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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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2
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Grønberg C, Sitsel O, Lindahl E, Gourdon P, Andersson M. Membrane Anchoring and Ion-Entry Dynamics in P-type ATPase Copper Transport. Biophys J 2016; 111:2417-2429. [PMID: 27926843 PMCID: PMC5153542 DOI: 10.1016/j.bpj.2016.10.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/29/2016] [Accepted: 10/17/2016] [Indexed: 12/23/2022] Open
Abstract
Cu+-specific P-type ATPase membrane protein transporters regulate cellular copper levels. The lack of crystal structures in Cu+-binding states has limited our understanding of how ion entry and binding are achieved. Here, we characterize the molecular basis of Cu+ entry using molecular-dynamics simulations, structural modeling, and in vitro and in vivo functional assays. Protein structural rearrangements resulting in the exposure of positive charges to bulk solvent rather than to lipid phosphates indicate a direct molecular role of the putative docking platform in Cu+ delivery. Mutational analyses and simulations in the presence and absence of Cu+ predict that the ion-entry path involves two ion-binding sites: one transient Met148-Cys382 site and one intramembranous site formed by trigonal coordination to Cys384, Asn689, and Met717. The results reconcile earlier biochemical and x-ray absorption data and provide a molecular understanding of ion entry in Cu+-transporting P-type ATPases.
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Affiliation(s)
| | | | - Erik Lindahl
- Biochemistry & Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Pontus Gourdon
- University of Copenhagen, Copenhagen, Denmark; Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Magnus Andersson
- Theoretical Physics and Swedish e-Science Research Center, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden.
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3
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Lasala R, Coudray N, Abdine A, Zhang Z, Lopez-Redondo M, Kirshenbaum R, Alexopoulos J, Zolnai Z, Stokes DL, Ubarretxena-Belandia I. Sparse and incomplete factorial matrices to screen membrane protein 2D crystallization. J Struct Biol 2014; 189:123-34. [PMID: 25478971 DOI: 10.1016/j.jsb.2014.11.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 11/18/2014] [Accepted: 11/24/2014] [Indexed: 01/09/2023]
Abstract
Electron crystallography is well suited for studying the structure of membrane proteins in their native lipid bilayer environment. This technique relies on electron cryomicroscopy of two-dimensional (2D) crystals, grown generally by reconstitution of purified membrane proteins into proteoliposomes under conditions favoring the formation of well-ordered lattices. Growing these crystals presents one of the major hurdles in the application of this technique. To identify conditions favoring crystallization a wide range of factors that can lead to a vast matrix of possible reagent combinations must be screened. However, in 2D crystallization these factors have traditionally been surveyed in a relatively limited fashion. To address this problem we carried out a detailed analysis of published 2D crystallization conditions for 12 β-barrel and 138 α-helical membrane proteins. From this analysis we identified the most successful conditions and applied them in the design of new sparse and incomplete factorial matrices to screen membrane protein 2D crystallization. Using these matrices we have run 19 crystallization screens for 16 different membrane proteins totaling over 1300 individual crystallization conditions. Six membrane proteins have yielded diffracting 2D crystals suitable for structure determination, indicating that these new matrices show promise to accelerate the success rate of membrane protein 2D crystallization.
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Affiliation(s)
- R Lasala
- New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA
| | - N Coudray
- New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA
| | - A Abdine
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Z Zhang
- New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA
| | - M Lopez-Redondo
- Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA
| | - R Kirshenbaum
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - J Alexopoulos
- Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA
| | - Z Zolnai
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - D L Stokes
- New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA; Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA
| | - I Ubarretxena-Belandia
- New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA; Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA.
