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Duan H, Zhou Y, Shi X, Luo Q, Gao J, Liang L, Liu W, Peng L, Deng D, Hu J. Allosteric and transport modulation of human concentrative nucleoside transporter 3 at the atomic scale. Phys Chem Chem Phys 2021; 23:25401-25413. [PMID: 34751688 DOI: 10.1039/d1cp03756k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Nucleosides are important precursors of nucleotide synthesis in cells, and nucleoside transporters play an important role in many physiological processes by mediating transmembrane transport and absorption. During nucleoside transport, such proteins undergo a significant conformational transition between the outward- and inward-facing states, which leads to alternating access of the substrate-binding site to either side of the membrane. In this work, a variety of molecular simulation methods have been applied to comparatively investigate the motion modes of human concentrative nucleoside transporter 3 (hCNT3) in three states, as well as global and local cavity conformational changes; and finally, a possible elevator-like transport mechanism consistent with experimental data was proposed. The results of the Gaussian network model (GNM) and anisotropic network model (ANM) show that hCNT3 as a whole tends to contract inwards and shift towards a membrane inside, exhibiting an allosteric process that is more energetically favorable than the rigid conversion. To reveal the complete allosteric process of hCNT3 in detail, a series of intermediate conformations were obtained by an adaptive anisotropic network model (aANM). One of the simulated intermediate states is similar to that of a crystal structure, which indicates that the allosteric process is reliable; the state with lower energy is slightly inclined to the inward-facing structure rather than the expected intermediate crystal structure. The final HOLE analysis showed that except for the outward-facing state, the transport channels were gradually enlarged, which was conductive to the directional transport of nucleosides. Our work provides a theoretical basis for the multistep elevator-like transportation mechanism of nucleosides, which helps to further understand the dynamic recognition between nucleoside substrates and hCNT3 as well as the design of nucleoside anticancer drugs.
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Affiliation(s)
- Huaichuan Duan
- School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China.
| | - Yanxia Zhou
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, Department of Obstetrics, West China Second Hospital, Sichuan University, Chengdu, China.
| | - Xiaodong Shi
- School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China.
| | - Qing Luo
- School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China.
| | - Jiaxing Gao
- School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China.
| | - Li Liang
- School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China.
| | - Wei Liu
- School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China.
| | - Lianxin Peng
- School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China.
| | - Dong Deng
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, Department of Obstetrics, West China Second Hospital, Sichuan University, Chengdu, China.
| | - Jianping Hu
- School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China.
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2
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Abstract
Nucleosides play central roles in all facets of life, from metabolism to cellular signaling. Because of their physiochemical properties, nucleosides are lipid bilayer impermeable and thus rely on dedicated transport systems to cross biological membranes. In humans, two unrelated protein families mediate nucleoside membrane transport: the concentrative and equilibrative nucleoside transporter families. The objective of this review is to provide a broad outlook on the current status of nucleoside transport research. We will discuss the role played by nucleoside transporters in human health and disease, with emphasis placed on recent structural advancements that have revealed detailed molecular principles of these important cellular transport systems and exploitable pharmacological features.
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Affiliation(s)
- Nicholas J. Wright
- Department of Biochemistry, Duke University Medical Center, 303 Research Drive, Durham, North Carolina, 27710, USA
| | - Seok-Yong Lee
- Department of Biochemistry, Duke University Medical Center, 303 Research Drive, Durham, North Carolina, 27710, USA
- Correspondence and requests for materials should be addressed to: S.-Y. Lee., , tel: 919-684-1005, fax: 919-684-8885
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3
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Zhou Y, Liao L, Wang C, Li J, Chi P, Xiao Q, Liu Q, Guo L, Sun L, Deng D. Cryo-EM structure of the human concentrative nucleoside transporter CNT3. PLoS Biol 2020; 18:e3000790. [PMID: 32776918 PMCID: PMC7440666 DOI: 10.1371/journal.pbio.3000790] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 08/20/2020] [Accepted: 07/20/2020] [Indexed: 01/17/2023] Open
Abstract
Concentrative nucleoside transporters (CNTs), members of the solute carrier (SLC) 28 transporter family, facilitate the salvage of nucleosides and therapeutic nucleoside derivatives across the plasma membrane. Despite decades of investigation, the structures of human CNTs remain unknown. We determined the cryogenic electron microscopy (cryo-EM) structure of human CNT (hCNT) 3 at an overall resolution of 3.6 Å. As with its bacterial homologs, hCNT3 presents a trimeric architecture with additional N-terminal transmembrane helices to stabilize the conserved central domains. The conserved binding sites for the substrate and sodium ions unravel the selective nucleoside transport and distinct coupling mechanism. Structural comparison of hCNT3 with bacterial homologs indicates that hCNT3 is stabilized in an inward-facing conformation. This study provides the molecular determinants for the transport mechanism of hCNTs and potentially facilitates the design of nucleoside drugs.
