1
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Burgardt NI, Melian NA, González Flecha FL. Copper resistance in the cold: Genome analysis and characterisation of a P IB-1 ATPase in Bizionia argentinensis. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13278. [PMID: 38943264 PMCID: PMC11213822 DOI: 10.1111/1758-2229.13278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 04/19/2024] [Indexed: 07/01/2024]
Abstract
Copper homeostasis is a fundamental process in organisms, characterised by unique pathways that have evolved to meet specific needs while preserving core resistance mechanisms. While these systems are well-documented in model bacteria, information on copper resistance in species adapted to cold environments is scarce. This study investigates the potential genes related to copper homeostasis in the genome of Bizionia argentinensis (JUB59-T), a psychrotolerant bacterium isolated from Antarctic seawater. We identified several genes encoding proteins analogous to those crucial for copper homeostasis, including three sequences of copper-transport P1B-type ATPases. One of these, referred to as BaCopA1, was chosen for cloning and expression in Saccharomyces cerevisiae. BaCopA1 was successfully integrated into yeast membranes and subsequently extracted with detergent. The purified BaCopA1 demonstrated the ability to catalyse ATP hydrolysis at low temperatures. Structural models of various BaCopA1 conformations were generated and compared with mesophilic and thermophilic homologous structures. The significant conservation of critical residues and structural similarity among these proteins suggest a shared reaction mechanism for copper transport. This study is the first to report a psychrotolerant P1B-ATPase that has been expressed and purified in a functional form.
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Affiliation(s)
- Noelia I. Burgardt
- Laboratorio de Biofísica Molecular, Facultad de Farmacia y Bioquímica, Instituto de Química y Fisicoquímica BiológicasUniversidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y TécnicasBuenos AiresArgentina
- Present address:
Departamento de Ciencia y TecnologíaUniversidad Nacional de QuilmesBernalArgentina
| | - Noelia A. Melian
- Laboratorio de Biofísica Molecular, Facultad de Farmacia y Bioquímica, Instituto de Química y Fisicoquímica BiológicasUniversidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y TécnicasBuenos AiresArgentina
| | - F. Luis González Flecha
- Laboratorio de Biofísica Molecular, Facultad de Farmacia y Bioquímica, Instituto de Química y Fisicoquímica BiológicasUniversidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y TécnicasBuenos AiresArgentina
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2
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Ongey EL, Banerjee A. In vitro reconstitution of transition metal transporters. J Biol Chem 2024:107589. [PMID: 39032653 DOI: 10.1016/j.jbc.2024.107589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 06/28/2024] [Accepted: 07/03/2024] [Indexed: 07/23/2024] Open
Abstract
Transition metal ions are critically important across all kingdoms of life. The chemical properties of iron, copper, zinc, manganese, cobalt, and nickel make them very attractive for use as cofactors in metalloenzymes and/or metalloproteins. Their versatile chemistry in aqueous solution enables them to function both as an electron donors and acceptors, and thus participate in both reduction and oxidation reactions respectively. Transition metal ions can also function as nonredox mutidentate coordination sites that play essential roles in macromolecular structure and function. Malfunction in transition metal transport and homeostasis has been linked to a wide number of human diseases including cancer, diabetes and neurodegenerative disorders. Transition metal transporters are central players in the physiology of transition metals whereby they move transition metals in and out of cellular compartments. In this review, we provide a comprehensive overview of in vitro reconstitution of the activity of integral membrane transition metal transporters and discuss strategies that have been successfully implemented to overcome the challenges. We also discuss recent advances in our understanding of transition metal transport mechanisms and the techniques that are currently employed to decipher the molecular basis of transport activities of these proteins. Deep mechanistic insights into transition metal transport systems will be essential to understand their malfunction in human diseases and target them for potential therapeutic strategies.
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Affiliation(s)
- Elvis L Ongey
- Cell Biology and Neurobiology Branch, National Institutes of Child Health and Human, Development, National Institutes of Health, Bethesda, MD-20892
| | - Anirban Banerjee
- Cell Biology and Neurobiology Branch, National Institutes of Child Health and Human, Development, National Institutes of Health, Bethesda, MD-20892.
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3
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Gaschignard G, Millet M, Bruley A, Benzerara K, Dezi M, Skouri-Panet F, Duprat E, Callebaut I. AlphaFold2-guided description of CoBaHMA, a novel family of bacterial domains within the heavy-metal-associated superfamily. Proteins 2024; 92:776-794. [PMID: 38258321 DOI: 10.1002/prot.26668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/22/2023] [Accepted: 01/01/2024] [Indexed: 01/24/2024]
Abstract
Three-dimensional (3D) structure information, now available at the proteome scale, may facilitate the detection of remote evolutionary relationships in protein superfamilies. Here, we illustrate this with the identification of a novel family of protein domains related to the ferredoxin-like superfold, by combining (i) transitive sequence similarity searches, (ii) clustering approaches, and (iii) the use of AlphaFold2 3D structure models. Domains of this family were initially identified in relation with the intracellular biomineralization of calcium carbonates by Cyanobacteria. They are part of the large heavy-metal-associated (HMA) superfamily, departing from the latter by specific sequence and structural features. In particular, most of them share conserved basic amino acids (hence their name CoBaHMA for Conserved Basic residues HMA), forming a positively charged surface, which is likely to interact with anionic partners. CoBaHMA domains are found in diverse modular organizations in bacteria, existing in the form of monodomain proteins or as part of larger proteins, some of which are membrane proteins involved in transport or lipid metabolism. This suggests that the CoBaHMA domains may exert a regulatory function, involving interactions with anionic lipids. This hypothesis might have a particular resonance in the context of the compartmentalization observed for cyanobacterial intracellular calcium carbonates.
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Affiliation(s)
- Geoffroy Gaschignard
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Maxime Millet
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Apolline Bruley
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Karim Benzerara
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Manuela Dezi
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Feriel Skouri-Panet
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Elodie Duprat
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
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4
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Dmitriev OY, Patry J. Structure and mechanism of the human copper transporting ATPases: Fitting the pieces into a moving puzzle. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184306. [PMID: 38408697 DOI: 10.1016/j.bbamem.2024.184306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/07/2024] [Accepted: 02/18/2024] [Indexed: 02/28/2024]
Abstract
Human copper transporters ATP7B and ATP7A deliver copper to biosynthetic pathways and maintain copper homeostasis in the cell. These enzymes combine several challenges for structural biology because they are large low abundance membrane proteins with many highly mobile domains and long disordered loops. No method has yet succeeded in solving the structure of the complete fully functional protein. Still, X-ray crystallography, Cryo-EM and NMR helped to piece together a structure based model of the enzyme activity and regulation by copper. We review the structures of ATP7B and ATP7A with an emphasis on the mechanistic insights into the unique aspects of the transport function and regulation of the human copper ATPases that have emerged from more than twenty years of research.
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Affiliation(s)
- Oleg Y Dmitriev
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada.
| | - Jaala Patry
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
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5
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Li J, Zhang Z, Shi G. Genome-Wide Identification and Expression Profiling of Heavy Metal ATPase (HMA) Genes in Peanut: Potential Roles in Heavy Metal Transport. Int J Mol Sci 2024; 25:613. [PMID: 38203784 PMCID: PMC10779257 DOI: 10.3390/ijms25010613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/29/2023] [Accepted: 12/31/2023] [Indexed: 01/12/2024] Open
Abstract
The heavy metal ATPase (HMA) family belongs to the P-type ATPase superfamily and plays an essential role in the regulation of metal homeostasis in plants. However, the gene family has not been fully investigated in peanut. Here, a genome-wide identification and bioinformatics analysis was performed on AhHMA genes in peanut, and the expression of 12 AhHMA genes in response to Cu, Zn, and Cd was evaluated in two peanut cultivars (Silihong and Fenghua 1) differing in Cd accumulation. A total of 21 AhHMA genes were identified in the peanut genome, including ten paralogous gene pairs derived from whole-genome duplication, and an additional gene resulting from tandem duplication. AhHMA proteins could be divided into six groups (I-VI), belonging to two clades (Zn/Co/Cd/Pb-ATPases and Cu/Ag-ATPases). Most AhHMA proteins within the same clade or group generally have a similar structure. However, significant divergence exists in the exon/intron organization even between duplicated gene pairs. RNA-seq data showed that most AhHMA genes are preferentially expressed in roots, shoots, and reproductive tissues. qRT-PCR results revealed that AhHMA1.1/1.2, AhHMA3.1/3.2, AhHMA7.1/7.4, and AhHMA8.1 might be involved in Zn transport in peanut plants, while AhHMA3.2 and AhHMA7.5 might be involved in Cd transport. Our findings provide clues to further characterize the functions of AhHMA genes in metal uptake and translocation in peanut plants.
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Affiliation(s)
| | | | - Gangrong Shi
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China; (J.L.); (Z.Z.)
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6
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Li W, Wang L, Li X, Zheng X, Cohen MF, Liu YX. Sequence-based Functional Metagenomics Reveals Novel Natural Diversity of Functional CopA in Environmental Microbiomes. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:1182-1194. [PMID: 36089219 PMCID: PMC11082258 DOI: 10.1016/j.gpb.2022.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 06/15/2023]
Abstract
Exploring the natural diversity of functional genes/proteins from environmental DNA in high throughput remains challenging. In this study, we developed a sequence-based functional metagenomics procedure for mining the diversity of copper (Cu) resistance gene copA in global microbiomes, by combining the metagenomic assembly technology, local BLAST, evolutionary trace analysis (ETA), chemical synthesis, and conventional functional genomics. In total, 87 metagenomes were collected from a public database and subjected to copA detection, resulting in 93,899 hits. Manual curation of 1214 hits of high confidence led to the retrieval of 517 unique CopA candidates, which were further subjected to ETA. Eventually, 175 novel copA sequences of high quality were discovered. Phylogenetic analysis showed that almost all these putative CopA proteins were distantly related to known CopA proteins, with 55 sequences from totally unknown species. Ten novel and three known copA genes were chemically synthesized for further functional genomic tests using the Cu-sensitive Escherichia coli (ΔcopA). The growth test and Cu uptake determination showed that five novel clones had positive effects on host Cu resistance and uptake. One recombinant harboring copA-like 15 (copAL15) successfully restored Cu resistance of the host with a substantially enhanced Cu uptake. Two novel copA genes were fused with the gfp gene and expressed in E. coli for microscopic observation. Imaging results showed that they were successfully expressed and their proteins were localized to the membrane. The results here greatly expand the diversity of known CopA proteins, and the sequence-based procedure developed overcomes biases in length, screening methods, and abundance of conventional functional metagenomics.
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Affiliation(s)
- Wenjun Li
- Hebei Key Laboratory of Soil Ecology, Centre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Likun Wang
- Hebei Key Laboratory of Soil Ecology, Centre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Xiaofang Li
- Hebei Key Laboratory of Soil Ecology, Centre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China.
| | - Xin Zheng
- Hebei Key Laboratory of Soil Ecology, Centre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Michael F Cohen
- Department of Biology, Sonoma State University, Rohnert Park, CA 94928, USA
| | - Yong-Xin Liu
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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7
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Hendrix J, Epperson LE, Tong EI, Chan YL, Hasan NA, Dawrs SN, Norton GJ, Virdi R, Crooks JL, Chan ED, Honda JR, Strong M. Complete genome assembly of Hawai'i environmental nontuberculous mycobacteria reveals unexpected co-isolation with methylobacteria. PLoS One 2023; 18:e0291072. [PMID: 37703253 PMCID: PMC10499228 DOI: 10.1371/journal.pone.0291072] [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: 02/24/2023] [Accepted: 08/22/2023] [Indexed: 09/15/2023] Open
Abstract
Nontuberculous mycobacteria (NTM) are ubiquitous environmental opportunistic pathogens that can cause chronic lung disease. Within the United States, Hawai'i has the highest incidence of NTM lung disease, though the precise reasons are yet to be fully elucidated. One possibility is the high prevalence of NTM in the Hawai'i environment acting as a potential reservoir for opportunistic NTM infections. Through our previous initiatives to collect and characterize NTM in Hawai'i, community scientists of Hawai'i have collected thousands of environmental samples for sequencing. Here, these community scientists were invited for the first time into a high school lab in O'ahu for a genomic sequencing workshop, where participants sequenced four of the collected isolate genomic samples using the Oxford Nanopore Technologies MinION sequencer. Participants generated high quality long read data that when combined with short read Illumina data yielded complete bacterial genomic assemblies suitable for in-depth analysis. The gene annotation analysis identified a suite of genes that might help NTM thrive in the Hawai'i environment. Further, we found evidence of co-occurring methylobacteria, revealed from the sequencing data, suggesting that in some cases methylobacteria and NTM may coexist in the same niche, challenging previously accepted paradigms. The sequencing efforts presented here generated novel insights regarding the potential survival strategies and microbial interactions of NTM in the geographic hot spot of Hawai'i. We highlight the contributions of community scientists and present an activity that can be reimplemented as a workshop or classroom activity by other research groups to engage their local communities.