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4
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Abstract
Copper ATPases, in analogy with other members of the P-ATPase superfamily, contain a catalytic headpiece including an aspartate residue reacting with ATP to form a phosphoenzyme intermediate, and transmembrane helices containing cation-binding sites [TMBS (transmembrane metal-binding sites)] for catalytic activation and cation translocation. Following phosphoenzyme formation by utilization of ATP, bound copper undergoes displacement from the TMBS to the lumenal membrane surface, with no H+ exchange. Although PII-type ATPases sustain active transport of alkali/alkali-earth ions (i.e. Na+, Ca2+) against electrochemical gradients across defined membranes, PIB-type ATPases transfer transition metal ions (i.e. Cu+) from delivery to acceptor proteins and, prominently in mammalian cells, undergo trafficking from/to various membrane compartments. A specific component of copper ATPases is the NMBD (N-terminal metal-binding domain), containing up to six copper-binding sites in mammalian (ATP7A and ATP7B) enzymes. Copper occupancy of NMBD sites and interaction with the ATPase headpiece are required for catalytic activation. Furthermore, in the presence of copper, the NMBD allows interaction with protein kinase D, yielding phosphorylation of serine residues, ATP7B trafficking and protection from proteasome degradation. A specific feature of ATP7A is glycosylation and stabilization on plasma membranes. Cisplatin, a platinum-containing anti-cancer drug, binds to copper sites of ATP7A and ATP7B, and undergoes vectorial displacement in analogy with copper.
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5
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Blackburn NJ, Yan N, Lutsenko S. Copper in Eukaryotes. BINDING, TRANSPORT AND STORAGE OF METAL IONS IN BIOLOGICAL CELLS 2014. [DOI: 10.1039/9781849739979-00524] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Copper is essential for normal growth and development of eukaryotic organisms. Numerous physiological processes rely on sufficient availability of copper: from indispensable reactions such as mitochondrial respiration to more highly specialized processes such as pigment development in a skin. Copper misbalance has been linked to a variety of metabolic and neurodegenerative disorders in humans. Complex cellular machinery has evolved to mediate copper uptake, compartmentalization and incorporation into target proteins. Extensive studies revealed a predominant utilization of methionines and histidines by copper handling molecules for copper capture at the extracellular surface and delivery to cuproenzymes in the lumen of cellular compartments, respectively. Cu(I) is a predominant form within the cell, and copper binding and distribution inside the cell at the cytosolic sites relies heavily on cysteines. The selectivity and directionality of copper transfer reactions is determined by thermodynamic and kinetic factors as well as spatial distribution of copper donors and acceptors. In this chapter, we review current structural and mechanistic data on copper transport and distribution in yeast and mammalian cells and highlight important issues and questions for future studies.
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Affiliation(s)
- Ninian J. Blackburn
- Institute of Environmental Health, Oregon Health and Sciences University Portland, OR 97239 USA
| | - Nan Yan
- Department of Physiology, The Johns Hopkins University School of Medicine Baltimore, MD 21205 USA
| | - Svetlana Lutsenko
- Department of Physiology, The Johns Hopkins University School of Medicine Baltimore, MD 21205 USA
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6
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Meloni G, Zhang L, Rees DC. Transmembrane type-2-like Cu2+ site in the P1B-3-type ATPase CopB: implications for metal selectivity. ACS Chem Biol 2014; 9:116-21. [PMID: 24144006 DOI: 10.1021/cb400603t] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Metal selectivity in P1B-type ATPase transporters is determined by conserved amino acid residues in their transmembrane helices responsible for metal binding and transport across the cellular membrane. The Cu(2+)-selective CopB from Archaeoglobus fulgidus has been investigated to explore the coordination chemistry of the transition metal binding sites in P1B-3-type ATPases. Electronic absorption, electron paramagnetic resonance, and X-ray absorption spectroscopic studies indicate the presence of a high-affinity transmembrane Type-2-like Cu(2+) center in which a single cupric ion is coordinated in a distorted square pyramidal geometry by mixed nitrogen/oxygen and sulfur ligands.