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Affiliation(s)
- Yanxia Zhou
- Division of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, China
| | - Lianghuan Liao
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Centre for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Chen Wang
- Division of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, China
| | - Jialu Li
- Division of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, China
| | - Pengliang Chi
- Division of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, China
| | - Qingjie Xiao
- Division of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, China
| | - Qingting Liu
- Division of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, China
| | - Li Guo
- Division of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, China
| | - Linfeng Sun
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Centre for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, China
- * E-mail: (LS); (DD)
| | - Dong Deng
- Division of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, China
- * E-mail: (LS); (DD)
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4
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Okamura Y, Yasukawa S, Narimatsu H, Boku N, Fukutomi A, Konishi M, Morinaga S, Toyama H, Kaneoka Y, Shimizu Y, Nakamori S, Sata N, Yamakita K, Takahashi A, Kainuma O, Hishinuma S, Yamaguchi R, Nagino M, Hirano S, Yanagisawa A, Mori K, Uesaka K. Human equilibrative nucleoside transporter-1 expression is a predictor in patients with resected pancreatic cancer treated with adjuvant S-1 chemotherapy. Cancer Sci 2020; 111:548-560. [PMID: 31778273 PMCID: PMC7004513 DOI: 10.1111/cas.14258] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/20/2019] [Accepted: 11/22/2019] [Indexed: 02/06/2023] Open
Abstract
The high expression of human equilibrative nucleoside transporter-1 (hENT1) and the low expression of dihydropyrimidine dehydrogenase (DPD) are reported to predict a favorable prognosis in patients treated with gemcitabine (GEM) and 5-fluorouracil (5FU) as the adjuvant setting, respectively. The expression of hENT1 and DPD were analyzed in patients registered in the JASPAC 01 trial, which showed a better survival of S-1 over GEM as adjuvant chemotherapy after resection for pancreatic cancer, and their possible roles for predicting treatment outcomes and selecting a chemotherapeutic agent were investigated. Intensity of hENT1 and DPD expression was categorized into no, weak, moderate or strong by immunohistochemistry staining, and the patients were classified into high (strong/moderate) and low (no/weak) groups. Specimens were available for 326 of 377 (86.5%) patients. High expression of hENT1 and DPD was detected in 100 (30.7%) and 63 (19.3%) of 326 patients, respectively. In the S-1 arm, the median overall survival (OS) with low hENT1, 58.0 months, was significantly better than that with high hENT1, 30.9 months (hazard ratio 1.75, P = 0.007). In contrast, there were no significant differences in OS between DPD low and high groups in the S-1 arm and neither the expression levels of hENT1 nor DPD revealed a relationship with treatment outcomes in the GEM arm. The present study did not show that the DPD and hENT1 are useful biomarkers for choosing S-1 or GEM as adjuvant chemotherapy. However, hENT1 expression is a significant prognostic factor for survival in the S-1 arm.