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Affiliation(s)
- Jo Hendrix
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, United States of America
- Computational Bioscience Program, University of Colorado, Anschutz Medical Campus, Aurora, CO, United States of America
| | - L. Elaine Epperson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, United States of America
| | - Eric I. Tong
- ‘Iolani School, Honolulu, Hawai’i, United States of America
| | - Yvonne L. Chan
- ‘Iolani School, Honolulu, Hawai’i, United States of America
| | - Nabeeh A. Hasan
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, United States of America
| | - Stephanie N. Dawrs
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, United States of America
| | - Grant J. Norton
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, United States of America
| | - Ravleen Virdi
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, United States of America
| | - James L. Crooks
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, CO, United States of America
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, United States of America
| | - Edward D. Chan
- Department of Medicine and Academic Affairs, National Jewish Health, Denver, CO, United States of America
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
- Department of Medicine, Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, CO, United States of America
| | - Jennifer R. Honda
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas Health Science Center at Tyler, Tyler, TX, United States of America
| | - Michael Strong
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, United States of America
- Computational Bioscience Program, University of Colorado, Anschutz Medical Campus, Aurora, CO, United States of America
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8
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Abeyrathna SS, Abeyrathna NS, Basak P, Irvine GW, Zhang L, Meloni G. Plastic recognition and electrogenic uniport translocation of 1 st-, 2 nd-, and 3 rd-row transition and post-transition metals by primary-active transmembrane P 1B-2-type ATPase pumps. Chem Sci 2023; 14:6059-6078. [PMID: 37293658 PMCID: PMC10246665 DOI: 10.1039/d3sc00347g] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/10/2023] [Indexed: 06/10/2023] Open
Abstract
Transmembrane P1B-type ATPase pumps catalyze the extrusion of transition metal ions across cellular lipid membranes to maintain essential cellular metal homeostasis and detoxify toxic metals. Zn(ii)-pumps of the P1B-2-type subclass, in addition to Zn2+, select diverse metals (Pb2+, Cd2+ and Hg2+) at their transmembrane binding site and feature promiscuous metal-dependent ATP hydrolysis in the presence of these metals. Yet, a comprehensive understanding of the transport of these metals, their relative translocation rates, and transport mechanism remain elusive. We developed a platform for the characterization of primary-active Zn(ii)-pumps in proteoliposomes to study metal selectivity, translocation events and transport mechanism in real-time, employing a "multi-probe" approach with fluorescent sensors responsive to diverse stimuli (metals, pH and membrane potential). Together with atomic-resolution investigation of cargo selection by X-ray absorption spectroscopy (XAS), we demonstrate that Zn(ii)-pumps are electrogenic uniporters that preserve the transport mechanism with 1st-, 2nd- and 3rd-row transition metal substrates. Promiscuous coordination plasticity, guarantees diverse, yet defined, cargo selectivity coupled to their translocation.
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Affiliation(s)
- Sameera S Abeyrathna
- Department of Chemistry and Biochemistry, The University of Texas at Dallas Richardson TX 75080 USA
| | - Nisansala S Abeyrathna
- Department of Chemistry and Biochemistry, The University of Texas at Dallas Richardson TX 75080 USA
| | - Priyanka Basak
- Department of Chemistry and Biochemistry, The University of Texas at Dallas Richardson TX 75080 USA
| | - Gordon W Irvine
- Department of Chemistry and Biochemistry, The University of Texas at Dallas Richardson TX 75080 USA
| | - Limei Zhang
- Department of Biochemistry and Redox Biology Center and the Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln Lincoln NE 68588 USA
| | - Gabriele Meloni
- Department of Chemistry and Biochemistry, The University of Texas at Dallas Richardson TX 75080 USA
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9
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Yang GM, Xu L, Wang RM, Tao X, Zheng ZW, Chang S, Ma D, Zhao C, Dong Y, Wu S, Guo J, Wu ZY. Structures of the human Wilson disease copper transporter ATP7B. Cell Rep 2023; 42:112417. [PMID: 37074913 DOI: 10.1016/j.celrep.2023.112417] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 02/22/2023] [Accepted: 04/05/2023] [Indexed: 04/20/2023] Open
Abstract
The P-type ATPase ATP7B exports cytosolic copper and plays an essential role in the regulation of cellular copper homeostasis. Mutants of ATP7B cause Wilson disease (WD), an autosomal recessive disorder of copper metabolism. Here, we present cryoelectron microscopy (cryo-EM) structures of human ATP7B in the E1 state in the apo, the putative copper-bound, and the putative cisplatin-bound forms. In ATP7B, the N-terminal sixth metal-binding domain (MBD6) binds at the cytosolic copper entry site of the transmembrane domain (TMD), facilitating the delivery of copper from the MBD6 to the TMD. The sulfur-containing residues in the TMD of ATP7B mark the copper transport pathway. By comparing structures of the E1 state human ATP7B and E2-Pi state frog ATP7B, we propose the ATP-driving copper transport model of ATP7B. These structures not only advance our understanding of the mechanisms of ATP7B-mediated copper export but can also guide the development of therapeutics for the treatment of WD.
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Affiliation(s)
- Guo-Min Yang
- Department of Medical Genetics and Center for Rare Diseases, and Department of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Lingyi Xu
- Department of Biophysics, and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Rou-Min Wang
- Department of Medical Genetics and Center for Rare Diseases, and Department of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Xin Tao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Zi-Wei Zheng
- Department of Medical Genetics and Center for Rare Diseases, and Department of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Shenghai Chang
- Department of Biophysics, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Center of Cryo Electron Microscopy, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Demin Ma
- Department of Biophysics, and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Cheng Zhao
- Department of Biophysics, and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Yi Dong
- Department of Medical Genetics and Center for Rare Diseases, and Department of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Shan Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.
| | - Jiangtao Guo
- Department of Biophysics, and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Department of Cardiology, Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China; Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, Zhejiang 311121, China; NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Science and Brain-machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310016, China.
| | - Zhi-Ying Wu
- Department of Medical Genetics and Center for Rare Diseases, and Department of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China; Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, Zhejiang 311121, China; NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Science and Brain-machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang 310016, China.
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10
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Azfar M, van Veen S, Houdou M, Hamouda NN, Eggermont J, Vangheluwe P. P5B-ATPases in the mammalian polyamine transport system and their role in disease. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119354. [PMID: 36064065 DOI: 10.1016/j.bbamcr.2022.119354] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 06/15/2023]
Abstract
Polyamines (PAs) are physiologically relevant molecules that are ubiquitous in all organisms. The vitality of PAs to the healthy functioning of a cell is due to their polycationic nature causing them to interact with a vast plethora of cellular players and partake in numerous cellular pathways. Naturally, the homeostasis of such essential molecules is tightly regulated in a strictly controlled interplay between intracellular synthesis and degradation, uptake from and secretion to the extracellular compartment, as well as intracellular trafficking. Not surprisingly, dysregulated PA homeostasis and signaling are implicated in multiple disorders, ranging from cancer to neurodegeneration; leading many to propose rectifying the PA balance as a potential therapeutic strategy. Despite being well characterized in bacteria, fungi and plants, the molecular identity and properties of the PA transporters in animals are poorly understood. This review brings together the current knowledge of the cellular function of the mammalian PA transport system (PTS). We will focus on the role of P5B-ATPases ATP13A2-5 which are PA transporters in the endosomal system that have emerged as key players in cellular PA uptake and organelle homeostasis. We will discuss recent breakthroughs on their biochemical and structural properties as well as their implications for disease and therapy.
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Affiliation(s)
- Mujahid Azfar
- Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, KU Leuven, B-3000 Leuven, Belgium
| | - Sarah van Veen
- Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, KU Leuven, B-3000 Leuven, Belgium
| | - Marine Houdou
- Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, KU Leuven, B-3000 Leuven, Belgium
| | - Norin Nabil Hamouda
- Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium
| | - Jan Eggermont
- Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium
| | - Peter Vangheluwe
- Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, KU Leuven, B-3000 Leuven, Belgium.
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11
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Raya D, Shreya A, Kumar A, Giri SK, Salem DR, Gnimpieba EZ, Gadhamshetty V, Dhiman SS. Molecular regulation of conditioning film formation and quorum quenching in sulfate reducing bacteria. Front Microbiol 2022; 13:1008536. [PMID: 36386676 PMCID: PMC9659907 DOI: 10.3389/fmicb.2022.1008536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 09/26/2022] [Indexed: 09/19/2023] Open
Abstract
Sensing surface topography, an upsurge of signaling biomolecules, and upholding cellular homeostasis are the rate-limiting spatio-temporal events in microbial attachment and biofilm formation. Initially, a set of highly specialized proteins, viz. conditioning protein, directs the irreversible attachment of the microbes. Later signaling molecules, viz. autoinducer, take over the cellular communication phenomenon, resulting in a mature microbial biofilm. The mandatory release of conditioning proteins and autoinducers corroborated the existence of two independent mechanisms operating sequentially for biofilm development. However, both these mechanisms are significantly affected by the availability of the cofactor, e.g., Copper (Cu). Generally, the Cu concentration beyond threshold levels is detrimental to the anaerobes except for a few species of sulfate-reducing bacteria (SRB). Remarkably SRB has developed intricate ways to resist and thrive in the presence of Cu by activating numerous genes responsible for modifying the presence of more toxic Cu(I) to Cu(II) within the periplasm, followed by their export through the outer membrane. Therefore, the determinants of Cu toxicity, sequestration, and transportation are reconnoitered for their contribution towards microbial adaptations and biofilm formation. The mechanistic details revealing Cu as a quorum quencher (QQ) are provided in addition to the three pathways involved in the dissolution of cellular communications. This review articulates the Machine Learning based data curing and data processing for designing novel anti-biofilm peptides and for an in-depth understanding of QQ mechanisms. A pioneering data set has been mined and presented on the functional properties of the QQ homolog in Oleidesulfovibrio alaskensis G20 and residues regulating the multicopper oxidase properties in SRB.