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Affiliation(s)
- Gabriele Meloni
- Division of Chemistry and Chemical Engineering and ‡Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California 91125, United States of America
| | - Limei Zhang
- Division of Chemistry and Chemical Engineering and ‡Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California 91125, United States of America
| | - Douglas C. Rees
- Division of Chemistry and Chemical Engineering and ‡Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California 91125, United States of America
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Hu Q, Wu X, Jiang Y, Liu Y, Liang Y, Liu X, Yin H, Baba N. Differential gene expression and bioinformatics analysis of copper resistance gene afe_1073 in Acidithiobacillus ferrooxidans. Biol Trace Elem Res 2013; 152:91-7. [PMID: 23344975 DOI: 10.1007/s12011-012-9589-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 12/20/2012] [Indexed: 01/13/2023]
Abstract
Copper resistance of acidophilic bacteria is very significant in bioleaching of copper ore since high concentration of copper are harmful to the growth of organisms. Copper resistance gene afe_1073 was putatively considered to be involved in copper homeostasis in Acidithiobacillus ferrooxidans ATCC23270. In the present study, differential expression of afe_1073 in A. ferrooxidans strain DY26 and DC was assessed with quantitative reverse transcription polymerase chain reaction. The results showed the expression of afe_1073 in two strains increased with the increment of copper concentrations. The expression of DY26 was lower than that of DC at the same copper concentration although A. ferrooxidans strain DY26 possessed higher copper resistance than strain DC. In addition, bioinformatics analysis showed AFE_1073 was a typical transmembrane protein P1b1-ATPase, which could reduce the harm of Cu(+) by pumping it out from the cell. There were two mutation sites in AFE_1073 between DY26 and DC and one may change the hydrophobicity of AFE_1073, which could enhance the ability of DY26 to pump out Cu(+). Therefore, DY26 needed less gene expression of afe_1073 for resisting copper toxicity than that of DC at the same copper stress. Our study will be beneficial to understanding the copper resistance mechanism of A. ferrooxidans.
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Affiliation(s)
- Qi Hu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, China 410083
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8
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Abstract
P(IB)-type ATPases transport heavy metals (Cu(2+), Cu(+), Ag(+), Zn(2+), Cd(2+), Co(2+)) across biomembranes, playing a key role in homeostasis and in the mechanisms of biotolerance of these metals. Three genes coding for putative P(IB)-type ATPases are present in the genome of Thermus thermophilus (HB8 and HB27): the TTC1358, TTC1371, and TTC0354 genes; these genes are annotated, respectively, as two copper transporter (CopA and CopB) genes and a zinc-cadmium transporter (Zn(2+)/Cd(2+)-ATPase) gene. We cloned and expressed the three proteins with 8His tags using a T. thermophilus expression system. After purification, each of the proteins was shown to have phosphodiesterase activity at 65°C with ATP and p-nitrophenyl phosphate (pNPP) as substrates. CopA was found to have greater activity in the presence of Cu(+), while CopB was found to have greater activity in the presence of Cu(2+). The putative Zn(2+)/Cd(2+)-ATPase was truncated at the N terminus and was, surprisingly, activated in vitro by copper but not by zinc or cadmium. When expressed in Escherichia coli, however, the putative Zn(2+)/Cd(2+)-ATPase could be isolated as a full-length protein and the ATPase activity was increased by the addition of Zn(2+) and Cd(2+) as well as by Cu(+). Mutant strains in which each of the three P-type ATPases was deleted singly were constructed. In each case, the deletion increased the sensitivity of the strain to growth in the presence of copper in the medium, indicating that each of the three can pump copper out of the cells and play a role in copper detoxification.
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9
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Rosenzweig AC, Argüello JM. Toward a molecular understanding of metal transport by P(1B)-type ATPases. CURRENT TOPICS IN MEMBRANES 2012; 69:113-36. [PMID: 23046649 DOI: 10.1016/b978-0-12-394390-3.00005-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The P(1B) family of P-type ATPases couples the transport of cytoplasmic transition metals across biological membranes to the hydrolysis of ATP. These ubiquitous transporters function in maintaining cytoplasmic metal quotas and in the assembly of metalloproteins, and have been classified into subfamilies (P(1B-1)-P(1B-5)) on the basis of their transported substrates (Cu(+), Zn(2+), Cu(2+), and Co(2+)) and signature sequences in their transmembrane segments. In addition, each subgroup presents a characteristic membrane topology and specific regulatory cytoplasmic metal-binding domains. In recent years, significant major aspects of their transport mechanism have been described, including the stoichiometry of transport and the delivery of substrates to transport sites by metallochaperones. Toward understanding their structure, the metal coordination by transport sites has been characterized for Cu(+) and Zn(2+)-ATPases. In addition, atomic resolution structures have been determined, providing key insight into the elements that enable transition metal transport. Because the Cu(+)-transporting ATPases are found in humans and are linked to disease, this subfamily has been the focus of intense study. As a result, significant progress has been made toward understanding Cu(+)-ATPase function on the molecular level, using both the human proteins and the bacterial homologs, most notably the CopA proteins from Archaeoglobus fulgidus, Bacillus subtilis, and Thermotoga maritima. This chapter thus focuses on the mechanistic and structural information obtained by studying these latter Cu(+)-ATPases, with some consideration of how these aspects might differ for the other subfamilies of P(1B)-ATPases.
