitro blue tetrazolium (NBT) can rapidly react with ·O2- to form a hydrophobic formazan precipitate. In this study, by deliberately utilizing this reaction, Pt asymmetrically decorated on a TiO2 nanochannel membrane (Pt/TiNM) is explored to fabricate an electrochemical immunosensing platform with outstanding selectivity and ultrahigh sensitivity. Using NBT as the substrate, hydrophobic formazan precipitation induces a substantial block of ionic diffusion flux in nanochannels. Using alpha fetoprotein (AFP) as the target analyte, the established immunorecognition event was used to induce MoS2-Ab2 conjugates. Thanks to the excellent light-shielding ability of MoS2 nanosheets, the production of ·O2- radicals from the photocatalysis of Pt/TiNM is effectively depressed because of the attenuated arrival of light. The reduced formazan precipitation results in ionic transport changes in nanochannels, which in turn enables the selective recognition of AFP down to 2 ng mL-1. This target-modulated sensing strategy is also capable of sensing other immune targets, thus paving a new way for designing nanochannel-based sensing platforms.
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Affiliation(s)
- Xia Zhao
- College of Sciences, Northeastern University, Shenyang 110819, China
| | - Jingwen Xu
- College of Sciences, Northeastern University, Shenyang 110819, China
| | - Zhenqing Dai
- College of Sciences, Northeastern University, Shenyang 110819, China
| | - Junli Guo
- College of Sciences, Northeastern University, Shenyang 110819, China
| | - Huijie Xu
- College of Sciences, Northeastern University, Shenyang 110819, China
| | - Junjian Zhao
- College of Sciences, Northeastern University, Shenyang 110819, China
| | - Yan-Yan Song
- College of Sciences, Northeastern University, Shenyang 110819, China
| | - Zhida Gao
- College of Sciences, Northeastern University, Shenyang 110819, China
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5
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Guan F, Li T, Dong W, Guo R, Chai H, Chen Z, Ren Z, Li Y, Ye S. Novel insights into the allosteric gating mechanism of MthK channel. Natl Sci Rev 2022; 9:nwac072. [PMID: 36072506 PMCID: PMC9440719 DOI: 10.1093/nsr/nwac072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 02/28/2022] [Accepted: 03/29/2022] [Indexed: 11/29/2022] Open
Abstract
Allostery is a fundamental element during channel gating in response to an appropriate stimulus by which events occurring at one site are transmitted to distal sites to regulate activity. To address how binding of the first Ca2+ ion at one of the eight chemically identical subunits facilitates the other Ca2+-binding events in MthK, a Ca2+-gated K+ channel containing a conserved ligand-binding RCK domain, we analysed a large collection of MthK structures and performed the corresponding thermodynamic and electrophysiological measurements. These structural and functional studies led us to conclude that the conformations of the Ca2+-binding sites alternate between two quaternary states and exhibit significant differences in Ca2+ affinity. We further propose an allosteric model of the MthK-gating mechanism by which a cascade of structural events connect the initial Ca2+-binding to the final changes of the ring structure that open the ion-conduction pore. This mechanical model reveals the exquisite design that achieves the allosteric gating and could be of general relevance for the action of other ligand-gated ion channels containing the RCK domain.