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Affiliation(s)
- Dheeraj Raya
- Department of Civil and Environmental Engineering, South Dakota Mines, Rapid City, SD, United States
- 2DBEST Research Center, South Dakota Mines, Rapid City, SD, United States
| | - Aritree Shreya
- Department of Civil and Environmental Engineering, South Dakota Mines, Rapid City, SD, United States
- 2DBEST Research Center, South Dakota Mines, Rapid City, SD, United States
| | - Anil Kumar
- Centre for Medical Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Shiv Kumar Giri
- Department of Biotechnology, Maharaja Agrasen University, Baddi, Himachal Pradesh, India
| | - David R. Salem
- Chemical and Biological Engineering, South Dakota Mines, Rapid City, SD, United States
| | - Etienne Z. Gnimpieba
- 2DBEST Research Center, South Dakota Mines, Rapid City, SD, United States
- Department of Biomedical Engineering, University of South Dakota, Vermillion, SD, United States
| | - Venkataramana Gadhamshetty
- Department of Civil and Environmental Engineering, South Dakota Mines, Rapid City, SD, United States
- 2DBEST Research Center, South Dakota Mines, Rapid City, SD, United States
| | - Saurabh Sudha Dhiman
- Department of Civil and Environmental Engineering, South Dakota Mines, Rapid City, SD, United States
- 2DBEST Research Center, South Dakota Mines, Rapid City, SD, United States
- Department of Chemistry, Biology and Health Sciences, South Dakota Mines, Rapid City, SD, United States
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12
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Orädd F, Steffen JH, Gourdon P, Andersson M. Copper binding leads to increased dynamics in the regulatory N-terminal domain of full-length human copper transporter ATP7B. PLoS Comput Biol 2022; 18:e1010074. [PMID: 36070320 PMCID: PMC9484656 DOI: 10.1371/journal.pcbi.1010074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 09/19/2022] [Accepted: 08/17/2022] [Indexed: 11/25/2022] Open
Abstract
ATP7B is a human copper-transporting P1B-type ATPase that is involved in copper homeostasis and resistance to platinum drugs in cancer cells. ATP7B consists of a copper-transporting core and a regulatory N-terminal tail that contains six metal-binding domains (MBD1-6) connected by linker regions. The MBDs can bind copper, which changes the dynamics of the regulatory domain and activates the protein, but the underlying mechanism remains unknown. To identify possible copper-specific structural dynamics involved in transport regulation, we constructed a model of ATP7B spanning the N-terminal tail and core catalytic domains and performed molecular dynamics (MD) simulations with (holo) and without (apo) copper ions bound to the MBDs. In the holo protein, MBD2, MBD3 and MBD5 showed enhanced mobilities, which resulted in a more extended N-terminal regulatory region. The observed separation of MBD2 and MBD3 from the core protein supports a mechanism where copper binding activates the ATP7B protein by reducing interactions among MBD1-3 and between MBD1-3 and the core protein. We also observed an increased interaction between MBD5 and the core protein that brought the copper-binding site of MBD5 closer to the high-affinity internal copper-binding site in the core protein. The simulation results assign specific, mechanistic roles to the metal-binding domains involved in ATP7B regulation that are testable in experimental settings. Living organisms depend upon active transport against gradients across biological membranes for survival. Such transport can be accomplished by ATP-dependent membrane protein transporters for which the activity must be regulated to maintain optimal concentrations in the cellular compartments. The regulatory mechanisms often involve structural responses inherent to the protein structure, which because of their dynamic nature can be hard to assess experimentally. A prime example is regulation of cellular copper levels by a copper-binding tail in the human copper transporter ATP7B. Dysregulation can cause severe diseases, for example the copper metabolism disorder Wilson’s disease, which is caused by mutations in ATP7B regulation machinery. Due to the practical difficulties in working with membrane proteins, most studies of ATP7B have been conducted in the absence of the membrane-bound protein core. Here, we used computer simulations of full-length ATP7B to study how structural dynamics in the regulatory tail differ between copper-bound and copper-free states. Copper induced increased dynamics in the tail, resulting in an overall movement towards the ion-binding site in the protein core. The simulations identified several, hitherto not reported, interactions between the regulatory tail and the protein core that can be targeted experimentally to enhance our understanding of this medically relevant regulatory mechanism.
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Affiliation(s)
- Fredrik Orädd
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Jonas Hyld Steffen
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pontus Gourdon
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Experimental Medical Science, Lund University, Lund, Sweden
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13
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Salustros N, Grønberg C, Abeyrathna NS, Lyu P, Orädd F, Wang K, Andersson M, Meloni G, Gourdon P. Structural basis of ion uptake in copper-transporting P 1B-type ATPases. Nat Commun 2022; 13:5121. [PMID: 36045128 PMCID: PMC9433437 DOI: 10.1038/s41467-022-32751-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/16/2022] [Indexed: 11/30/2022] Open
Abstract
Copper is essential for living cells, yet toxic at elevated concentrations. Class 1B P-type (P1B-) ATPases are present in all kingdoms of life, facilitating cellular export of transition metals including copper. P-type ATPases follow an alternating access mechanism, with inward-facing E1 and outward-facing E2 conformations. Nevertheless, no structural information on E1 states is available for P1B-ATPases, hampering mechanistic understanding. Here, we present structures that reach 2.7 Å resolution of a copper-specific P1B-ATPase in an E1 conformation, with complementing data and analyses. Our efforts reveal a domain arrangement that generates space for interaction with ion donating chaperones, and suggest a direct Cu+ transfer to the transmembrane core. A methionine serves a key role by assisting the release of the chaperone-bound ion and forming a cargo entry site together with the cysteines of the CPC signature motif. Collectively, the findings provide insights into P1B-mediated transport, likely applicable also to human P1B-members.
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Affiliation(s)
- Nina Salustros
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen, Denmark
| | - Christina Grønberg
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen, Denmark
| | - Nisansala S Abeyrathna
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800W Campbell Rd., Richardson, TX, 75080, USA
| | - Pin Lyu
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen, Denmark
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen, Denmark
| | - Fredrik Orädd
- Department of Chemistry, Umeå University, Linneaus Väg 10, SE-901 87, Umeå, Sweden
| | - Kaituo Wang
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen, Denmark
| | - Magnus Andersson
- Department of Chemistry, Umeå University, Linneaus Väg 10, SE-901 87, Umeå, Sweden
| | - Gabriele Meloni
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800W Campbell Rd., Richardson, TX, 75080, USA
| | - Pontus Gourdon
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen, Denmark.
- Department of Experimental Medical Science, Lund University, Sölvegatan 19, SE-221 84, Lund, Sweden.
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14
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Fruergaard MU, Dach I, Andersen JL, Ozol M, Shasavar A, Quistgaard EM, Poulsen H, Fedosova NU, Nissen P. The Na,K-ATPase in complex with beryllium fluoride mimics an ATPase phosphorylated state. J Biol Chem 2022; 298:102317. [PMID: 35926706 PMCID: PMC9485054 DOI: 10.1016/j.jbc.2022.102317] [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: 04/16/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 10/29/2022] Open
Abstract
The Na+,K+-ATPase generates electrochemical gradients of Na+ and K+ across the plasma membrane via a functional cycle that includes various phosphoenzyme intermediates. However, the structure and function of these intermediates and how metal fluorides mimick them require further investigation. Here, we describe a 4.0 Å resolution crystal structure and functional properties of the pig kidney Na+,K+-ATPase stabilized by the inhibitor beryllium fluoride (denoted E2-BeFx). E2-BeFx is expected to mimic properties of the E2P phosphoenzyme, yet with unknown characteristics of ion and ligand binding. The structure resembles the E2P form obtained by phosphorylation from inorganic phosphate (Pi) and stabilized by cardiotonic steroids, including a low-affinity Mg2+ site near ion binding site II. Our anomalous Fourier analysis of the crystals soaked in Rb+ (a K+ congener) followed by a low-resolution rigid-body refinement (6.9-7.5 Å) revealed pre-occlusion transitions leading to activation of the dephosphorylation reaction. We show that the Mg2+ location indicates a site of initial K+ recognition and acceptance upon binding to the outward-open E2P state after Na+ release. Furthermore, using binding and activity studies, we find that the BeFx-inhibited enzyme is also able to bind ADP/ATP and Na+. These results relate the E2-BeFx complex to a transient K+- and ADP-sensitive E*P intermediate of the functional cycle of the Na+,K+-ATPase, prior to E2P.
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Affiliation(s)
- Marlene U Fruergaard
- DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Dept. Molecular Biology and Genetics, DK - 8000 Aarhus C, Denmark
| | - Ingrid Dach
- DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Dept. Molecular Biology and Genetics, DK - 8000 Aarhus C, Denmark
| | - Jacob L Andersen
- DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Dept. Molecular Biology and Genetics, DK - 8000 Aarhus C, Denmark; Department of Biomedicine, Aarhus University, DK - 8000 Aarhus C, Denmark
| | - Mette Ozol
- DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Dept. Molecular Biology and Genetics, DK - 8000 Aarhus C, Denmark
| | - Azadeh Shasavar
- DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Dept. Molecular Biology and Genetics, DK - 8000 Aarhus C, Denmark
| | - Esben M Quistgaard
- DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Dept. Molecular Biology and Genetics, DK - 8000 Aarhus C, Denmark
| | - Hanne Poulsen
- DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Dept. Molecular Biology and Genetics, DK - 8000 Aarhus C, Denmark
| | - Natalya U Fedosova
- Department of Biomedicine, Aarhus University, DK - 8000 Aarhus C, Denmark.
| | - Poul Nissen
- DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Dept. Molecular Biology and Genetics, DK - 8000 Aarhus C, Denmark.
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15
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Bitter RM, Oh S, Deng Z, Rahman S, Hite RK, Yuan P. Structure of the Wilson disease copper transporter ATP7B. SCIENCE ADVANCES 2022; 8:eabl5508. [PMID: 35245129 PMCID: PMC8896786 DOI: 10.1126/sciadv.abl5508] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/10/2022] [Indexed: 05/31/2023]
Abstract
ATP7A and ATP7B, two homologous copper-transporting P1B-type ATPases, play crucial roles in cellular copper homeostasis, and mutations cause Menkes and Wilson diseases, respectively. ATP7A/B contains a P-type ATPase core consisting of a membrane transport domain and three cytoplasmic domains, the A, P, and N domains, and a unique amino terminus comprising six consecutive metal-binding domains. Here, we present a cryo-electron microscopy structure of frog ATP7B in a copper-free state. Interacting with both the A and P domains, the metal-binding domains are poised to exert copper-dependent regulation of ATP hydrolysis coupled to transmembrane copper transport. A ring of negatively charged residues lines the cytoplasmic copper entrance that is presumably gated by a conserved basic residue sitting at the center. Within the membrane, a network of copper-coordinating ligands delineates a stepwise copper transport pathway. This work provides the first glimpse into the structure and function of ATP7 proteins and facilitates understanding of disease mechanisms and development of rational therapies.
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Affiliation(s)
- Ryan M. Bitter
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - SeCheol Oh
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Zengqin Deng
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Suhaila Rahman
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Richard K. Hite
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Peng Yuan
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA
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16
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Placenti MA, Roman EA, González Flecha FL, González-Lebrero RM. Functional characterization of Legionella pneumophila Cu + transport ATPase. The activation by Cu + and ATP. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183822. [PMID: 34826402 DOI: 10.1016/j.bbamem.2021.183822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/08/2021] [Accepted: 11/17/2021] [Indexed: 06/13/2023]
Abstract
Cu+-ATPases are integral membrane proteins belonging to the IB subfamily of the P-type ATPases that couple Cu+ transport to the hydrolysis of ATP. As some structural and functional particularities arise for Cu+-ATPases, several authors suggest that some of the reaction steps of the Albers-Post model postulated for other P-ATPases may be different. In this work we describe a functional characterization of Legionella pneumophila Cu+-ATPase (LpCopA), the first PIB-ATPase whose structure was determined by X-ray crystallography. Cu+-ATPase activity of the enzyme presents a maximum at ∼37 °C and pH 6.6-6.8. Phospholipids enhance LpCopA Cu+-ATPase activity in a non-essential mode where optimal activity is achieved at an asolectin molar fraction of 0.15 and an amphiphile-protein ratio of ~30,000. As described for other P-ATPases, Mg2+ acts as an essential activator. Furthermore, Cu+-ATPase activity dependence on [Cu+] and [ATP] can both be described by a sum of two hyperbolic functions. Based on that, and the [Cu+] and [ATP] dependencies of the best fitting parameters of the hyperbolae pointed above, we propose a minimal reaction scheme for the catalytic mechanism that shares the basic reaction steps of the Albers-Post model for P-type ATPases. The reaction scheme postulated contemplates two different binding affinities for a single ATP (apparent affinities of 0.66 and 550 μM at [Cu+] → ∞) and binding of at least 2 Cu+ with different affinities as well (apparent affinities of 1.4 and 102.5 μM at [ATP] → ∞).