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Affiliation(s)
- Amy C Rosenzweig
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
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10
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Ponomarev SY, Click TH, Kaminski GA. Electrostatic polarization is crucial in reproducing Cu(I) interaction energies and hydration. J Phys Chem B 2011; 115:10079-85. [PMID: 21761909 DOI: 10.1021/jp2051933] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have explored the suitability of fixed-charges and polarizable force fields for modeling interactions of the monovalent Cu(I) ion. Parameters for this ion have been tested and refitted within the fixed-charges OPLS-AA and polarizable force field (PFF) frameworks. While this ion plays an important role in many protein interactions, the attention to it in developing empirical force fields is limited. Our PFF parameters for the copper ion worked very well for the Cu(I) interactions with water, while both the original OPLS2005 and our refitted OPLS versions moderately underestimated the copper-water interaction energy. However, the greatest problem in using the nonpolarizable fixed-charges OPLS force field was observed while calculating interaction energies and distances for Cu(I)-benzene complexes. The OPLS2005 model underestimates the interaction energy by a factor of 4. Refitting the OPLS parameters reduced this underestimation to a factor of 2.2-2.4, but only at a cost of distorting the complex geometry. At the same time, the polarizable calculations had an error of about 4%. Moreover, we then used the PFF and nonpolarizable refitted OPLS models for finding free energy of hydration for copper ion via molecular dynamics simulations. While the OPLS calculations lead to a 22% error in the solvation energy, the PFF result was off by only 1.8%. This was achieved with no refitting of the parameters but simply by employing the model developed for the Cu(I) interaction with a single water molecule. We believe that the presented results not only lead to a conclusion about a qualitatively greater suitability of polarizable force fields for simulating molecular interactions with ions but also attest to the excellent level of transferability of PFF parameters.
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Affiliation(s)
- Sergei Y Ponomarev
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts 01609, USA
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11
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Crystal structure of a copper-transporting PIB-type ATPase. Nature 2011; 475:59-64. [PMID: 21716286 DOI: 10.1038/nature10191] [Citation(s) in RCA: 244] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Accepted: 05/11/2011] [Indexed: 01/19/2023]
Abstract
Heavy-metal homeostasis and detoxification is crucial for cell viability. P-type ATPases of the class IB (PIB) are essential in these processes, actively extruding heavy metals from the cytoplasm of cells. Here we present the structure of a PIB-ATPase, a Legionella pneumophila CopA Cu(+)-ATPase, in a copper-free form, as determined by X-ray crystallography at 3.2 Å resolution. The structure indicates a three-stage copper transport pathway involving several conserved residues. A PIB-specific transmembrane helix kinks at a double-glycine motif displaying an amphipathic helix that lines a putative copper entry point at the intracellular interface. Comparisons to Ca(2+)-ATPase suggest an ATPase-coupled copper release mechanism from the binding sites in the membrane via an extracellular exit site. The structure also provides a framework to analyse missense mutations in the human ATP7A and ATP7B proteins associated with Menkes' and Wilson's diseases.
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12
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Lam VH, Lee JH, Silverio A, Chan H, Gomolplitinant KM, Povolotsky TL, Orlova E, Sun EI, Welliver CH, Saier MH. Pathways of transport protein evolution: recent advances. Biol Chem 2011; 392:5-12. [PMID: 21194372 DOI: 10.1515/bc.2011.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
We herein report recent advances in our understanding of transport protein evolution. Numerous families of complex transmembrane transport proteins are believed to have arisen from short channel-forming amphipathic or hydrophobic peptides by various types of intragenic duplication events. Distinct pathways distinguish families, demonstrating independent origins for some, and allowing assignment of others to superfamilies. Some families have diversified in topology, whereas others have remained uniform. An example of 'retroevolution' was discovered where a more complex carrier gave rise to a structurally and functionally simpler channel. The results described in this review article expand our understanding of protein evolution.