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Affiliation(s)
- Fenghui Guan
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin300072, China
- The Cancer Hospital of the University of Chinese Academy of Sciences, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang310022, China
| | - Tianyu Li
- State Key Laboratory of Drug Research and Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing100049, China
| | - Wei Dong
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058Zhejiang, China
| | - Rui Guo
- Department of Logistics, Tianjin University, 92 Weijin Road, Nankai District, Tianjin300072, China
| | - Hao Chai
- State Key Laboratory of Drug Research and Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing100049, China
| | - Zhiqiu Chen
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing100049, China
| | - Zhong Ren
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL60607, USA
- Renz Research Inc., Westmont, IL60559, USA
| | - Yang Li
- State Key Laboratory of Drug Research and Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing100049, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, China
| | - Sheng Ye
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin300072, China
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058Zhejiang, China
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6
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Suma A, Granata D, Thomson AS, Carnevale V, Rothberg BS. Polyamine blockade and binding energetics in the MthK potassium channel. J Gen Physiol 2021; 152:151703. [PMID: 32342093 PMCID: PMC7335011 DOI: 10.1085/jgp.201912527] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/24/2020] [Indexed: 11/20/2022] Open
Abstract
Polyamines such as spermidine and spermine are found in nearly all cells, at concentrations ranging up to 0.5 mM. These cations are endogenous regulators of cellular K+ efflux, binding tightly in the pores of inwardly rectifying K+ (Kir) channels in a voltage-dependent manner. Although the voltage dependence of Kir channel polyamine blockade is thought to arise at least partially from the energetically coupled movements of polyamine and K+ ions through the pore, the nature of physical interactions between these molecules is unclear. Here we analyze the polyamine-blocking mechanism in the model K+ channel MthK, using a combination of electrophysiology and computation. Spermidine (SPD3+) and spermine (SPM4+) each blocked current through MthK channels in a voltage-dependent manner, and blockade by these polyamines was described by a three-state kinetic scheme over a wide range of polyamine concentrations. In the context of the scheme, both SPD3+ and SPM4+ access a blocking site with similar effective gating valences (0.84 ± 0.03 e0 for SPD3+ and 0.99 ± 0.04 e0 for SPM4+), whereas SPM4+ binds in the blocked state with an ∼20-fold higher affinity than SPD3+ (Kd = 28.1 ± 3.1 µM for SPD3+ and 1.28 ± 0.20 µM for SPM4+), consistent with a free energy difference of 1.8 kcal/mol. Molecular simulations of the MthK pore in complex with either SPD3+ or SPM4+ are consistent with the leading amine interacting with the hydroxyl groups of T59, at the selectivity filter threshold, with access to this site governed by outward movement of K+ ions. These coupled movements can account for a large fraction of the voltage dependence of blockade. In contrast, differences in binding energetics between SPD3+ and SPM4+ may arise from distinct electrostatic interactions between the polyamines and carboxylate oxygens on the side chains of E92 and E96, located in the pore-lining helix.
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Affiliation(s)
- Antonio Suma
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA
| | - Daniele Granata
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA
| | - Andrew S Thomson
- Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA
| | - Vincenzo Carnevale
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA
| | - Brad S Rothberg
- Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA
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7
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Fan C, Sukomon N, Flood E, Rheinberger J, Allen TW, Nimigean CM. Ball-and-chain inactivation in a calcium-gated potassium channel. Nature 2020; 580:288-293. [PMID: 32269335 PMCID: PMC7153497 DOI: 10.1038/s41586-020-2116-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 01/15/2020] [Indexed: 01/21/2023]
Abstract
Inactivation is the process by which ion channels terminate ion flux through their pores while the opening stimulus is still present1. In neurons, inactivation of both sodium and potassium channels is crucial for the generation of action potentials and regulation of firing frequency1,2. A cytoplasmic domain of either the channel or an accessory subunit is thought to plug the open pore to inactivate the channel via a 'ball-and-chain' mechanism3-7. Here we use cryo-electron microscopy to identify the molecular gating mechanism in calcium-activated potassium channels by obtaining structures of the MthK channel from Methanobacterium thermoautotrophicum-a purely calcium-gated and inactivating channel-in a lipid environment. In the absence of Ca2+, we obtained a single structure in a closed state, which was shown by atomistic simulations to be highly flexible in lipid bilayers at ambient temperature, with large rocking motions of the gating ring and bending of pore-lining helices. In Ca2+-bound conditions, we obtained several structures, including multiple open-inactivated conformations, further indication of a highly dynamic protein. These different channel conformations are distinguished by rocking of the gating rings with respect to the transmembrane region, indicating symmetry breakage across the channel. Furthermore, in all conformations displaying open channel pores, the N terminus of one subunit of the channel tetramer sticks into the pore and plugs it, with free energy simulations showing that this is a strong interaction. Deletion of this N terminus leads to functionally non-inactivating channels and structures of open states without a pore plug, indicating that this previously unresolved N-terminal peptide is responsible for a ball-and-chain inactivation mechanism.