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Affiliation(s)
- M Agueda Placenti
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química y Fisicoquímica Biológicas, Buenos Aires, Argentina
| | - Ernesto A Roman
- Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química y Fisicoquímica Biológicas, Buenos Aires, Argentina; Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Buenos Aires, Argentina
| | - F Luis González Flecha
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química y Fisicoquímica Biológicas, Buenos Aires, Argentina.
| | - Rodolfo M González-Lebrero
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química y Fisicoquímica Biológicas, Buenos Aires, Argentina.
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17
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Grønberg C, Hu Q, Mahato DR, Longhin E, Salustros N, Duelli A, Lyu P, Bågenholm V, Eriksson J, Rao KU, Henderson DI, Meloni G, Andersson M, Croll T, Godaly G, Wang K, Gourdon P. Structure and ion-release mechanism of P IB-4-type ATPases. eLife 2021; 10:73124. [PMID: 34951590 PMCID: PMC8880997 DOI: 10.7554/elife.73124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/17/2021] [Indexed: 11/13/2022] Open
Abstract
Transition metals, such as zinc, are essential micronutrients in all organisms, but also highly toxic in excessive amounts. Heavy-metal transporting P-type (PIB) ATPases are crucial for homeostasis, conferring cellular detoxification and redistribution through transport of these ions across cellular membranes. No structural information is available for the PIB-4-ATPases, the subclass with the broadest cargo scope, and hence even their topology remains elusive. Here we present structures and complementary functional analyses of an archetypal PIB‑4‑ATPase, sCoaT from Sulfitobacter sp. NAS14-1. The data disclose the architecture, devoid of classical so-called heavy metal binding domains, and provides fundamentally new insights into the mechanism and diversity of heavy-metal transporters. We reveal several novel P-type ATPase features, including a dual role in heavy-metal release and as an internal counter ion of an invariant histidine. We also establish that the turn-over of PIB‑ATPases is potassium independent, contrasting to many other P-type ATPases. Combined with new inhibitory compounds, our results open up for efforts in e.g. drug discovery, since PIB-4-ATPases function as virulence factors in many pathogens.
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Affiliation(s)
- Christina Grønberg
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Qiaoxia Hu
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Elena Longhin
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nina Salustros
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Annette Duelli
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Pin Lyu
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Viktoria Bågenholm
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | | | | | | | - Gabriele Meloni
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, United States
| | | | - Tristan Croll
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Gabriela Godaly
- Department of Laboratory Medicine, Umeå University, Umeå, Sweden
| | - Kaituo Wang
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Pontus Gourdon
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
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18
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Guo Y, Xu Y, Bao Q, Shen C, Ni D, Hu P, Shi J. Endogenous Copper for Nanocatalytic Oxidative Damage and Self-Protection Pathway Breakage of Cancer. ACS NANO 2021; 15:16286-16297. [PMID: 34652919 DOI: 10.1021/acsnano.1c05451] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nanocatalytic medicine is one of the most recent advances in the development of nanomedicine, which catalyzes intratumoral chemical reactions to produce toxins such as reactive oxygen species in situ for cancer specific treatment by using exogenous-delivered catalysts such as Fenton agents. However, the overexpression of reductive glutathione and Cu-Zn superoxide dismutase in cancer cells will significantly counteract the therapeutic efficacy by reactive oxygen species-mediated oxidative damages. Additionally, the direct delivery of iron-based Fenton agents may arouse undesired detrimental effects such as anaphylactic reactions. In this study, instead of exogenously delivering Fenton agents, the endogenous copper ions from intracellular Cu-Zn superoxide dismutase have been employed as the source of Fenton-like agents by chelating the Cu ions from the superoxide dismutase using a common metal ion chelator, N,N,N',N'-tetrakis(2-pyridinylmethyl)-1,2-ethanediamine (TPEN), followed by the TPEN-Cu(II) chelate reduction to TPEN-Cu(I) by reductive glutathione. Briefly, TPEN was loaded in a disulfide bond-containing link poly(acrylic acid) shell-coated hybrid mesoporous silica/organosilicate (MSN@MON) nanocomposite as a reductive glutathione-responsive nanoplatform, which features inter-related triple functions: intratumoral reductive glutathione-responsive link poly(acrylic acid) disruption and TPEN release; the accompanying reductive glutathione consumption and Cu-Zn superoxide dismutase deactivation by TPEN chelating Cu ions from this superoxide dismutase; and the Fenton reaction catalyzed by TPEN-Cu(I) chelate as a Fenton-like agent generated from TPEN-Cu(II) reduction by the remaining reductive glutathione in cancer cells, thereby cutting off the self-protection pathway of cancer cells under severe oxidation stress and ensuring cancer cell apoptosis by reactive oxygen species produced by the catalytic Fenton-like reactions. Such a nanocatalyst demonstrates excellent biosafety and augmented therapeutic efficacy by simultaneous nanocatalytic oxidative damage and intrinsic protection pathway breakage of cancer cells.
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Affiliation(s)
- Yuedong Guo
- State Key Laboratory of High Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Yingying Xu
- State Key Laboratory of High Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Qunqun Bao
- Shanghai Tenth People's Hospital, School of medicine, Tongji University, Shanghai 200072, P. R. China
| | - Chao Shen
- BD Bioscience, Shanghai 200050, P. R. China
| | - Dalong Ni
- Department of Orthopedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200020, P. R. China
| | - Ping Hu
- State Key Laboratory of High Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050, P. R. China
- Shanghai Tenth People's Hospital, School of medicine, Tongji University, Shanghai 200072, P. R. China
| | - Jianlin Shi
- State Key Laboratory of High Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050, P. R. China
- Shanghai Tenth People's Hospital, School of medicine, Tongji University, Shanghai 200072, P. R. China
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19
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Bartels K, Lasitza‐Male T, Hofmann H, Löw C. Single-Molecule FRET of Membrane Transport Proteins. Chembiochem 2021; 22:2657-2671. [PMID: 33945656 PMCID: PMC8453700 DOI: 10.1002/cbic.202100106] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/03/2021] [Indexed: 12/31/2022]
Abstract
Uncovering the structure and function of biomolecules is a fundamental goal in structural biology. Membrane-embedded transport proteins are ubiquitous in all kingdoms of life. Despite structural flexibility, their mechanisms are typically studied by ensemble biochemical methods or by static high-resolution structures, which complicate a detailed understanding of their dynamics. Here, we review the recent progress of single molecule Förster Resonance Energy Transfer (smFRET) in determining mechanisms and timescales of substrate transport across membranes. These studies do not only demonstrate the versatility and suitability of state-of-the-art smFRET tools for studying membrane transport proteins but they also highlight the importance of membrane mimicking environments in preserving the function of these proteins. The current achievements advance our understanding of transport mechanisms and have the potential to facilitate future progress in drug design.
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Affiliation(s)
- Kim Bartels
- Centre for Structural Systems Biology (CSSB)DESY and European Molecular Biology Laboratory HamburgNotkestrasse 8522607HamburgGermany
| | - Tanya Lasitza‐Male
- Department of Structural BiologyWeizmann Institute of ScienceHerzl St. 2347610001RehovotIsrael
| | - Hagen Hofmann
- Department of Structural BiologyWeizmann Institute of ScienceHerzl St. 2347610001RehovotIsrael
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB)DESY and European Molecular Biology Laboratory HamburgNotkestrasse 8522607HamburgGermany
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20
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Abeyrathna N, Abeyrathna S, Morgan MT, Fahrni CJ, Meloni G. Transmembrane Cu(I) P-type ATPase pumps are electrogenic uniporters. Dalton Trans 2021; 49:16082-16094. [PMID: 32469032 DOI: 10.1039/d0dt01380c] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Cu(i) P-type ATPases are transmembrane primary active ion pumps that catalyze the extrusion of copper ions across cellular membranes. Their activity is critical in controlling copper levels in all kingdoms of life. Biochemical and structural characterization established the structural framework by which Cu-pumps perform their function. However, the details of the overall mechanism of transport (uniporter vs. cotransporter) and electrogenicity still remain elusive. In this work, we developed a platform to reconstitute the model Cu(i)-pump from E. coli (EcCopA) in artificial lipid bilayer small unilamellar vesicles (SUVs) to quantitatively characterize the metal substrate, putative counter-ions and charge translocation. By encapsulating in the liposome lumen fluorescence detector probes (CTAP-3, pyranine and oxonol VI) responsive to diverse stimuli (Cu(i), pH and membrane potential), we correlated substrate, secondary-ion translocation and charge movement events in EcCopA proteoliposomes. This platform centered on multiple fluorescence reporters allowed study of the mechanism and translocation kinetic parameters in real-time for wild-type EcCopA and inactive mutants. The maximal initial Cu(i) transport rate of 165 nmol Cu(i) mg-1 min-1 and KM, Cu(I) = 0.15 ± 0.07 μM was determined with this analysis. We reveal that Cu(i) pumps are primary-active uniporters and electrogenic. The Cu(i) translocation cycle does not require proton counter-transport resulting in electrogenic generation of transmembrane potential upon translocation of one Cu(i) per ATP hydrolysis cycle. Thus, mechanistic differences between Cu(i) pumps and other better characterized P-type ATPases are discussed. The platform opens the venue to study translocation events and mechanisms of transport in other transition metal P-type ATPase pumps.
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Affiliation(s)
- Nisansala Abeyrathna
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX 75080, USA.
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21
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Herbert FC, Abeyrathna SS, Abeyrathna NS, Wijesundara YH, Brohlin OR, Carraro F, Amenitsch H, Falcaro P, Luzuriaga MA, Durand-Silva A, Diwakara SD, Smaldone RA, Meloni G, Gassensmith JJ. Stabilization of supramolecular membrane protein-lipid bilayer assemblies through immobilization in a crystalline exoskeleton. Nat Commun 2021; 12:2202. [PMID: 33850135 PMCID: PMC8044103 DOI: 10.1038/s41467-021-22285-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 02/25/2021] [Indexed: 11/09/2022] Open
Abstract
Artificial native-like lipid bilayer systems constructed from phospholipids assembling into unilamellar liposomes allow the reconstitution of detergent-solubilized transmembrane proteins into supramolecular lipid-protein assemblies called proteoliposomes, which mimic cellular membranes. Stabilization of these complexes remains challenging because of their chemical composition, the hydrophobicity and structural instability of membrane proteins, and the lability of interactions between protein, detergent, and lipids within micelles and lipid bilayers. In this work we demonstrate that metastable lipid, protein-detergent, and protein-lipid supramolecular complexes can be successfully generated and immobilized within zeolitic-imidazole framework (ZIF) to enhance their stability against chemical and physical stressors. Upon immobilization in ZIF bio-composites, blank liposomes, and model transmembrane metal transporters in detergent micelles or embedded in proteoliposomes resist elevated temperatures, exposure to chemical denaturants, aging, and mechanical stresses. Extensive morphological and functional characterization of the assemblies upon exfoliation reveal that all these complexes encapsulated within the framework maintain their native morphology, structure, and activity, which is otherwise lost rapidly without immobilization.
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Affiliation(s)
- Fabian C Herbert
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX, USA
| | - Sameera S Abeyrathna
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX, USA
| | - Nisansala S Abeyrathna
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX, USA
| | - Yalini H Wijesundara
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX, USA
| | - Olivia R Brohlin
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX, USA
| | - Francesco Carraro
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Graz, Austria
| | - Heinz Amenitsch
- Institute of Inorganic Chemistry, Graz University of Technology, Graz, Austria
| | - Paolo Falcaro
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Graz, Austria
| | - Michael A Luzuriaga
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX, USA
| | - Alejandra Durand-Silva
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX, USA
| | - Shashini D Diwakara
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX, USA
| | - Ronald A Smaldone
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX, USA
| | - Gabriele Meloni
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX, USA.
| | - Jeremiah J Gassensmith
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX, USA.
- Department of Bioengineering, The University of Texas at Dallas, Richardson, TX, USA.