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Affiliation(s)
- Vincent H Lam
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
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13
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Morth JP, Pedersen BP, Buch-Pedersen MJ, Andersen JP, Vilsen B, Palmgren MG, Nissen P. A structural overview of the plasma membrane Na+,K+-ATPase and H+-ATPase ion pumps. Nat Rev Mol Cell Biol 2011; 12:60-70. [PMID: 21179061 DOI: 10.1038/nrm3031] [Citation(s) in RCA: 253] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Plasma membrane ATPases are primary active transporters of cations that maintain steep concentration gradients. The ion gradients and membrane potentials derived from them form the basis for a range of essential cellular processes, in particular Na(+)-dependent and proton-dependent secondary transport systems that are responsible for uptake and extrusion of metabolites and other ions. The ion gradients are also both directly and indirectly used to control pH homeostasis and to regulate cell volume. The plasma membrane H(+)-ATPase maintains a proton gradient in plants and fungi and the Na(+),K(+)-ATPase maintains a Na(+) and K(+) gradient in animal cells. Structural information provides insight into the function of these two distinct but related P-type pumps.
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Affiliation(s)
- J Preben Morth
- Danish National Research Foundation, Centre for Membrane Pumps in Cells and Disease - PUMPKIN, Denmark
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14
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Raimunda D, González-Guerrero M, Leeber BW, Argüello JM. The transport mechanism of bacterial Cu+-ATPases: distinct efflux rates adapted to different function. Biometals 2011; 24:467-75. [PMID: 21210186 DOI: 10.1007/s10534-010-9404-3] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Accepted: 12/22/2010] [Indexed: 12/11/2022]
Abstract
Cu(+)-ATPases play a key role in bacterial Cu(+) homeostasis by participating in Cu(+) detoxification and cuproprotein assembly. Characterization of Archaeoglobus fulgidus CopA, a model protein within the subfamily of P(1B-1) type ATPases, has provided structural and mechanistic details on this group of transporters. Atomic resolution structures of cytoplasmic regulatory metal binding domains (MBDs) and catalytic actuator, phosphorylation, and nucleotide binding domains are available. These, in combination with whole protein structures resulting from cryo-electron microscopy analyses, have enabled the initial modeling of these transporters. Invariant residues in helixes 6, 7 and 8 form two transmembrane metal binding sites (TM-MBSs). These bind Cu(+) with high affinity in a trigonal planar geometry. The cytoplasmic Cu(+) chaperone CopZ transfers the metal directly to the TM-MBSs; however, loading both of the TM-MBSs requires binding of nucleotides to the enzyme. In agreement with the classical transport mechanism of P-type ATPases, occupancy of both transmembrane sites by cytoplasmic Cu(+) is a requirement for enzyme phosphorylation and subsequent transport into the periplasmic or extracellular milieus. Recent transport studies have shown that all Cu(+)-ATPases drive cytoplasmic Cu(+) efflux, albeit with quite different transport rates in tune with their various physiological roles. Archetypical Cu(+)-efflux pumps responsible for Cu(+) tolerance, like the Escherichia coli CopA, have turnover rates ten times higher than those involved in cuproprotein assembly (or alternative functions). This explains the incapability of the latter group to significantly contribute to the metal efflux required for survival in high copper environments.
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Affiliation(s)
- Daniel Raimunda
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA 01609, USA
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15
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Reversible Unfolding of a Thermophilic Membrane Protein in Phospholipid/Detergent Mixed Micelles. J Mol Biol 2010; 397:550-9. [DOI: 10.1016/j.jmb.2010.01.045] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Revised: 01/13/2010] [Accepted: 01/21/2010] [Indexed: 01/11/2023]
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16
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Barry AN, Shinde U, Lutsenko S. Structural organization of human Cu-transporting ATPases: learning from building blocks. J Biol Inorg Chem 2009; 15:47-59. [PMID: 19851794 DOI: 10.1007/s00775-009-0595-4] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 09/28/2009] [Indexed: 12/29/2022]
Abstract
Copper-transporting ATPases (Cu-ATPases) ATP7A and ATP7B play an essential role in human physiological function. Their primary function is to deliver copper to the secretory pathway and export excess copper from the cell for removal or further utilization. Cells employ Cu-ATPases in numerous physiological processes that include the biosynthesis of copper-dependent enzymes, lactation, and response to hypoxia. Biochemical studies of human Cu-ATPases and their orthologs have demonstrated that Cu-ATPases share many common structural and mechanistic characteristics with other members of the P-type ATPase family. Nevertheless, the Cu-ATPases have a unique coordinate environment for their ligands, copper and ATP, and additional domains that are required for sophisticated regulation of their intracellular localization and activity. Here, we review recent progress that has been made in understanding the structure of Cu-ATPases from the analysis of their individual domains and orthologs from microorganisms, and speculate about the implications of these findings for the function and regulation of human copper pumps.