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Affiliation(s)
- Chen Fan
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Nattakan Sukomon
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Emelie Flood
- School of Science, RMIT University, Melbourne, Victoria, Australia
| | - Jan Rheinberger
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
- Department of Structural Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Toby W Allen
- School of Science, RMIT University, Melbourne, Victoria, Australia
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA.
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA.
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8
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Orriss GL, To V, Moya-Torres A, Seabrook G, O'Neil J, Stetefeld J. Solution structure of the cytoplasmic domain of NhaP2 a K +/H + antiporter from Vibrio cholera. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183225. [PMID: 32126231 DOI: 10.1016/j.bbamem.2020.183225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 02/08/2020] [Accepted: 02/10/2020] [Indexed: 11/24/2022]
Abstract
NhaP2 is a K+/H+ antiporter from Vibrio cholerae which consists of a transmembrane domain and a cytoplasmic domain of approximately 200 amino acids, both of which are required for cholera infectivity. Here we present the solution structure for a 165 amino acid minimal cytoplasmic domain (P2MIN) form of the protein. The structure reveals a compact N-terminal domain which resembles a Regulator of Conductance of K+ channels (RCK) domain connected to a more open C-terminal domain via a flexible 20 amino acid linker. NMR titration experiments showed that the protein binds ATP through its N-terminal domain, which was further supported by waterLOGSY and Saturation Transfer Difference NMR experiments. The two-domain organisation of the protein was confirmed by BIOSAXS, which also revealed that there are no detectable-ATP-induced conformational changes in the protein structure. Finally, in contrast to all known RCK domain structures solved to date, the current work shows that the protein is a monomer.
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Affiliation(s)
- George L Orriss
- University of Manitoba, Department of Chemistry, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada
| | - Vu To
- University of Manitoba, Department of Chemistry, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada
| | - Aniel Moya-Torres
- University of Manitoba, Department of Chemistry, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada
| | - Genevieve Seabrook
- The OCI/UHN High Field NMR Facility, MaRS Toronto Medical Discovery Tower, 101 College Street, Toronto, Ontario M5C 1L7, Canada
| | - Joe O'Neil
- University of Manitoba, Department of Chemistry, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada
| | - Jörg Stetefeld
- University of Manitoba, Department of Chemistry, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada.
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9
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Teixeira-Duarte CM, Fonseca F, Morais-Cabral JH. Activation of a nucleotide-dependent RCK domain requires binding of a cation cofactor to a conserved site. eLife 2019; 8:50661. [PMID: 31868587 PMCID: PMC6957272 DOI: 10.7554/elife.50661] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 12/22/2019] [Indexed: 12/24/2022] Open
Abstract
RCK domains regulate the activity of K+ channels and transporters in eukaryotic and prokaryotic organisms by responding to ions or nucleotides. The mechanisms of RCK activation by Ca2+ in the eukaryotic BK and bacterial MthK K+ channels are well understood. However, the molecular details of activation in nucleotide-dependent RCK domains are not clear. Through a functional and structural analysis of the mechanism of ATP activation in KtrA, a RCK domain from the B. subtilis KtrAB cation channel, we have found that activation by nucleotide requires binding of cations to an intra-dimer interface site in the RCK dimer. In particular, divalent cations are coordinated by the γ-phosphates of bound-ATP, tethering the two subunits and stabilizing the active state conformation. Strikingly, the binding site residues are highly conserved in many different nucleotide-dependent RCK domains, indicating that divalent cations are a general cofactor in the regulatory mechanism of many nucleotide-dependent RCK domains.