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22
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An L, Luo X, Wu M, Feng L, Shi K, Wang G, Rosen BP, Li M. Comamonas testosteroni antA encodes an antimonite-translocating P-type ATPase. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 754:142393. [PMID: 33254899 PMCID: PMC7885177 DOI: 10.1016/j.scitotenv.2020.142393] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 09/11/2020] [Accepted: 09/13/2020] [Indexed: 05/31/2023]
Abstract
Antimony, like arsenic, is a toxic metalloid widely distributed in the environment. Microbial detoxification of antimony has recently been identified. Here we describe a novel bacterial P1B-type antimonite (Sb(III))-translocating ATPase from the antimony-mining bacterium Comamonas testosterone JL40 that confers resistance to Sb(III). In a comparative proteomics analysis of strain JL40, an operon (ant operon) was up-regulated by Sb(III). The ant operon includes three genes, antR, antC and antA. AntR belongs to the ArsR/SmtB family of metalloregulatory proteins that regulates expression of the ant operon. AntA belongs to the P1B family of the P-type cation-translocating ATPases. It has both similarities to and differences from other members of the P1B-1 subfamily and appears to be the first identified member of a distinct subfamily that we designate P1B-8. Expression AntA in E. coli AW3110 (Δars) conferred resistance to Sb(III) and reduced the intracellular concentration of Sb(III) but not As(III) or other metals. Everted membrane vesicles from cells expressing antA accumulated Sb(III) but not As(III), where uptake in everted vesicles reflects efflux from cells. AntC is a small protein with a potential Sb(III) binding site, and co-expression of AntC with AntA increased resistance to Sb(III). We propose that AntC functions as an Sb(III) chaperone to AntA, augmenting Sb(III) efflux. The identification of a novel Sb(III)-translocating ATPase enhances our understanding of the biogeochemical cycling of environmental antimony by bacteria.
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Affiliation(s)
- Lijin An
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xiong Luo
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Minghan Wu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Liling Feng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Kaixiang Shi
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Barry P Rosen
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, United States
| | - Mingshun Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.
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Orädd F, Andersson M. Tracking Membrane Protein Dynamics in Real Time. J Membr Biol 2021; 254:51-64. [PMID: 33409541 PMCID: PMC7936944 DOI: 10.1007/s00232-020-00165-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/11/2020] [Indexed: 12/14/2022]
Abstract
Abstract Membrane proteins govern critical cellular processes and are central to human health and associated disease. Understanding of membrane protein function is obscured by the vast ranges of structural dynamics—both in the spatial and time regime—displayed in the protein and surrounding membrane. The membrane lipids have emerged as allosteric modulators of membrane protein function, which further adds to the complexity. In this review, we discuss several examples of membrane dependency. A particular focus is on how molecular dynamics (MD) simulation have aided to map membrane protein dynamics and how enhanced sampling methods can enable observing the otherwise inaccessible biological time scale. Also, time-resolved X-ray scattering in solution is highlighted as a powerful tool to track membrane protein dynamics, in particular when combined with MD simulation to identify transient intermediate states. Finally, we discuss future directions of how to further develop this promising approach to determine structural dynamics of both the protein and the surrounding lipids. Graphic Abstract ![]()
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Affiliation(s)
- Fredrik Orädd
- Department of Chemistry, Umeå University, Umeå, Sweden
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24
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Abstract
Abstract
Transition metals such as zinc, copper and iron play vital roles in maintaining physiological functions and homeostasis of living systems. Molecular imaging, including two-photon imaging (TPI), bioluminescence imaging (BLI) and photoacoustic imaging (PAI), could act as non-invasive toolkits for capturing dynamic events in living cells, tissues and whole animals. Herein, we review the recent progress in the development of molecular probes for essential transition metals and their biological applications. We emphasize the contributions of metallostasis to health and disease, and discuss the future research directions about how to harness the great potential of metal sensors.
Graphic Abstract
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25
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Andrei A, Öztürk Y, Khalfaoui-Hassani B, Rauch J, Marckmann D, Trasnea PI, Daldal F, Koch HG. Cu Homeostasis in Bacteria: The Ins and Outs. MEMBRANES 2020; 10:E242. [PMID: 32962054 PMCID: PMC7558416 DOI: 10.3390/membranes10090242] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 12/16/2022]
Abstract
Copper (Cu) is an essential trace element for all living organisms and used as cofactor in key enzymes of important biological processes, such as aerobic respiration or superoxide dismutation. However, due to its toxicity, cells have developed elaborate mechanisms for Cu homeostasis, which balance Cu supply for cuproprotein biogenesis with the need to remove excess Cu. This review summarizes our current knowledge on bacterial Cu homeostasis with a focus on Gram-negative bacteria and describes the multiple strategies that bacteria use for uptake, storage and export of Cu. We furthermore describe general mechanistic principles that aid the bacterial response to toxic Cu concentrations and illustrate dedicated Cu relay systems that facilitate Cu delivery for cuproenzyme biogenesis. Progress in understanding how bacteria avoid Cu poisoning while maintaining a certain Cu quota for cell proliferation is of particular importance for microbial pathogens because Cu is utilized by the host immune system for attenuating pathogen survival in host cells.
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Affiliation(s)
- Andreea Andrei
- Institut für Biochemie und Molekularbiologie, ZBMZ, Medizinische Fakultät, Albert-Ludwigs Universität Freiburg; Stefan Meier Str. 17, 79104 Freiburg, Germany; (A.A.); (Y.O.); (J.R.); (D.M.)
- Fakultät für Biologie, Albert-Ludwigs Universität Freiburg; Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Yavuz Öztürk
- Institut für Biochemie und Molekularbiologie, ZBMZ, Medizinische Fakultät, Albert-Ludwigs Universität Freiburg; Stefan Meier Str. 17, 79104 Freiburg, Germany; (A.A.); (Y.O.); (J.R.); (D.M.)
| | | | - Juna Rauch
- Institut für Biochemie und Molekularbiologie, ZBMZ, Medizinische Fakultät, Albert-Ludwigs Universität Freiburg; Stefan Meier Str. 17, 79104 Freiburg, Germany; (A.A.); (Y.O.); (J.R.); (D.M.)
| | - Dorian Marckmann
- Institut für Biochemie und Molekularbiologie, ZBMZ, Medizinische Fakultät, Albert-Ludwigs Universität Freiburg; Stefan Meier Str. 17, 79104 Freiburg, Germany; (A.A.); (Y.O.); (J.R.); (D.M.)
| | | | - Fevzi Daldal
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Hans-Georg Koch
- Institut für Biochemie und Molekularbiologie, ZBMZ, Medizinische Fakultät, Albert-Ludwigs Universität Freiburg; Stefan Meier Str. 17, 79104 Freiburg, Germany; (A.A.); (Y.O.); (J.R.); (D.M.)
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26
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Tadini-Buoninsegni F. Protein Adsorption on Solid Supported Membranes: Monitoring the Transport Activity of P-Type ATPases. Molecules 2020; 25:molecules25184167. [PMID: 32933017 PMCID: PMC7570688 DOI: 10.3390/molecules25184167] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 02/07/2023] Open
Abstract
P-type ATPases are a large family of membrane transporters that are found in all forms of life. These enzymes couple ATP hydrolysis to the transport of various ions or phospholipids across cellular membranes, thereby generating and maintaining crucial electrochemical potential gradients. P-type ATPases have been studied by a variety of methods that have provided a wealth of information about the structure, function, and regulation of this class of enzymes. Among the many techniques used to investigate P-type ATPases, the electrical method based on solid supported membranes (SSM) was employed to investigate the transport mechanism of various ion pumps. In particular, the SSM method allows the direct measurement of charge movements generated by the ATPase following adsorption of the membrane-bound enzyme on the SSM surface and chemical activation by a substrate concentration jump. This kind of measurement was useful to identify electrogenic partial reactions and localize ion translocation in the reaction cycle of the membrane transporter. In the present review, we discuss how the SSM method has contributed to investigate some key features of the transport mechanism of P-type ATPases, with a special focus on sarcoplasmic reticulum Ca2+-ATPase, mammalian Cu+-ATPases (ATP7A and ATP7B), and phospholipid flippase ATP8A2.
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27
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León-Torres A, Arango E, Castillo E, Soto CY. CtpB is a plasma membrane copper (I) transporting P-type ATPase of Mycobacterium tuberculosis. Biol Res 2020; 53:6. [PMID: 32054527 PMCID: PMC7017476 DOI: 10.1186/s40659-020-00274-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 01/30/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The intracellular concentration of heavy-metal cations, such as copper, nickel, and zinc is pivotal for the mycobacterial response to the hostile environment inside macrophages. To date, copper transport mediated by P-type ATPases across the mycobacterial plasma membrane has not been sufficiently explored. RESULTS In this work, the ATPase activity of the putative Mycobacterium tuberculosis P1B-type ATPase CtpB was associated with copper (I) transport from mycobacterial cells. Although CtpB heterologously expressed in M. smegmatis induced tolerance to toxic concentrations of Cu2+ and a metal preference for Cu+, the disruption of ctpB in M. tuberculosis cells did not promote impaired cell growth or heavy-metal accumulation in whole mutant cells in cultures under high doses of copper. In addition, the Cu+ ATPase activity of CtpB embedded in the plasma membrane showed features of high affinity/slow turnover ATPases, with enzymatic parameters KM 0.19 ± 0.04 µM and Vmax 2.29 ± 0.10 nmol/mg min. In contrast, the ctpB gene transcription was activated in cells under culture conditions that mimicked the hostile intraphagosomal environment, such as hypoxia, nitrosative and oxidative stress, but not under high doses of copper. CONCLUSIONS The overall results suggest that M. tuberculosis CtpB is associated with Cu+ transport from mycobacterial cells possibly playing a role different from copper detoxification.
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Affiliation(s)
- Andrés León-Torres
- Chemistry Department, Faculty of Sciences, Universidad Nacional de Colombia, Carrera 30 N° 45-03, Ciudad Universitaria, Bogotá, Colombia
| | - Epifania Arango
- Chemistry Department, Faculty of Sciences, Universidad Nacional de Colombia, Carrera 30 N° 45-03, Ciudad Universitaria, Bogotá, Colombia
| | - Eliana Castillo
- Chemistry Department, Faculty of Sciences, Universidad Nacional de Colombia, Carrera 30 N° 45-03, Ciudad Universitaria, Bogotá, Colombia
| | - Carlos Y Soto
- Chemistry Department, Faculty of Sciences, Universidad Nacional de Colombia, Carrera 30 N° 45-03, Ciudad Universitaria, Bogotá, Colombia.
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28
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Yun Y, Hong SA, Kim KK, Baek D, Lee D, Londhe AM, Lee M, Yu J, McEachin ZT, Bassell GJ, Bowser R, Hales CM, Cho SR, Kim J, Pae AN, Cheong E, Kim S, Boulis NM, Bae S, Ha Y. CRISPR-mediated gene correction links the ATP7A M1311V mutations with amyotrophic lateral sclerosis pathogenesis in one individual. Commun Biol 2020; 3:33. [PMID: 31959876 PMCID: PMC6970999 DOI: 10.1038/s42003-020-0755-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 12/17/2019] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a severe disease causing motor neuron death, but a complete cure has not been developed and related genes have not been defined in more than 80% of cases. Here we compared whole genome sequencing results from a male ALS patient and his healthy parents to identify relevant variants, and chose one variant in the X-linked ATP7A gene, M1311V, as a strong disease-linked candidate after profound examination. Although this variant is not rare in the Ashkenazi Jewish population according to results in the genome aggregation database (gnomAD), CRISPR-mediated gene correction of this mutation in patient-derived and re-differentiated motor neurons drastically rescued neuronal activities and functions. These results suggest that the ATP7A M1311V mutation has a potential responsibility for ALS in this patient and might be a potential therapeutic target, revealed here by a personalized medicine strategy.