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Affiliation(s)
- Yukiyasu Okamura
- Division of Hepato‐Biliary‐Pancreatic SurgeryShizuoka Cancer Center HospitalNagaizumiJapan
| | | | - Hiroto Narimatsu
- Cancer Prevention and Control DivisionKanagawa Cancer CenterYokohamaJapan
| | - Narikazu Boku
- Gastrointestinal Medical OncologyNational Cancer Center HospitalTokyoJapan
| | - Akira Fukutomi
- Gastrointestinal OncologyShizuoka Cancer CenterShizuokaJapan
| | - Masaru Konishi
- Hepato‐Biliary‐Pancreatic SurgeryNational Cancer Center Hospital EastKashiwaJapan
| | - Soichiro Morinaga
- Department of Gastrointestinal SurgeryKanagawa Cancer CenterYokohamaJapan
| | | | | | | | - Shoji Nakamori
- SurgeryNational Hospital Organization Osaka National HospitalOsakaJapan
| | - Naohiro Sata
- Gastrointestinal SurgeryJichi Medical UniversityShimotsukeJapan
| | - Keisuke Yamakita
- Division of Metabolism and Biosystemic ScienceDepartment of MedicineAsahikawa Medical UniversityAsahikawaJapan
| | | | - Osamu Kainuma
- Gastrointestinal SurgeryChiba Cancer CenterChibaJapan
| | | | | | - Masato Nagino
- Division of Surgical OncologyDepartment of SurgeryNagoya University Graduate of School of MedicineNagoyaJapan
| | - Satoshi Hirano
- Gastroenterological Surgery IIFaculty of MedicineHokkaido UniversitySapporoJapan
| | | | - Keita Mori
- Clinical Trial Coordination Office BiostatisticianShizuoka Cancer Center HospitalNagaizumiJapan
| | - Katsuhiko Uesaka
- Division of Hepato‐Biliary‐Pancreatic SurgeryShizuoka Cancer Center HospitalNagaizumiJapan
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5
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Stecula A, Schlessinger A, Giacomini KM, Sali A. Human Concentrative Nucleoside Transporter 3 (hCNT3, SLC28A3) Forms a Cyclic Homotrimer. Biochemistry 2017; 56:3475-3483. [PMID: 28661652 DOI: 10.1021/acs.biochem.7b00339] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Many anticancer and antiviral drugs are purine or pyrimidine analogues, which use membrane transporters to cross cellular membranes. Concentrative nucleoside transporters (CNTs) mediate the salvage of nucleosides and the transport of therapeutic nucleoside analogues across plasma membranes by coupling the transport of ligands to the sodium gradient. Of the three members of the human CNT family, CNT3 has the broadest selectivity and the widest expression profile. However, the molecular mechanisms of the transporter, including how it interacts with and translocates structurally diverse nucleosides and nucleoside analogues, are unclear. Recently, the crystal structure of vcCNT showed that the prokaryotic homologue of CNT3 forms a homotrimer. In this study, we successfully expressed and purified the wild type human homologue, hCNT3, demonstrating the homotrimer by size exclusion profiles and glutaraldehyde cross-linking. Further, by creating a series of cysteine mutants at highly conserved positions guided by comparative structure models, we cross-linked hCNT3 protomers in a cell-based assay, thus showing the existence of hCNT3 homotrimers in human cells. The presence and absence of cross-links at specific locations along TM9 informs us of important structural differences between vcCNT and hCNT3. Comparative modeling of the trimerization domain and sequence coevolution analysis both indicate that oligomerization is critical to the stability and function of hCNT3. In particular, trimerization appears to shorten the translocation path for nucleosides across the plasma membrane and may allow modulation of the transport function via allostery.
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Affiliation(s)
- Adrian Stecula
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco , San Francisco, California 94158, United States
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Kathleen M Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco , San Francisco, California 94158, United States.,California Institute for Quantitative Biosciences, University of California, San Francisco , San Francisco, California 94158, United States.,Department of Pharmaceutical Chemistry, University of California, San Francisco , San Francisco, California 94158, United States.,Institute for Human Genetics, University of California, San Francisco , San Francisco, California 94158, United States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco , San Francisco, California 94158, United States.,California Institute for Quantitative Biosciences, University of California, San Francisco , San Francisco, California 94158, United States.,Department of Pharmaceutical Chemistry, University of California, San Francisco , San Francisco, California 94158, United States
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6
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The SLC28 (CNT) and SLC29 (ENT) nucleoside transporter families: a 30-year collaborative odyssey. Biochem Soc Trans 2017; 44:869-76. [PMID: 27284054 DOI: 10.1042/bst20160038] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Indexed: 01/18/2023]
Abstract
Specialized nucleoside transporter (NT) proteins are required for passage of nucleosides and hydrophilic nucleoside analogues across biological membranes. Physiologic nucleosides serve as central salvage metabolites in nucleotide biosynthesis, and nucleoside analogues are used as chemotherapeutic agents in the treatment of cancer and antiviral diseases. The nucleoside adenosine modulates numerous cellular events via purino-receptor cell signalling pathways. Human NTs are divided into two structurally unrelated protein families: the SLC28 concentrative nucleoside transporter (CNT) family and the SLC29 equilibrative nucleoside transporter (ENT) family. Human CNTs are inwardly directed Na(+)-dependent nucleoside transporters found predominantly in intestinal and renal epithelial and other specialized cell types. Human ENTs mediate bidirectional fluxes of purine and pyrimidine nucleosides down their concentration gradients and are ubiquitously found in most, possibly all, cell types. Both protein families are evolutionarily old: CNTs are present in both eukaryotes and prokaryotes; ENTs are widely distributed in mammalian, lower vertebrate and other eukaryote species. This mini-review describes a 30-year collaboration with Professor Stephen Baldwin to identify and understand the structures and functions of these physiologically and clinically important transport proteins.