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Affiliation(s)
- Celso M Teixeira-Duarte
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal.,Programa Doutoral em Biologia Molecular e Celular (MCbiology), Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Fátima Fonseca
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
| | - João H Morais-Cabral
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
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10
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Lorenzo-Ceballos Y, Carrasquel-Ursulaez W, Castillo K, Alvarez O, Latorre R. Calcium-driven regulation of voltage-sensing domains in BK channels. eLife 2019; 8:44934. [PMID: 31509109 PMCID: PMC6763263 DOI: 10.7554/elife.44934] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 09/10/2019] [Indexed: 12/17/2022] Open
Abstract
Allosteric interactions between the voltage-sensing domain (VSD), the Ca2+-binding sites, and the pore domain govern the mammalian Ca2+- and voltage-activated K+ (BK) channel opening. However, the functional relevance of the crosstalk between the Ca2+- and voltage-sensing mechanisms on BK channel gating is still debated. We examined the energetic interaction between Ca2+ binding and VSD activation by investigating the effects of internal Ca2+ on BK channel gating currents. Our results indicate that Ca2+ sensor occupancy has a strong impact on VSD activation through a coordinated interaction mechanism in which Ca2+ binding to a single α-subunit affects all VSDs equally. Moreover, the two distinct high-affinity Ca2+-binding sites contained in the C-terminus domains, RCK1 and RCK2, contribute equally to decrease the free energy necessary to activate the VSD. We conclude that voltage-dependent gating and pore opening in BK channels is modulated to a great extent by the interaction between Ca2+ sensors and VSDs.
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Affiliation(s)
- Yenisleidy Lorenzo-Ceballos
- Doctorado en Ciencias Mención Neurociencia, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile.,Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
| | - Willy Carrasquel-Ursulaez
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
| | - Karen Castillo
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
| | - Osvaldo Alvarez
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile.,Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Ramon Latorre
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
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11
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Howard RJ, Carnevale V, Delemotte L, Hellmich UA, Rothberg BS. Permeating disciplines: Overcoming barriers between molecular simulations and classical structure-function approaches in biological ion transport. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:927-942. [PMID: 29258839 DOI: 10.1016/j.bbamem.2017.12.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 12/08/2017] [Accepted: 12/14/2017] [Indexed: 11/20/2022]
Abstract
Ion translocation across biological barriers is a fundamental requirement for life. In many cases, controlling this process-for example with neuroactive drugs-demands an understanding of rapid and reversible structural changes in membrane-embedded proteins, including ion channels and transporters. Classical approaches to electrophysiology and structural biology have provided valuable insights into several such proteins over macroscopic, often discontinuous scales of space and time. Integrating these observations into meaningful mechanistic models now relies increasingly on computational methods, particularly molecular dynamics simulations, while surfacing important challenges in data management and conceptual alignment. Here, we seek to provide contemporary context, concrete examples, and a look to the future for bridging disciplinary gaps in biological ion transport. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain.
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Affiliation(s)
- Rebecca J Howard
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, 17121 Solna, Sweden.
| | - Vincenzo Carnevale
- Institute for Computational Molecular Science, Department of Chemistry, Temple University, Philadelphia, PA 19122, USA.
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Theoretical Physics, KTH Royal Institute of Technology, Box 1031, 17121 Solna, Sweden.
| | - Ute A Hellmich
- Johannes Gutenberg University Mainz, Institute for Pharmacy and Biochemistry, Johann-Joachim-Becherweg 30, 55128 Mainz, Germany; Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt, Germany.
| | - Brad S Rothberg
- Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA.