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Affiliation(s)
- Yeomin Yun
- Department of Neurosurgery, Spine & Spinal Cord Institute, College of Medicine, Yonsei University, Seoul, 03722, South Korea
- Brain Korea 21 PLUS Project for Medical Science, College of Medicine, Yonsei University, Seoul, 03722, South Korea
| | - Sung-Ah Hong
- Department of Chemistry, Hanyang University, Seoul, 04763, South Korea
- Research Institute for Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Ka-Kyung Kim
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Daye Baek
- Department of Neurosurgery, Spine & Spinal Cord Institute, College of Medicine, Yonsei University, Seoul, 03722, South Korea
- Brain Korea 21 PLUS Project for Medical Science, College of Medicine, Yonsei University, Seoul, 03722, South Korea
| | - Dongsu Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, South Korea
| | - Ashwini M Londhe
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology, PO Box 131, Cheongryang, Seoul, 130-650, South Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul, 02792, South Korea
| | - Minhyung Lee
- Stem Cell Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, South Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, 34113, South Korea
| | - Jihyeon Yu
- Department of Chemistry, Hanyang University, Seoul, 04763, South Korea
| | - Zachary T McEachin
- Laboratory of Translational Cell Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Gary J Bassell
- Laboratory of Translational Cell Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Cell Biology, Emory University, Atlanta, GA, 30322, USA
| | - Robert Bowser
- Department of Neurobiology, Barrow Neurological Institute and St. Joseph's Hospital and Medical Center, Phoenix, AZ, 85013, USA
| | - Chadwick M Hales
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA
| | - Sung-Rae Cho
- Brain Korea 21 PLUS Project for Medical Science, College of Medicine, Yonsei University, Seoul, 03722, South Korea
- Department and Research Institute of Rehabilitation Medicine, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Janghwan Kim
- Stem Cell Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, South Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, 34113, South Korea
| | - Ae Nim Pae
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology, PO Box 131, Cheongryang, Seoul, 130-650, South Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul, 02792, South Korea
| | - Eunji Cheong
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, South Korea
| | - Sangwoo Kim
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Nicholas M Boulis
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Sangsu Bae
- Department of Chemistry, Hanyang University, Seoul, 04763, South Korea.
- Research Institute for Natural Sciences, Hanyang University, Seoul, 04763, South Korea.
| | - Yoon Ha
- Department of Neurosurgery, Spine & Spinal Cord Institute, College of Medicine, Yonsei University, Seoul, 03722, South Korea.
- Brain Korea 21 PLUS Project for Medical Science, College of Medicine, Yonsei University, Seoul, 03722, South Korea.
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29
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Petruzzelli R, Polishchuk RS. Activity and Trafficking of Copper-Transporting ATPases in Tumor Development and Defense against Platinum-Based Drugs. Cells 2019; 8:E1080. [PMID: 31540259 PMCID: PMC6769697 DOI: 10.3390/cells8091080] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/10/2019] [Accepted: 09/12/2019] [Indexed: 02/06/2023] Open
Abstract
Membrane trafficking pathways emanating from the Golgi regulate a wide range of cellular processes. One of these is the maintenance of copper (Cu) homeostasis operated by the Golgi-localized Cu-transporting ATPases ATP7A and ATP7B. At the Golgi, these proteins supply Cu to newly synthesized enzymes which use this metal as a cofactor to catalyze a number of vitally important biochemical reactions. However, in response to elevated Cu, the Golgi exports ATP7A/B to post-Golgi sites where they promote sequestration and efflux of excess Cu to limit its potential toxicity. Growing tumors actively consume Cu and employ ATP7A/B to regulate the availability of this metal for oncogenic enzymes such as LOX and LOX-like proteins, which confer higher invasiveness to malignant cells. Furthermore, ATP7A/B activity and trafficking allow tumor cells to detoxify platinum (Pt)-based drugs (like cisplatin), which are used for the chemotherapy of different solid tumors. Despite these noted activities of ATP7A/B that favor oncogenic processes, the mechanisms that regulate the expression and trafficking of Cu ATPases in malignant cells are far from being completely understood. This review summarizes current data on the role of ATP7A/B in the regulation of Cu and Pt metabolism in malignant cells and outlines questions and challenges that should be addressed to understand how ATP7A and ATP7B trafficking mechanisms might be targeted to counteract tumor development.
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Affiliation(s)
- Raffaella Petruzzelli
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy.
| | - Roman S Polishchuk
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy.
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30
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Rogne P, Andersson D, Grundström C, Sauer-Eriksson E, Linusson A, Wolf-Watz M. Nucleation of an Activating Conformational Change by a Cation-π Interaction. Biochemistry 2019; 58:3408-3412. [PMID: 31339702 DOI: 10.1021/acs.biochem.9b00538] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
As a key molecule in biology, adenosine triphosphate (ATP) has numerous crucial functions in, for instance, energetics, post-translational modifications, nucleotide biosynthesis, and cofactor metabolism. Here, we have discovered an intricate interplay between the enzyme adenylate kinase and its substrate ATP. The side chain of an arginine residue was found to be an efficient sensor of the aromatic moiety of ATP through the formation of a strong cation-π interaction. In addition to recognition, the interaction was found to have dual functionality. First, it nucleates the activating conformational transition of the ATP binding domain and also affects the specificity in the distant AMP binding domain. In light of the functional consequences resulting from the cation-π interaction, it is possible that the mode of ATP recognition may be a useful tool in enzyme design.
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Affiliation(s)
- Per Rogne
- Department of Chemistry , Umeå University , SE-901 87 Umeå , Sweden
| | - David Andersson
- Department of Chemistry , Umeå University , SE-901 87 Umeå , Sweden
| | | | | | - Anna Linusson
- Department of Chemistry , Umeå University , SE-901 87 Umeå , Sweden
| | - Magnus Wolf-Watz
- Department of Chemistry , Umeå University , SE-901 87 Umeå , Sweden
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31
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Indexed: 12/23/2022]
Abstract
Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Matti Javanainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences, Flemingovo naḿesti 542/2, 16610 Prague, Czech Republic
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Waldemar Kulig
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Tomasz Róg
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Ilpo Vattulainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
- MEMPHYS-Center
for Biomembrane Physics
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32
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Guo J, Yuan H, Chen Y, Chen Z, Zhao M, Zou L, Liu Y, Liu Z, Zhao Q, Guo Z, He W. A ratiometric fluorescent sensor for tracking Cu(I) fluctuation in endoplasmic reticulum. Sci China Chem 2019. [DOI: 10.1007/s11426-018-9424-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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33
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Lekeux G, Crowet JM, Nouet C, Joris M, Jadoul A, Bosman B, Carnol M, Motte P, Lins L, Galleni M, Hanikenne M. Homology modeling and in vivo functional characterization of the zinc permeation pathway in a heavy metal P-type ATPase. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:329-341. [PMID: 30418580 PMCID: PMC6305203 DOI: 10.1093/jxb/ery353] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 10/01/2018] [Indexed: 05/26/2023]
Abstract
The P1B ATPase heavy metal ATPase 4 (HMA4) is responsible for zinc and cadmium translocation from roots to shoots in Arabidopsis thaliana. It couples ATP hydrolysis to cytosolic domain movements, enabling metal transport across the membrane. The detailed mechanism of metal permeation by HMA4 through the membrane remains elusive. Here, homology modeling of the HMA4 transmembrane region was conducted based on the crystal structure of a ZntA bacterial homolog. The analysis highlighted amino acids forming a metal permeation pathway, whose importance was subsequently investigated functionally through mutagenesis and complementation experiments in plants. Although the zinc pathway displayed overall conservation among the two proteins, significant differences were observed, especially in the entrance area with altered electronegativity and the presence of a ionic interaction/hydrogen bond network. The analysis also newly identified amino acids whose mutation results in total or partial loss of the protein function. In addition, comparison of zinc and cadmium accumulation in shoots of A. thaliana complemented lines revealed a number of HMA4 mutants exhibiting different abilities in zinc and cadmium translocation. These observations could be instrumental to design low cadmium-accumulating crops, hence decreasing human cadmium exposure.
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Affiliation(s)
- Gilles Lekeux
- InBioS - Center for Protein Engineering (CIP), Biological Macromolecules, University of Liège, Liège, Belgium
- InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, Liège, Belgium
| | - Jean-Marc Crowet
- Laboratory of Molecular Biophysics at Interfaces, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Cécile Nouet
- InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, Liège, Belgium
| | - Marine Joris
- InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, Liège, Belgium
| | - Alice Jadoul
- InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, Liège, Belgium
| | - Bernard Bosman
- InBioS - PhytoSystems, Laboratory of Plant and Microbial Ecology, Department of Biology, Ecology, Evolution, University of Liège, Liège, Belgium
| | - Monique Carnol
- InBioS - PhytoSystems, Laboratory of Plant and Microbial Ecology, Department of Biology, Ecology, Evolution, University of Liège, Liège, Belgium
| | - Patrick Motte
- InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, Liège, Belgium
| | - Laurence Lins
- Laboratory of Molecular Biophysics at Interfaces, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Moreno Galleni
- InBioS - Center for Protein Engineering (CIP), Biological Macromolecules, University of Liège, Liège, Belgium
| | - Marc Hanikenne
- InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, Liège, Belgium
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34
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Isolation and Characterization of Nanobodies against a Zinc-Transporting P-Type ATPase. Antibodies (Basel) 2018; 7:antib7040039. [PMID: 31544889 PMCID: PMC6698960 DOI: 10.3390/antib7040039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 10/31/2018] [Accepted: 11/04/2018] [Indexed: 11/24/2022] Open
Abstract
P-type ATPases form a large and ubiquitous superfamily of ion and lipid transporters that use ATP (adenosine triphosphate) to carry out their function. The IB subclass (PIB-ATPases) allows flux of heavy metals and are key players in metal detoxification, critical for human health, crops, and survival of pathogens. Nevertheless, PIB-ATPases remain poorly understood at a molecular level. In this study, nanobodies (Nbs) are selected against the zinc-transporting PIB-ATPase ZntA from Shigella sonnei (SsZntA), aiming at developing tools to assist the characterization of the structure and function of this class of transporters. We identify six different Nbs that bind detergent stabilized SsZntA. We further assess the effect of the Nbs on the catalytic function of SsZntA, and find that five nanobodies associate without affecting the function, while one nanobody significantly reduces the ATPase activity. This study paves the way for more refined mechanistical and structural studies of zinc-transporting PIB-ATPases.