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7
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Visualizing multistep elevator-like transitions of a nucleoside transporter. Nature 2017; 545:66-70. [PMID: 28424521 PMCID: PMC5567992 DOI: 10.1038/nature22057] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 03/09/2017] [Indexed: 02/06/2023]
Abstract
Membrane transporters move substrates across the membrane by alternating access of their binding sites between the opposite sides of the membrane. An emerging model of this process is the elevator mechanism, in which a substrate-binding transport domain moves a large distance across the membrane. This mechanism has been characterized by a transition between two states, but the conformational path that leads to the transition is not yet known, largely because the available structural information has been limited to the two end states. Here we present crystal structures of the inward-facing, intermediate, and outward-facing states of a concentrative nucleoside transporter from Neisseria wadsworthii. Notably, we determined the structures of multiple intermediate conformations, in which the transport domain is captured halfway through its elevator motion. Our structures present a trajectory of the conformational transition in the elevator model, revealing multiple intermediate steps and state-dependent conformational changes within the transport domain that are associated with the elevator-like motion.
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8
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Mulinta R, Yao SYM, Ng AML, Cass CE, Young JD. Substituted cysteine accessibility method (SCAM) analysis of the transport domain of human concentrative nucleoside transporter 3 (hCNT3) and other family members reveals features of structural and functional importance. J Biol Chem 2017; 292:9505-9522. [PMID: 28385889 PMCID: PMC5465479 DOI: 10.1074/jbc.m116.743997] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 03/31/2017] [Indexed: 12/13/2022] Open
Abstract
The human SLC28 family of concentrative nucleoside transporter (CNT) proteins has three members: hCNT1, hCNT2, and hCNT3. Na+-coupled hCNT1 and hCNT2 transport pyrimidine and purine nucleosides, respectively, whereas hCNT3 transports both pyrimidine and purine nucleosides utilizing Na+ and/or H+ electrochemical gradients. Escherichia coli CNT family member NupC resembles hCNT1 in permeant selectivity but is H+-coupled. Using heterologous expression in Xenopus oocytes and the engineered cysteine-less hCNT3 protein hCNT3(C-), substituted cysteine accessibility method analysis with the membrane-impermeant thiol reactive reagent p-chloromercuribenzene sulfonate was performed on the transport domain (interfacial helix 2, hairpin 1, putative transmembrane domain (TM) 7, and TM8), as well as TM9 of the scaffold domain of the protein. This systematic scan of the entire C-terminal half of hCNT3(C-) together with parallel studies of the transport domain of wild-type hCNT1 and the corresponding TMs of cysteine-less NupC(C-) yielded results that validate the newly developed structural homology model of CNT membrane architecture for human CNTs, revealed extended conformationally mobile regions within transport-domain TMs, identified pore-lining residues of functional importance, and provided evidence of an emerging novel elevator-type mechanism of transporter function.