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12
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Affiliation(s)
- Brad S Rothberg
- Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
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13
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Giraldez T, Rothberg BS. Understanding the conformational motions of RCK gating rings. J Gen Physiol 2017; 149:431-441. [PMID: 28246116 PMCID: PMC5379921 DOI: 10.1085/jgp.201611726] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 01/17/2017] [Indexed: 12/16/2022] Open
Abstract
A timely review of the structural basis of Ca2+-activated K+ channel modulation by regulator of conduction of K+ (RCK) domains Regulator of conduction of K+ (RCK) domains are ubiquitous regulators of channel and transporter activity in prokaryotes and eukaryotes. In humans, RCK domains form an integral component of large-conductance calcium-activated K channels (BK channels), key modulators of nerve, muscle, and endocrine cell function. In this review, we explore how the study of RCK domains in bacterial and human channels has contributed to our understanding of the structural basis of channel function. This knowledge will be critical in identifying mechanisms that underlie BK channelopathies that lead to epilepsy and other diseases, as well as regions of the channel that might be successfully targeted to treat such diseases.
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Affiliation(s)
- Teresa Giraldez
- Department of Basic Medical Sciences, Institute of Biomedical Technologies and Centre for Biomedical Research of the Canary Islands, Universidad de La Laguna, La Laguna 38071, Spain
| | - Brad S Rothberg
- Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140
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Davis SJ, Scott LL, Ordemann G, Philpo A, Cohn J, Pierce-Shimomura JT. Putative calcium-binding domains of the Caenorhabditis elegans BK channel are dispensable for intoxication and ethanol activation. GENES BRAIN AND BEHAVIOR 2016; 14:454-65. [PMID: 26113050 DOI: 10.1111/gbb.12229] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 06/16/2015] [Accepted: 06/22/2015] [Indexed: 01/17/2023]
Abstract
Alcohol modulates the highly conserved, voltage- and calcium-activated potassium (BK) channel, which contributes to alcohol-mediated behaviors in species from worms to humans. Previous studies have shown that the calcium-sensitive domains, RCK1 and the Ca(2+) bowl, are required for ethanol activation of the mammalian BK channel in vitro. In the nematode Caenorhabditis elegans, ethanol activates the BK channel in vivo, and deletion of the worm BK channel, SLO-1, confers strong resistance to intoxication. To determine if the conserved RCK1 and calcium bowl domains were also critical for intoxication and basal BK channel-dependent behaviors in C. elegans, we generated transgenic worms that express mutated SLO-1 channels predicted to have the RCK1, Ca(2+) bowl or both domains rendered insensitive to calcium. As expected, mutating these domains inhibited basal function of SLO-1 in vivo as neck and body curvature of these mutants mimicked that of the BK null mutant. Unexpectedly, however, mutating these domains singly or together in SLO-1 had no effect on intoxication in C. elegans. Consistent with these behavioral results, we found that ethanol activated the SLO-1 channel in vitro with or without these domains. By contrast, in agreement with previous in vitro findings, C. elegans harboring a human BK channel with mutated calcium-sensing domains displayed resistance to intoxication. Thus, for the worm SLO-1 channel, the putative calcium-sensitive domains are critical for basal in vivo function but unnecessary for in vivo ethanol action.