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Affiliation(s)
- Amanda N Barry
- Department of Physiology, Johns Hopkins University, Baltimore, MD 21205, USA
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17
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Völlmecke C, Kötting C, Gerwert K, Lübben M. Spectroscopic investigation of the reaction mechanism of CopB-B, the catalytic fragment from an archaeal thermophilic ATP-driven heavy metal transporter. FEBS J 2009; 276:6172-86. [PMID: 19780839 DOI: 10.1111/j.1742-4658.2009.07320.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The mechanism of ATP hydrolysis of a shortened variant of the heavy metal-translocating P-type ATPase CopB of Sulfolobus solfataricus was studied. The catalytic fragment, named CopB-B, comprises the nucleotide binding and phosphorylation domains. We demonstrated stoichiometric high-affinity binding of one nucleotide to the protein (K(diss) 1-20 microm). Mg is not necessary for nucleotide association but is essential for the phosphatase activity. Binding and hydrolysis of ATP released photolytically from the caged precursor nitrophenylethyl-ATP was measured at 30 degrees C by infrared spectroscopy, demonstrating that phosphate groups are not involved in nucleotide binding. The hydrolytic kinetics was biphasic, and provides evidence for at least one reaction intermediate. Modelling of the forward reaction gave rise to three kinetic states connected by two intrinsic rate constants. The lower kinetic constant (k(1) = 4.7 x 10(-3) s(-1) at 30 degrees C) represents the first and rate-limiting reaction, probably reflecting the transition between the open and closed conformations of the domain pair. The subsequent step has a faster rate (k(2) = 17 x 10(-3) s(-1) at 30 degrees C), leading to product formation. Although the latter appears to be a single step, it probably comprises several reactions with presently unresolved intermediates. Based on these data, we suggest a model of the hydrolytic mechanism.
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18
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Hatori Y, Lewis D, Toyoshima C, Inesi G. Reaction cycle of Thermotoga maritima copper ATPase and conformational characterization of catalytically deficient mutants. Biochemistry 2009; 48:4871-80. [PMID: 19364131 PMCID: PMC2756213 DOI: 10.1021/bi900338n] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
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Copper transport ATPases sustain important roles in homeostasis of heavy metals and delivery of copper to metalloenzymes. The copper transport ATPase from Thermotoga maritima (CopA) provides a useful system for mechanistic studies, due to its heterologous expression and stability. Its sequence comprises 726 amino acids, including the N-terminal metal binding domain (NMBD), three catalytic domains (A, N, and P), and a copper transport domain formed by eight helices, including the transmembrane metal binding site (TMBS). We performed functional characterization and conformational analysis by proteolytic digestion of WT and mutated (NMBD deletion or mutation) T. maritima CopA, comparing it with Archaeoglobus fulgidus CopA and Ca2+ ATPase. A specific feature of T. maritima CopA is ATP utilization in the absence of copper, to form a low-turnover phosphoenzyme intermediate, with a conformation similar to that obtained by phosphorylation with Pi or phosphate analogues. On the other hand, formation of an activated state requires copper binding to both NMBD and TMBS, with consequent conformational changes involving the NMBD and A domain. Proteolytic digestion analysis demonstrates A domain movements similar to those of other P-type ATPases to place the conserved TGES motif in the optimal position for catalytic assistance. We also studied an H479Q mutation (analogous to one of human copper ATPase ATP7B in Wilson disease) that inhibits ATPase activity. We found that, in spite of the H479Q mutation within the nucleotide binding domain, the mutant still binds ATP, yielding a phosphorylation transition state conformation. However, covalent phosphoryl transfer is not completed, and no catalytic turnover is observed.