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35
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Yang Y, Tang J, Abbaraju PL, Jambhrunkar M, Song H, Zhang M, Lei C, Fu J, Gu Z, Liu Y, Yu C. Hybrid Nanoreactors: Enabling an Off‐the‐Shelf Strategy for Concurrently Enhanced Chemo‐immunotherapy. Angew Chem Int Ed Engl 2018; 57:11764-11769. [DOI: 10.1002/anie.201807595] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Yannan Yang
- Australian Institute for Bioengineering and NanotechnologyThe University of Queensland St Lucia Brisbane QLD 4072 Australia
| | - Jie Tang
- Australian Institute for Bioengineering and NanotechnologyThe University of Queensland St Lucia Brisbane QLD 4072 Australia
| | - Prasanna Lakshmi Abbaraju
- Australian Institute for Bioengineering and NanotechnologyThe University of Queensland St Lucia Brisbane QLD 4072 Australia
| | - Manasi Jambhrunkar
- Australian Institute for Bioengineering and NanotechnologyThe University of Queensland St Lucia Brisbane QLD 4072 Australia
| | - Hao Song
- Australian Institute for Bioengineering and NanotechnologyThe University of Queensland St Lucia Brisbane QLD 4072 Australia
| | - Min Zhang
- Australian Institute for Bioengineering and NanotechnologyThe University of Queensland St Lucia Brisbane QLD 4072 Australia
| | - Chang Lei
- Australian Institute for Bioengineering and NanotechnologyThe University of Queensland St Lucia Brisbane QLD 4072 Australia
| | - Jianye Fu
- Australian Institute for Bioengineering and NanotechnologyThe University of Queensland St Lucia Brisbane QLD 4072 Australia
| | - Zhengying Gu
- Australian Institute for Bioengineering and NanotechnologyThe University of Queensland St Lucia Brisbane QLD 4072 Australia
| | - Yang Liu
- Australian Institute for Bioengineering and NanotechnologyThe University of Queensland St Lucia Brisbane QLD 4072 Australia
| | - Chengzhong Yu
- Australian Institute for Bioengineering and NanotechnologyThe University of Queensland St Lucia Brisbane QLD 4072 Australia
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36
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Yang Y, Tang J, Abbaraju PL, Jambhrunkar M, Song H, Zhang M, Lei C, Fu J, Gu Z, Liu Y, Yu C. Hybrid Nanoreactors: Enabling an Off-the-Shelf Strategy for Concurrently Enhanced Chemo-immunotherapy. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807595] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yannan Yang
- Australian Institute for Bioengineering and Nanotechnology; The University of Queensland; St Lucia Brisbane QLD 4072 Australia
| | - Jie Tang
- Australian Institute for Bioengineering and Nanotechnology; The University of Queensland; St Lucia Brisbane QLD 4072 Australia
| | - Prasanna Lakshmi Abbaraju
- Australian Institute for Bioengineering and Nanotechnology; The University of Queensland; St Lucia Brisbane QLD 4072 Australia
| | - Manasi Jambhrunkar
- Australian Institute for Bioengineering and Nanotechnology; The University of Queensland; St Lucia Brisbane QLD 4072 Australia
| | - Hao Song
- Australian Institute for Bioengineering and Nanotechnology; The University of Queensland; St Lucia Brisbane QLD 4072 Australia
| | - Min Zhang
- Australian Institute for Bioengineering and Nanotechnology; The University of Queensland; St Lucia Brisbane QLD 4072 Australia
| | - Chang Lei
- Australian Institute for Bioengineering and Nanotechnology; The University of Queensland; St Lucia Brisbane QLD 4072 Australia
| | - Jianye Fu
- Australian Institute for Bioengineering and Nanotechnology; The University of Queensland; St Lucia Brisbane QLD 4072 Australia
| | - Zhengying Gu
- Australian Institute for Bioengineering and Nanotechnology; The University of Queensland; St Lucia Brisbane QLD 4072 Australia
| | - Yang Liu
- Australian Institute for Bioengineering and Nanotechnology; The University of Queensland; St Lucia Brisbane QLD 4072 Australia
| | - Chengzhong Yu
- Australian Institute for Bioengineering and Nanotechnology; The University of Queensland; St Lucia Brisbane QLD 4072 Australia
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37
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Autzen HE, Koldsø H, Stansfeld PJ, Gourdon P, Sansom MSP, Nissen P. Interactions of a Bacterial Cu(I)-ATPase with a Complex Lipid Environment. Biochemistry 2018; 57:4063-4073. [DOI: 10.1021/acs.biochem.8b00326] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Henriette E. Autzen
- Centre for Membrane Pumps in Cells and Disease (PUMPkin), Danish National Research Foundation, 8000 Aarhus, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds vej 10C, 8000 Aarhus C, Denmark
| | - Heidi Koldsø
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Phillip J. Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Pontus Gourdon
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Poul Nissen
- Centre for Membrane Pumps in Cells and Disease (PUMPkin), Danish National Research Foundation, 8000 Aarhus, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds vej 10C, 8000 Aarhus C, Denmark
- Danish Research Institute of Translational Neuroscience (DANDRITE), Nordic-EMBL Partnership for Molecular Medicine, Aarhus University, 8000 Aarhus C, Denmark
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38
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Birch J, Axford D, Foadi J, Meyer A, Eckhardt A, Thielmann Y, Moraes I. The fine art of integral membrane protein crystallisation. Methods 2018; 147:150-162. [PMID: 29778646 DOI: 10.1016/j.ymeth.2018.05.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 05/13/2018] [Accepted: 05/15/2018] [Indexed: 11/29/2022] Open
Abstract
Integral membrane proteins are among the most fascinating and important biomolecules as they play a vital role in many biological functions. Knowledge of their atomic structures is fundamental to the understanding of their biochemical function and key in many drug discovery programs. However, over the years, structure determination of integral membrane proteins has proven to be far from trivial, hence they are underrepresented in the protein data bank. Low expression levels, insolubility and instability are just a few of the many hurdles one faces when studying these proteins. X-ray crystallography has been the most used method to determine atomic structures of membrane proteins. However, the production of high quality membrane protein crystals is always very challenging, often seen more as art than a rational experiment. Here we review valuable approaches, methods and techniques to successful membrane protein crystallisation.
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Affiliation(s)
- James Birch
- Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE, UK
| | - James Foadi
- Department of Mathematical Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Arne Meyer
- XtalConcepts GmbH, Schnackenburgallee 13, 22525 Hamburg, Germany
| | - Annette Eckhardt
- XtalConcepts GmbH, Schnackenburgallee 13, 22525 Hamburg, Germany
| | - Yvonne Thielmann
- Max Planck Institute of Biophysics, Molecular Membrane Biology, Max-von-Laue-Strasse 3, 60438 Frankfurt, Germany
| | - Isabel Moraes
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK; Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE, UK; National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK.
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39
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Ponnandai Shanmugavel K, Petranovic D, Wittung-Stafshede P. Probing functional roles of Wilson disease protein (ATP7B) copper-binding domains in yeast. Metallomics 2018; 9:981-988. [PMID: 28653724 DOI: 10.1039/c7mt00101k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
After Ctr1-mediated uptake into human cells, copper (Cu) ions are transported by the cytoplasmic Cu chaperone Atox1 to the Wilson disease protein (ATP7B) in the Golgi network. Cu transfer occurs via direct protein-protein interactions and leads to incorporation of Cu into Cu-dependent enzymes. ATP7B is a large multi-domain membrane-spanning protein which, in contrast to homologs, has six cytoplasmic metal-binding domains (MBDs). The reason for multiple MBDs is proposed to be indirect modulation of activity but mechanistic studies of full-length ATP7B are limited. We here developed a system that probes Cu flow through human Atox1 and ATP7B proteins when expressed in yeast. Using this assay, we assessed the roles of the different MBDs in ATP7B and found that the presence of the most N-terminal MBD increased, whereas the third MBD decreased, overall ATP7B-mediated Cu transport activity. Upon removal of all MBDs in ATP7B, the ability to transport Cu disappeared. The designed system can be expanded to include other yeast viability parameters and will be a useful tool for further mechanistic insights on human Cu transport as well as diseases involving Cu imbalance.
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Affiliation(s)
| | - Dina Petranovic
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden. and Novo Nordisk Foundation, Center for Biosustainability, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Pernilla Wittung-Stafshede
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden.
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40
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Abstract
Fungal cells colonize and proliferate in distinct niches, from soil and plants to diverse tissues in human hosts. Consequently, fungi are challenged with the goal of obtaining nutrients while simultaneously elaborating robust regulatory mechanisms to cope with a range of availability of nutrients, from scarcity to excess. Copper is essential for life but also potentially toxic. In this review we describe the sophisticated homeostatic mechanisms by which fungi acquire, utilize, and control this biochemically versatile trace element. Fungal pathogens, which can occupy distinct host tissues that have their own intrinsic requirements for copper homeostasis, have evolved mechanisms to acquire copper to successfully colonize the host, disseminate to other tissues, and combat host copper bombardment mechanisms that would otherwise mitigate virulence.
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Affiliation(s)
| | | | - Dennis J Thiele
- Department of Pharmacology and Cancer Biology.,Department of Molecular Genetics and Microbiology, and.,Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710;
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41
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Cu +-specific CopB transporter: Revising P 1B-type ATPase classification. Proc Natl Acad Sci U S A 2018; 115:2108-2113. [PMID: 29440418 DOI: 10.1073/pnas.1721783115] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The copper-transporting P1B-ATPases, which play a key role in cellular copper homeostasis, have been divided traditionally into two subfamilies, the P1B-1-ATPases or CopAs and the P1B-3-ATPases or CopBs. CopAs selectively export Cu+ whereas previous studies and bioinformatic analyses have suggested that CopBs are specific for Cu2+ export. Biochemical and spectroscopic characterization of Sphaerobacter thermophilus CopB (StCopB) show that, while it does bind Cu2+, the binding site is not the prototypical P1B-ATPase transmembrane site and does not involve sulfur coordination as proposed previously. Most important, StCopB exhibits metal-stimulated ATPase activity in response to Cu+, but not Cu2+, indicating that it is actually a Cu+ transporter. X-ray absorption spectroscopic studies indicate that Cu+ is coordinated by four sulfur ligands, likely derived from conserved cysteine and methionine residues. The histidine-rich N-terminal region of StCopB is required for maximal activity, but is inhibitory in the presence of divalent metal ions. Finally, reconsideration of the P1B-ATPase classification scheme suggests that the P1B-1- and P1B-3-ATPase subfamilies both comprise Cu+ transporters. These results are completely consistent with the known presence of only Cu+ within the reducing environment of the cytoplasm, which should eliminate the need for a Cu2+ P1B-ATPase.
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42
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Adiban J, Jamali Y, Rafii-Tabar H. Simulation of the effect of an external GHz electric field on the potential energy profile of Ca2+
ions in the selectivity filter of the CaV
Ab channel. Proteins 2018; 86:414-422. [DOI: 10.1002/prot.25456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 12/06/2017] [Accepted: 01/08/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Jamal Adiban
- Department of Medical Physics and Biomedical Engineering; School of Medicine, Shahid Beheshti University of Medical Sciences; Tehran Iran
| | - Yousef Jamali
- Department of Applied Mathematics; School of Mathematical Sciences, Tarbiat Modares University; Tehran Iran
- School of Nano-Science; Institute for Research in Fundamental Sciences (IPM); Tehran Iran
| | - Hashem Rafii-Tabar
- Department of Medical Physics and Biomedical Engineering; School of Medicine, Shahid Beheshti University of Medical Sciences; Tehran Iran
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43
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Ravishankar H, Barth A, Andersson M. Probing the activity of a recombinant Zn 2+ -transporting P-type ATPase. Biopolymers 2017; 109. [PMID: 29168553 DOI: 10.1002/bip.23087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/16/2017] [Accepted: 10/25/2017] [Indexed: 01/25/2023]
Abstract
P-type ATPase proteins maintain cellular homeostasis and uphold critical concentration gradients by ATP-driven ion transport across biological membranes. Characterization of single-cycle dynamics by time-resolved X-ray scattering techniques in solution could resolve structural intermediates not amendable to for example crystallization or cryo-electron microscopy sample preparation. To pave way for such time-resolved experiments, we used biochemical activity measurements, Attenuated Total Reflectance (ATR) and time-dependent Fourier-Transform Infra-Red (FTIR) spectroscopy to identify optimal conditions for activating a Zn2+ -transporting Type-I ATPase from Shigella sonnei (ssZntA) at high protein concentration using caged ATP. The highest total activity was observed at a protein concentration of 25 mg/mL, at 310 K, pH 7, and required the presence of 20% (v/v) glycerol as stabilizing agent. Neither the presence of caged ATP nor increasing lipid-to-protein ratio affected the hydrolysis activity significantly. This work also paves way for characterization of recombinant metal-transporting (Type-I) ATPase mutants with medical relevance.
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Affiliation(s)
- H Ravishankar
- Science for Life Laboratory, Department of Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, Solna, SE-171 21, Sweden
| | - A Barth
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE-106 91, Sweden
| | - M Andersson
- Science for Life Laboratory, Department of Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, Solna, SE-171 21, Sweden
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44
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Dyla M, Terry DS, Kjaergaard M, Sørensen TLM, Lauwring Andersen J, Andersen JP, Rohde Knudsen C, Altman RB, Nissen P, Blanchard SC. Dynamics of P-type ATPase transport revealed by single-molecule FRET. Nature 2017; 551:346-351. [PMID: 29144454 DOI: 10.1038/nature24296] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 09/18/2017] [Indexed: 01/05/2023]
Abstract
Phosphorylation-type (P-type) ATPases are ubiquitous primary transporters that pump cations across cell membranes through the formation and breakdown of a phosphoenzyme intermediate. Structural investigations suggest that the transport mechanism is defined by conformational changes in the cytoplasmic domains of the protein that are allosterically coupled to transmembrane helices so as to expose ion binding sites to alternate sides of the membrane. Here, we have used single-molecule fluorescence resonance energy transfer to directly observe conformational changes associated with the functional transitions in the Listeria monocytogenes Ca2+-ATPase (LMCA1), an orthologue of eukaryotic Ca2+-ATPases. We identify key intermediates with no known crystal structures and show that Ca2+ efflux by LMCA1 is rate-limited by phosphoenzyme formation. The transport process involves reversible steps and an irreversible step that follows release of ADP and extracellular release of Ca2+.