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Affiliation(s)
- Ras Mulinta
- From the Membrane Protein Disease Research Group, Departments of Physiology and
| | - Sylvia Y M Yao
- From the Membrane Protein Disease Research Group, Departments of Physiology and
| | - Amy M L Ng
- From the Membrane Protein Disease Research Group, Departments of Physiology and
| | - Carol E Cass
- Oncology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada and.,the Cross Cancer Institute, Edmonton, Alberta T6G 2H7, Canada
| | - James D Young
- From the Membrane Protein Disease Research Group, Departments of Physiology and
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9
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Johnson ZL, Lee JH, Lee K, Lee M, Kwon DY, Hong J, Lee SY. Structural basis of nucleoside and nucleoside drug selectivity by concentrative nucleoside transporters. eLife 2014; 3:e03604. [PMID: 25082345 PMCID: PMC4139061 DOI: 10.7554/elife.03604] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Concentrative nucleoside transporters (CNTs) are responsible for cellular entry of nucleosides, which serve as precursors to nucleic acids and act as signaling molecules. CNTs also play a crucial role in the uptake of nucleoside-derived drugs, including anticancer and antiviral agents. Understanding how CNTs recognize and import their substrates could not only lead to a better understanding of nucleoside-related biological processes but also the design of nucleoside-derived drugs that can better reach their targets. Here, we present a combination of X-ray crystallographic and equilibrium-binding studies probing the molecular origins of nucleoside and nucleoside drug selectivity of a CNT from Vibrio cholerae. We then used this information in chemically modifying an anticancer drug so that it is better transported by and selective for a single human CNT subtype. This work provides proof of principle for utilizing transporter structural and functional information for the design of compounds that enter cells more efficiently and selectively. DOI:http://dx.doi.org/10.7554/eLife.03604.001 DNA molecules are made from four bases—often named ‘G’, ‘A’, ‘C’, and ‘T’—that are arranged along a backbone made of sugars and phosphate groups. Chemicals called nucleosides are essentially the same as these four building blocks of DNA (and other similar molecules) but without the phosphate groups. Proteins called nucleoside transporters are found in the membranes that surround cells and can pump nucleosides into the cell. These transporters also allow drugs that are made from modified nucleosides to enter cells; however, it was previously unclear how different transporters recognized and imported specific nucleosides. Like other proteins, nucleoside transporters are basically strings of amino acids that have folded into a specific three-dimensional shape. A protein's shape is often important for defining what that protein can do, as often other molecules must bind to proteins—much like a key fitting into a lock. Johnson et al. have now revealed the three-dimensional structure of one nucleoside transporter protein bound to different nucleosides and nucleoside-derived chemicals, including three anti-cancer drugs and one anti-viral drug. Some of these chemicals were shown to bind more strongly to the transporter protein than others, and examining the three-dimensional structures revealed that the different chemicals interacted with slightly different amino acids in the transporter protein. Johnson et al. then used this information to chemically modify an anticancer drug so that it is transported more easily into cells and is imported by only one of the subtypes of nucleoside transporters that are found in humans. This provides proof of principle that information about the structure and function of a transporter protein can help to redesign chemicals such that they can enter cells more efficiently, and to tailor them for transport by specific transporters. A similar approach may in the future allow researchers to design new nucleoside-derived drugs that are better at getting inside specific cells and, as such, provide effective treatments against cancers and viral infections. DOI:http://dx.doi.org/10.7554/eLife.03604.002
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Affiliation(s)
- Zachary Lee Johnson
- Department of Biochemistry, Duke University Medical Center, Durham, United States
| | - Jun-Ho Lee
- Department of Biochemistry, Duke University Medical Center, Durham, United States
| | - Kiyoun Lee
- Department of Chemistry, Duke University, Durham, United States
| | - Minhee Lee
- Department of Chemistry, Duke University, Durham, United States
| | - Do-Yeon Kwon
- Department of Chemistry, Duke University, Durham, United States
| | - Jiyong Hong