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Affiliation(s)
- Yuta Hatori
- California Pacific Medical Center Research Institute, San Francisco, California 94107, USA
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Villafane AA, Voskoboynik Y, Cuebas M, Ruhl I, Bini E. Response to excess copper in the hyperthermophile Sulfolobus solfataricus strain 98/2. Biochem Biophys Res Commun 2009; 385:67-71. [PMID: 19427833 DOI: 10.1016/j.bbrc.2009.05.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2009] [Accepted: 05/04/2009] [Indexed: 10/20/2022]
Abstract
Copper is an essential micronutrient, but toxic in excess. Sulfolobus solfataricus cells have the ability to adapt to fluctuations of copper levels in their external environment. To better understand the molecular mechanism behind the organismal response to copper, the expression of the cluster of genes copRTA, which encodes the copper-responsive transcriptional regulator CopR, the copper-binding protein CopT, and CopA, has been investigated and the whole operon has been shown to be cotranscribed at low levels from the copR promoter under all conditions, whereas increased transcription from the copTA promoter occurs in the presence of excess copper. Furthermore, the expression of the copper-transporting ATPase CopA over a 27-h interval has been monitored by quantitative real-time RT-PCR and compared to the pattern of cellular copper accumulation, as determined in a parallel analysis by Inductively Coupled Plasma Optical Emission spectrometry (ICP-OES). The results provide the basis for a model of the molecular mechanisms of copper homeostasis in Sulfolobus, which relies on copper efflux and sequestration.
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Affiliation(s)
- Aramis A Villafane
- Department of Biochemistry and Microbiology, and Biotechnology Center for Agriculture and the Environment, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901-8525, USA
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Structural model of the CopA copper ATPase of Enterococcus hirae based on chemical cross-linking. Biometals 2008; 22:363-75. [PMID: 18979168 DOI: 10.1007/s10534-008-9173-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2008] [Accepted: 10/13/2008] [Indexed: 10/21/2022]
Abstract
The CopA copper ATPase of Enterococcus hirae belongs to the family of heavy metal pumping CPx-type ATPases and shares 43% sequence similarity with the human Menkes and Wilson copper ATPases. Due to a lack of suitable protein crystals, only partial three-dimensional structures have so far been obtained for this family of ion pumps. We present a structural model of CopA derived by combining topological information obtained by intramolecular cross-linking with molecular modeling. Purified CopA was cross-linked with different bivalent reagents, followed by tryptic digestion and identification of cross-linked peptides by mass spectrometry. The structural proximity of tryptic fragments provided information about the structural arrangement of the hydrophilic protein domains, which was integrated into a three-dimensional model of CopA. Comparative modeling of CopA was guided by the sequence similarity to the calcium ATPase of the sarcoplasmic reticulum, Serca1, for which detailed structures are available. In addition, known partial structures of CPx-ATPase homologous to CopA were used as modeling templates. A docking approach was used to predict the orientation of the heavy metal binding domain of CopA relative to the core structure, which was verified by distance constraints derived from cross-links. The overall structural model of CopA resembles the Serca1 structure, but reveals distinctive features of CPx-type ATPases. A prominent feature is the positioning of the heavy metal binding domain. It features an orientation of the Cu binding ligands which is appropriate for the interaction with Cu-loaded metallochaperones in solution. Moreover, a novel model of the architecture of the intramembranous Cu binding sites could be derived.
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González-Guerrero M, Eren E, Rawat S, Stemmler TL, Argüello JM. Structure of the two transmembrane Cu+ transport sites of the Cu+ -ATPases. J Biol Chem 2008; 283:29753-9. [PMID: 18772137 DOI: 10.1074/jbc.m803248200] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Cu(+)-ATPases drive metal efflux from the cell cytoplasm. Paramount to this function is the binding of Cu(+) within the transmembrane region and its coupled translocation across the permeability barrier. Here, we describe the two transmembrane Cu(+) transport sites present in Archaeoglobus fulgidus CopA. Both sites can be independently loaded with Cu(+). However, their simultaneous occupation is associated with enzyme turnover. Site I is constituted by two Cys in transmembrane segment (TM) 6 and a Tyr in TM7. An Asn in TM7 and Met and Ser in TM8 form Site II. Single site x-ray spectroscopic analysis indicates a trigonal coordination in both sites. This architecture is distinct from that observed in Cu(+)-trafficking chaperones and classical cuproproteins. The high affinity of these sites for Cu(+) (Site I K(a)=1.3 fM(-1), Site II K(a)=1.1 fM(-1)), in conjunction with reversible direct Cu(+) transfer from chaperones, points to a transport mechanism where backward release of free Cu(+) to the cytoplasm is largely prevented.