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Affiliation(s)
- S J Davis
- Waggoner Center for Alcohol and Addiction Research, Institute for Neuroscience, Center for Learning and Memory, Center for Brain, Behavior and Evolution, and Department of Neuroscience, The University of Texas at Austin, Austin, TX, USA
| | - L L Scott
- Waggoner Center for Alcohol and Addiction Research, Institute for Neuroscience, Center for Learning and Memory, Center for Brain, Behavior and Evolution, and Department of Neuroscience, The University of Texas at Austin, Austin, TX, USA
| | - G Ordemann
- Waggoner Center for Alcohol and Addiction Research, Institute for Neuroscience, Center for Learning and Memory, Center for Brain, Behavior and Evolution, and Department of Neuroscience, The University of Texas at Austin, Austin, TX, USA
| | - A Philpo
- Waggoner Center for Alcohol and Addiction Research, Institute for Neuroscience, Center for Learning and Memory, Center for Brain, Behavior and Evolution, and Department of Neuroscience, The University of Texas at Austin, Austin, TX, USA
| | - J Cohn
- Waggoner Center for Alcohol and Addiction Research, Institute for Neuroscience, Center for Learning and Memory, Center for Brain, Behavior and Evolution, and Department of Neuroscience, The University of Texas at Austin, Austin, TX, USA
| | - J T Pierce-Shimomura
- Waggoner Center for Alcohol and Addiction Research, Institute for Neuroscience, Center for Learning and Memory, Center for Brain, Behavior and Evolution, and Department of Neuroscience, The University of Texas at Austin, Austin, TX, USA
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Abstract
BK channels are universal regulators of cell excitability, given their exceptional unitary conductance selective for K(+), joint activation mechanism by membrane depolarization and intracellular [Ca(2+)] elevation, and broad expression pattern. In this chapter, we discuss the structural basis and operational principles of their activation, or gating, by membrane potential and calcium. We also discuss how the two activation mechanisms interact to culminate in channel opening. As members of the voltage-gated potassium channel superfamily, BK channels are discussed in the context of archetypal family members, in terms of similarities that help us understand their function, but also seminal structural and biophysical differences that confer unique functional properties.
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Affiliation(s)
- A Pantazis
- David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, United States
| | - R Olcese
- David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, United States.
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Chin KH, Liang JM, Yang JG, Shih MS, Tu ZL, Wang YC, Sun XH, Hu NJ, Liang ZX, Dow JM, Ryan RP, Chou SH. Structural Insights into the Distinct Binding Mode of Cyclic Di-AMP with SaCpaA_RCK. Biochemistry 2015; 54:4936-51. [PMID: 26171638 DOI: 10.1021/acs.biochem.5b00633] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Cyclic di-AMP (c-di-AMP) is a relatively new member of the family of bacterial cyclic dinucleotide second messengers. It has attracted significant attention in recent years because of the abundant roles it plays in a variety of Gram-positive bacteria. The structural features that allow diverse bacterial proteins to bind c-di-AMP are not fully understood. Here we report the biophysical and structural studies of c-di-AMP in complex with a bacterial cation-proton antiporter (CpaA) RCK (regulator of the conductance of K(+)) protein from Staphylococcus aureus (Sa). The crystal structure of the SaCpaA_RCK C-terminal domain (CTD) in complex with c-di-AMP was determined to a resolution of 1.81 Å. This structure revealed two well-liganded water molecules, each interacting with one of the adenine bases by a unique H2Olp-π interaction to stabilize the complex. Sequence blasting using the SaCpaA_RCK primary sequence against the bacterial genome database returned many CpaA analogues, and alignment of these sequences revealed that the active site residues are all well-conserved, indicating a universal c-di-AMP binding mode for CpaA_RCK. A proteoliposome activity assay using the full-length SaCpaA membrane protein indicated that c-di-AMP binding alters its antiporter activity by approximately 40%. A comparison of this structure to all other reported c-di-AMP-receptor complex structures revealed that c-di-AMP binds to receptors in either a "U-shape" or "V-shape" mode. The two adenine rings are stabilized in the inner interaction zone by a variety of CH-π, cation-π, backbone-π, or H2Olp-π interaction, but more commonly in the outer interaction zone by hydrophobic CH-π or π-π interaction. The structures determined to date provide an understanding of the mechanisms by which a single c-di-AMP can interact with a variety of receptor proteins, and how c-di-AMP binds receptor proteins in a special way different from that of c-di-GMP.