- Department of Chemistry, Duke University, Durham, United States Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, United States
| | - Seok-Yong Lee
- Department of Biochemistry, Duke University Medical Center, Durham, United States
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10
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Johnson ZL, Cheong CG, Lee SY. Crystal structure of a concentrative nucleoside transporter from Vibrio cholerae at 2.4 Å. Nature 2012; 483:489-93. [PMID: 22407322 PMCID: PMC3310960 DOI: 10.1038/nature10882] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Accepted: 01/20/2012] [Indexed: 02/07/2023]
Abstract
Nucleosides are required for DNA and RNA synthesis, and the nucleoside adenosine has a function in a variety of signalling processes. Transport of nucleosides across cell membranes provides the major source of nucleosides in many cell types and is also responsible for the termination of adenosine signalling. As a result of their hydrophilic nature, nucleosides require a specialized class of integral membrane proteins, known as nucleoside transporters (NTs), for specific transport across cell membranes. In addition to nucleosides, NTs are important determinants for the transport of nucleoside-derived drugs across cell membranes. A wide range of nucleoside-derived drugs, including anticancer drugs (such as Ara-C and gemcitabine) and antiviral drugs (such as zidovudine and ribavirin), have been shown to depend, at least in part, on NTs for transport across cell membranes. Concentrative nucleoside transporters, members of the solute carrier transporter superfamily SLC28, use an ion gradient in the active transport of both nucleosides and nucleoside-derived drugs against their chemical gradients. The structural basis for selective ion-coupled nucleoside transport by concentrative nucleoside transporters is unknown. Here we present the crystal structure of a concentrative nucleoside transporter from Vibrio cholerae in complex with uridine at 2.4 Å. Our functional data show that, like its human orthologues, the transporter uses a sodium-ion gradient for nucleoside transport. The structure reveals the overall architecture of this class of transporter, unravels the molecular determinants for nucleoside and sodium binding, and provides a framework for understanding the mechanism of nucleoside and nucleoside drug transport across cell membranes.
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Affiliation(s)
- Zachary Lee Johnson
- Department of Biochemistry and Ion Channel Research Unit, Duke University Medical Center, 2 Genome Ct, Durham, North Carolina, 27710, USA
| | - Cheom-Gil Cheong
- Department of Biochemistry and Ion Channel Research Unit, Duke University Medical Center, 2 Genome Ct, Durham, North Carolina, 27710, USA
| | - Seok-Yong Lee
- Department of Biochemistry and Ion Channel Research Unit, Duke University Medical Center, 2 Genome Ct, Durham, North Carolina, 27710, USA
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11
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Cano-Soldado P, Gorraitz E, Errasti-Murugarren E, Casado FJ, Lostao MP, Pastor-Anglada M. Functional analysis of the human concentrative nucleoside transporter-1 variant hCNT1S546P provides insight into the sodium-binding pocket. Am J Physiol Cell Physiol 2012; 302:C257-66. [DOI: 10.1152/ajpcell.00198.2011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
SLC28 genes, encoding concentrative nucleoside transporter proteins (CNT), show little genetic variability, although a few single nucleotide polymorphisms (SNPs) have been associated with marked functional disturbances. In particular, human CNT1S546P had been reported to result in negligible thymidine uptake. In this study we have characterized the molecular mechanisms responsible for this apparent loss of function. The hCNT1S546P variant showed an appropriate endoplasmic reticulum export and insertion into the plasma membrane, whereas loss of nucleoside translocation ability affected all tested nucleoside and nucleoside-derived drugs. Site-directed mutagenesis analysis revealed that it is the lack of the serine residue itself responsible for the loss of hCNT1 function. This serine residue is highly conserved, and mutation of the analogous serine in hCNT2 (Ser541) and hCNT3 (Ser568) resulted in total and partial loss of function, respectively. Moreover, hCNT3, the only member that shows a 2Na+/1 nucleoside stoichiometry, showed altered Na+ binding properties associated with a shift in the Hill coefficient, consistent with one Na+ binding site being affected by the mutation. Two-electrode voltage-clamp studies using the hCNT1S546P mutant revealed the occurrence of Na+ leak, which was dependent on the concentration of extracellular Na+ indicating that, although the variant is unable to transport nucleosides, there is an uncoupled sodium transport.