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Affiliation(s)
- Manuel González-Guerrero
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts 01609, USA
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Hatori Y, Hirata A, Toyoshima C, Lewis D, Pilankatta R, Inesi G. Intermediate phosphorylation reactions in the mechanism of ATP utilization by the copper ATPase (CopA) of Thermotoga maritima. J Biol Chem 2008; 283:22541-9. [PMID: 18562314 PMCID: PMC2504886 DOI: 10.1074/jbc.m802735200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2008] [Revised: 06/05/2008] [Indexed: 11/24/2022] Open
Abstract
Recombinant and purified Thermotoga maritima CopA sustains ATPase velocity of 1.78-2.73 micromol/mg/min in the presence of Cu+ (pH 6, 60 degrees C) and 0.03-0.08 micromol/mg/min in the absence of Cu+. High levels of enzyme phosphorylation are obtained by utilization of [gamma-32P]ATP in the absence of Cu+. This phosphoenzyme decays at a much slower rate than observed with Cu.E1 approximately P. In fact, the phosphoenzyme is reduced to much lower steady state levels upon addition of Cu+, due to rapid hydrolytic cleavage. Negligible ATPase turnover is sustained by CopA following deletion of its N-metal binding domain (DeltaNMBD) or mutation of NMBD cysteines (CXXC). Nevertheless, high levels of phosphoenzyme are obtained by utilization of [gamma-3)P]ATP by the DeltaNMBD and CXXC mutants, with no effect of Cu+ either on its formation or hydrolytic cleavage. Phosphoenzyme formation (E2P) can also be obtained by utilization of Pi, and this reaction is inhibited by Cu+ (E2 to E1 transition) even in the DeltaNMBD mutant, evidently due to Cu+ binding at a (transport) site other than the NMBD. E2P undergoes hydrolytic cleavage faster in DeltaNMBD and slower in CXXC mutant. We propose that Cu+ binding to the NMBD is required to produce an "active" conformation of CopA, whereby additional Cu+ bound to an alternate (transmembrane transport) site initiates faster cycles including formation of Cu.E1 approximately P, followed by the E1 approximately P to E2-P conformational transition and hydrolytic cleavage of phosphate. An H479Q mutation (analogous to one found in Wilson disease) renders CopA unable to utilize ATP, whereas phosphorylation by Pi is retained.
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Affiliation(s)
- Yuta Hatori
- Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo 113-0032, Japan
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Cellular multitasking: the dual role of human Cu-ATPases in cofactor delivery and intracellular copper balance. Arch Biochem Biophys 2008; 476:22-32. [PMID: 18534184 DOI: 10.1016/j.abb.2008.05.005] [Citation(s) in RCA: 154] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Revised: 05/06/2008] [Accepted: 05/13/2008] [Indexed: 11/23/2022]
Abstract
The human copper-transporting ATPases (Cu-ATPases) are essential for dietary copper uptake, normal development and function of the CNS, and regulation of copper homeostasis in the body. In a cell, Cu-ATPases maintain the intracellular concentration of copper by transporting copper into intracellular exocytic vesicles. In addition, these P-type ATPases mediate delivery of copper to copper-dependent enzymes in the secretory pathway and in specialized cell compartments such as secretory granules or melanosomes. The multiple functions of human Cu-ATPase necessitate complex regulation of these transporters that is mediated through the presence of regulatory domains in their structure, posttranslational modification and intracellular trafficking, as well as interactions with the copper chaperone Atox1 and other regulatory molecules. In this review, we summarize the current information on the function and regulatory mechanisms acting on human Cu-ATPases ATP7A and ATP7B. Brief comparison with the Cu-ATPase orthologs from other species is included.
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