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Affiliation(s)
- Ko-Hsin Chin
- †National Chung Hsing University Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Juin-Ming Liang
- ‡Institute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Jauo-Guey Yang
- ‡Institute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Min-Shao Shih
- ‡Institute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Zhi-Le Tu
- ‡Institute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Yu-Chuang Wang
- ‡Institute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Xing-Han Sun
- ‡Institute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Nien-Jen Hu
- ‡Institute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Zhao-Xun Liang
- §School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - J Maxwell Dow
- ∥School of Microbiology, Biosciences Institute, University College Cork, Cork, Ireland
| | - Robert P Ryan
- ⊥Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, U.K
| | - Shan-Ho Chou
- †National Chung Hsing University Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan, ROC.,‡Institute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan, ROC
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Kuang Q, Purhonen P, Hebert H. Structure of potassium channels. Cell Mol Life Sci 2015; 72:3677-93. [PMID: 26070303 PMCID: PMC4565861 DOI: 10.1007/s00018-015-1948-5] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 05/09/2015] [Accepted: 06/03/2015] [Indexed: 12/25/2022]
Abstract
Potassium channels ubiquitously exist in nearly all kingdoms of life and perform diverse but important functions. Since the first atomic structure of a prokaryotic potassium channel (KcsA, a channel from Streptomyces lividans) was determined, tremendous progress has been made in understanding the mechanism of potassium channels and channels conducting other ions. In this review, we discuss the structure of various kinds of potassium channels, including the potassium channel with the pore-forming domain only (KcsA), voltage-gated, inwardly rectifying, tandem pore domain, and ligand-gated ones. The general properties shared by all potassium channels are introduced first, followed by specific features in each class. Our purpose is to help readers to grasp the basic concepts, to be familiar with the property of the different domains, and to understand the structure and function of the potassium channels better.
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Affiliation(s)
- Qie Kuang
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 14183, Huddinge, Sweden.
- School of Technology and Health, KTH Royal Institute of Technology, Novum, 14183, Huddinge, Sweden.
| | - Pasi Purhonen
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 14183, Huddinge, Sweden
| | - Hans Hebert
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 14183, Huddinge, Sweden
- School of Technology and Health, KTH Royal Institute of Technology, Novum, 14183, Huddinge, Sweden
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Kim H, Youn SJ, Kim SO, Ko J, Lee JO, Choi BS. Structural Studies of Potassium Transport Protein KtrA Regulator of Conductance of K+ (RCK) C Domain in Complex with Cyclic Diadenosine Monophosphate (c-di-AMP). J Biol Chem 2015; 290:16393-402. [PMID: 25957408 DOI: 10.1074/jbc.m115.641340] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Indexed: 11/06/2022] Open
Abstract
Although it was only recently identified as a second messenger, c-di-AMP was found to have fundamental importance in numerous bacterial functions such as ion transport. The potassium transporter protein, KtrA, was identified as a c-di-AMP receptor. However, the co-crystallization of c-di-AMP with the protein has not been studied. Here, we determined the crystal structure of the KtrA RCK_C domain in complex with c-di-AMP. The c-di-AMP nucleotide, which adopts a U-shaped conformation, is bound at the dimer interface of RCK_C close to helices α3 and α4. c-di-AMP interacts with KtrA RCK_C mainly by forming hydrogen bonds and hydrophobic interactions. c-di-AMP binding induces the contraction of the dimer, bringing the two monomers of KtrA RCK_C into close proximity. The KtrA RCK_C was able to interact with only c-di-AMP, but not with c-di-GMP, 3',3-cGAMP, ATP, and ADP. The structure of the KtrA RCK_C domain and c-di-AMP complex would expand our understanding about the mechanism of inactivation in Ktr transporters governed by c-di-AMP.
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Affiliation(s)
- Henna Kim
- From the Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Korea
| | - Suk-Jun Youn
- From the Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Korea
| | - Seong Ok Kim
- From the Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Korea
| | - Junsang Ko
- From the Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Korea
| | - Jie-Oh Lee
- From the Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Korea
| | - Byong-Seok Choi
- From the Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Korea
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