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Affiliation(s)
- Pedro Cano-Soldado
- Departament de Bioquímica i Biologia Molecular, Institut de Biomedicina (IBUB), Universitat de Barcelona and CIBER EHD, Barcelona
| | - Edurne Gorraitz
- Department of Food Science, Physiology and Toxicology, University of Navarra, Pamplona, Spain
| | - Ekaitz Errasti-Murugarren
- Departament de Bioquímica i Biologia Molecular, Institut de Biomedicina (IBUB), Universitat de Barcelona and CIBER EHD, Barcelona
| | - F. Javier Casado
- Departament de Bioquímica i Biologia Molecular, Institut de Biomedicina (IBUB), Universitat de Barcelona and CIBER EHD, Barcelona
| | - M. Pilar Lostao
- Department of Food Science, Physiology and Toxicology, University of Navarra, Pamplona, Spain
| | - Marçal Pastor-Anglada
- Departament de Bioquímica i Biologia Molecular, Institut de Biomedicina (IBUB), Universitat de Barcelona and CIBER EHD, Barcelona
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12
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Cano-Soldado P, Pastor-Anglada M. Transporters that translocate nucleosides and structural similar drugs: structural requirements for substrate recognition. Med Res Rev 2011; 32:428-57. [DOI: 10.1002/med.20221] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Pedro Cano-Soldado
- Departament de Bioquímica i Biologia Molecular; Institut de Biomedicina de la Universitat de Barcelona (IBUB); Universitat de Barcelona and CIBER EHD; Barcelona Spain
| | - Marçal Pastor-Anglada
- Departament de Bioquímica i Biologia Molecular; Institut de Biomedicina de la Universitat de Barcelona (IBUB); Universitat de Barcelona and CIBER EHD; Barcelona Spain
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13
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Effects of Na+ and H+ on steady-state and presteady-state currents of the human concentrative nucleoside transporter 3 (hCNT3). Pflugers Arch 2010; 460:617-32. [DOI: 10.1007/s00424-010-0846-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Revised: 04/13/2010] [Accepted: 05/04/2010] [Indexed: 11/26/2022]
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14
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Slugoski MD, Ng AML, Yao SYM, Lin CC, Mulinta R, Cass CE, Baldwin SA, Young JD. Substituted cysteine accessibility method analysis of human concentrative nucleoside transporter hCNT3 reveals a novel discontinuous region of functional importance within the CNT family motif (G/A)XKX3NEFVA(Y/M/F). J Biol Chem 2009; 284:17281-17292. [PMID: 19380585 DOI: 10.1074/jbc.m109.009704] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The human SLC28 family of integral membrane CNT (concentrative nucleoside transporter) proteins has three members, hCNT1, hCNT2, and hCNT3. Na(+)-coupled hCNT1 and hCNT2 transport pyrimidine and purine nucleosides, respectively, whereas hCNT3 mediates transport of both pyrimidine and purine nucleosides utilizing Na(+) and/or H(+) electrochemical gradients. These and other eukaryote CNTs are currently defined by a putative 13-transmembrane helix (TM) topology model with an intracellular N terminus and a glycosylated extracellular C terminus. Recent mutagenesis studies, however, have provided evidence supporting an alternative 15-TM membrane architecture. In the absence of CNT crystal structures, valuable information can be gained about residue localization and function using substituted cysteine accessibility method analysis with thiol-reactive reagents, such as p-chloromercuribenzene sulfonate. Using heterologous expression in Xenopus oocytes and the cysteineless hCNT3 protein hCNT3C-, substituted cysteine accessibility method analysis with p-chloromercuribenzene sulfonate was performed on the TM 11-13 region, including bridging extramembranous loops. The results identified residues of functional importance and, consistent with a new revised 15-TM CNT membrane architecture, suggest a novel membrane-associated topology for a region of the protein (TM 11A) that includes the highly conserved CNT family motif (G/A)XKX(3)NEFVA(Y/M/F).
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Affiliation(s)
| | - Amy M L Ng
- From the Departments of Physiology, Edmonton, Alberta T6G 2H7, Canada
| | - Sylvia Y M Yao
- From the Departments of Physiology, Edmonton, Alberta T6G 2H7, Canada
| | - Colin C Lin
- From the Departments of Physiology, Edmonton, Alberta T6G 2H7, Canada
| | - Ras Mulinta
- From the Departments of Physiology, Edmonton, Alberta T6G 2H7, Canada
| | - Carol E Cass
- Oncology, Membrane Protein Research Group, University of Alberta, Edmonton, Alberta T6G 2H7, Canada; Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada
| | - Stephen A Baldwin
- Astbury Centre for Structural Molecular Biology, Institute of Membrane and Systems Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - James D Young
- From the Departments of Physiology, Edmonton, Alberta T6G 2H7, Canada.
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