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Affiliation(s)
- Mateusz Dyla
- Centre for Membrane Pumps in Cells and Disease - PUMPKIN, Danish National Research Foundation & Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus University, DK-8000 Aarhus C, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark.,Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000 Aarhus C, Denmark
| | - Daniel S Terry
- Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, New York 10021, USA
| | - Magnus Kjaergaard
- Centre for Membrane Pumps in Cells and Disease - PUMPKIN, Danish National Research Foundation & Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus University, DK-8000 Aarhus C, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark.,Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000 Aarhus C, Denmark.,Aarhus Institute of Advanced Studies (AIAS), Aarhus University, DK-8000 Aarhus C, Denmark
| | - Thomas L-M Sørensen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Jacob Lauwring Andersen
- Centre for Membrane Pumps in Cells and Disease - PUMPKIN, Danish National Research Foundation & Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus University, DK-8000 Aarhus C, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Jens P Andersen
- Department of Biomedicine, Aarhus University, DK-8000 Aarhus C, Denmark
| | | | - Roger B Altman
- Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, New York 10021, USA
| | - Poul Nissen
- Centre for Membrane Pumps in Cells and Disease - PUMPKIN, Danish National Research Foundation & Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus University, DK-8000 Aarhus C, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark.,Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000 Aarhus C, Denmark
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, New York 10021, USA
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45
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Jayakanthan S, Braiterman LT, Hasan NM, Unger VM, Lutsenko S. Human copper transporter ATP7B (Wilson disease protein) forms stable dimers in vitro and in cells. J Biol Chem 2017; 292:18760-18774. [PMID: 28842499 DOI: 10.1074/jbc.m117.807263] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 08/21/2017] [Indexed: 11/06/2022] Open
Abstract
ATP7B is a copper-transporting P1B-type ATPase (Cu-ATPase) with an essential role in human physiology. Mutations in ATP7B cause the potentially fatal Wilson disease, and changes in ATP7B expression are observed in several cancers. Despite its physiologic importance, the biochemical information about ATP7B remains limited because of a complex multidomain organization of the protein. By analogy with the better characterized prokaryotic Cu-ATPases, ATP7B is assumed to be a single-chain monomer. We show that in eukaryotic cells, human ATP7B forms dimers that can be purified following solubilization. Deletion of the four N-terminal metal-binding domains, characteristic for human ATP7B, does not disrupt dimerization, i.e. the dimer interface is formed by the domains that are conserved among Cu-ATPases. Unlike the full-length ATP7B, which is targeted to the trans-Golgi network, 1-4ΔMBD-7B is targeted primarily to vesicles. This result and the analysis of differentially tagged ATP7B variants indicate that the dimeric structure is retained during ATP7B trafficking between the intracellular compartments. Purified dimeric species of 1-4ΔMBD-7B were characterized by a negative stain electron microscopy in the presence of ADP/MgCl2 Single-particle analysis yielded a low-resolution 3D model that provides the first insight into an overall architecture of a human Cu-ATPase, positions of the main domains, and a dimer interface.
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Affiliation(s)
| | - Lelita T Braiterman
- Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 and
| | | | - Vinzenz M Unger
- the Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
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46
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Abstract
Cellular potassium import systems play a fundamental role in osmoregulation, pH homeostasis and membrane potential in all domains of life. In bacteria, the kdp operon encodes a four subunit potassium pump that maintains intracellular homeostasis as well as cell shape and turgor under conditions where potassium is limiting1. This membrane complex, called KdpFABC, has one channel-like subunit (KdpA) belonging to the Superfamily of Potassium Transporters and another pump-like subunit (KdpB) belonging to the Superfamily of P-type ATPases. Although there is considerable structural and functional information about members from both superfamilies, the mechanism by which uphill potassium transport through KdpA is coupled with ATP hydrolysis by KdpB remains poorly understood. Here we report the 2.9 Å X-ray structure of the complete Escherichia coli KdpFABC complex with a potassium ion within the selectivity filter of KdpA as well as a water molecule at a canonical cation site in the transmembrane domain of KdpB. The structure also reveals two structural elements that appear to mediate the coupling between these two subunits. Specifically, a protein-embedded tunnel runs between these potassium and water sites and a helix controlling the cytoplasmic gate of KdpA is linked to the phosphorylation domain of KdpB. Based on these observations, we propose an unprecedented mechanism that repurposes protein channel architecture for active transport across biomembranes.
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Affiliation(s)
- Ching-Shin Huang
- Molecular Biophysics Graduate Program, New York University School of Medicine, Skirball Institute, 540 First Avenue, New York, New York 10016, USA
| | - Bjørn Panyella Pedersen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark.,Aarhus Institute of Advanced Studies, Aarhus University, Høegh-Guldbergs Gade 6B, DK-8000 Aarhus C, Denmark
| | - David L Stokes
- Department of Cell Biology, New York University School of Medicine, Skirball Institute, 540 First Avenue, New York, New York 10016, USA
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47
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Focht D, Croll TI, Pedersen BP, Nissen P. Improved Model of Proton Pump Crystal Structure Obtained by Interactive Molecular Dynamics Flexible Fitting Expands the Mechanistic Model for Proton Translocation in P-Type ATPases. Front Physiol 2017; 8:202. [PMID: 28443028 PMCID: PMC5387105 DOI: 10.3389/fphys.2017.00202] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 03/20/2017] [Indexed: 11/22/2022] Open
Abstract
The plasma membrane H+-ATPase is a proton pump of the P-type ATPase family and essential in plants and fungi. It extrudes protons to regulate pH and maintains a strong proton-motive force that energizes e.g., secondary uptake of nutrients. The only crystal structure of a H+-ATPase (AHA2 from Arabidopsis thaliana) was reported in 2007. Here, we present an improved atomic model of AHA2, obtained by a combination of model rebuilding through interactive molecular dynamics flexible fitting (iMDFF) and structural refinement based on the original data, but using up-to-date refinement methods. More detailed map features prompted local corrections of the transmembrane domain, in particular rearrangement of transmembrane helices 7 and 8, and the cytoplasmic N- and P-domains, and the new model shows improved overall quality and reliability scores. The AHA2 structure shows similarity to the Ca2+-ATPase E1 state, and provides a valuable starting point model for structural and functional analysis of proton transport mechanism of P-type H+-ATPases. Specifically, Asp684 protonation associated with phosphorylation and occlusion of the E1P state may result from hydrogen bond interaction with Asn106. A subsequent deprotonation associated with extracellular release in the E2P state may result from an internal salt bridge formation to an Arg655 residue, which in the present E1 state is stabilized in a solvated pocket. A release mechanism based on an in-built counter-cation was also later proposed for Zn2+-ATPase, for which structures have been determined in Zn2+ released E2P-like states with the salt bridge interaction formed.
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Affiliation(s)
- Dorota Focht
- Department of Molecular Biology and Genetics, Aarhus UniversityAarhus, Denmark.,DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus UniversityAarhus, Denmark.,PUMPkin, Danish National Research Foundation, Aarhus UniversityAarhus, Denmark
| | - Tristan I Croll
- Institute of Health Biomedical Innovation, Queensland University of TechnologyBrisbane, QLD, Australia
| | - Bjorn P Pedersen
- Department of Molecular Biology and Genetics, Aarhus UniversityAarhus, Denmark.,PUMPkin, Danish National Research Foundation, Aarhus UniversityAarhus, Denmark.,Aarhus Institute of Advanced Studies, Aarhus UniversityAarhus, Denmark
| | - Poul Nissen
- Department of Molecular Biology and Genetics, Aarhus UniversityAarhus, Denmark.,DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus UniversityAarhus, Denmark.,PUMPkin, Danish National Research Foundation, Aarhus UniversityAarhus, Denmark
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48
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Wijekoon CJK, Udagedara SR, Knorr RL, Dimova R, Wedd AG, Xiao Z. Copper ATPase CopA from Escherichia coli: Quantitative Correlation between ATPase Activity and Vectorial Copper Transport. J Am Chem Soc 2017; 139:4266-4269. [PMID: 28272878 DOI: 10.1021/jacs.6b12921] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Cu-ATPases are membrane copper transporters present in all kingdoms of life. They play a central role in Cu homeostasis by pumping Cu ions across cell membranes with energy derived from ATP hydrolysis. In this work, the Cu-ATPase CopA from Escherichia coli was expressed and purified in fully functional form and demonstrated to bind Cu(I) with subfemtomolar affinity. It was incorporated into the lipid membrane of giant unilamellar vesicles (GUVs) whose dimensions match those of eukaryotic cells. An 1H NMR approach provided a quantitative ATPase activity assay for the enzyme either dissolved in detergent or embedded in GUV membranes. The activity varied with the Cu(I) availability in an optimized assay solution for either environment, demonstrating a direct correlation between ATPase activity and Cu(I) transport. Quantitative analysis of the Cu content trapped by the GUVs is consistent with a Cu:ATP turnover ratio of 1.
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Affiliation(s)
- Chathuri J K Wijekoon
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne , Parkville, Victoria 3010, Australia
| | - Saumya R Udagedara
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne , Parkville, Victoria 3010, Australia
| | - Roland L Knorr
- Max Planck Institute of Colloids and Interfaces , Science Park Golm, 14424 Potsdam, Germany
| | - Rumiana Dimova
- Max Planck Institute of Colloids and Interfaces , Science Park Golm, 14424 Potsdam, Germany
| | - Anthony G Wedd
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne , Parkville, Victoria 3010, Australia
| | - Zhiguang Xiao
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne , Parkville, Victoria 3010, Australia.,The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville , Victoria 3010, Australia
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Tadini-Buoninsegni F, Smeazzetto S. Mechanisms of charge transfer in human copper ATPases ATP7A and ATP7B. IUBMB Life 2017; 69:218-225. [PMID: 28164426 DOI: 10.1002/iub.1603] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 12/26/2016] [Indexed: 12/30/2022]
Abstract
ATP7A and ATP7B are Cu+ -transporting ATPases of subclass IB and play a fundamental role in intracellular copper homeostasis. ATP7A/B transfer Cu+ ions across the membrane from delivery to acceptor proteins without establishing a free Cu+ gradient. Transfer of copper across the membrane is coupled to ATP hydrolysis. Current measurements on solid supported membranes (SSM) were performed to investigate the mechanism of copper-related charge transfer across ATP7A and ATP7B. SSM measurements demonstrated that electrogenic copper displacement occurs within ATP7A/B following addition of ATP and formation of the phosphorylated intermediate. Comparison of the time constants for cation displacement in ATP7A/B and sarcoplasmic reticulum Ca2+ -ATPase is consistent with the slower phosphoenzyme formation in copper ATPases. Moreover, ATP-dependent copper transfer in ATP7A/B is not affected by varying the pH, suggesting that net proton counter-transport may not occur in copper ATPases. Platinum anticancer drugs activate ATP7A/B and are subjected to ATP-dependent vectorial displacement with a mechanism analogous to that of copper. © 2016 IUBMB Life, 69(4):218-225, 2017.
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Affiliation(s)
| | - Serena Smeazzetto
- Department of Chemistry "Ugo Schiff,", University of Florence, Sesto Fiorentino, Italy
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50
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Öhrvik H, Aaseth J, Horn N. Orchestration of dynamic copper navigation – new and missing pieces. Metallomics 2017; 9:1204-1229. [DOI: 10.1039/c7mt00010c] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A general principle in all cells in the body is that an essential metal – here copper – is taken up at the plasma membrane, directed through cellular compartments for use in specific enzymes and pathways, stored in specific scavenging molecules if in surplus, and finally expelled from the cells.
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Affiliation(s)
- Helena Öhrvik
- Medical Biochemistry and Microbiology
- Uppsala University
- Sweden
| | - Jan Aaseth
- Innlandet Hospital Trust and Inland Norway University of Applied Sciences
- Norway
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