101
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Electron paramagnetic resonance characterization of the copper-resistance protein PcoC from Escherichia coli. J Biol Inorg Chem 2008; 13:899-907. [DOI: 10.1007/s00775-008-0377-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2007] [Accepted: 04/05/2008] [Indexed: 11/25/2022]
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102
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Ridge PG, Zhang Y, Gladyshev VN. Comparative genomic analyses of copper transporters and cuproproteomes reveal evolutionary dynamics of copper utilization and its link to oxygen. PLoS One 2008; 3:e1378. [PMID: 18167539 PMCID: PMC2147054 DOI: 10.1371/journal.pone.0001378] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2007] [Accepted: 12/05/2007] [Indexed: 12/11/2022] Open
Abstract
Copper is an essential trace element in many organisms and is utilized in all domains of life. It is often used as a cofactor of redox proteins, but is also a toxic metal ion. Intracellular copper must be carefully handled to prevent the formation of reactive oxygen species which pose a threat to DNA, lipids, and proteins. In this work, we examined patterns of copper utilization in prokaryotes by analyzing the occurrence of copper transporters and copper-containing proteins. Many organisms, including those that lack copper-dependent proteins, had copper exporters, likely to protect against copper ions that inadvertently enter the cell. We found that copper use is widespread among prokaryotes, but also identified several phyla that lack cuproproteins. This is in contrast to the use of other trace elements, such as selenium, which shows more scattered and reduced usage, yet larger selenoproteomes. Copper transporters had different patterns of occurrence than cuproproteins, suggesting that the pathways of copper utilization and copper detoxification are independent of each other. We present evidence that organisms living in oxygen-rich environments utilize copper, whereas the majority of anaerobic organisms do not. In addition, among copper users, cuproproteomes of aerobic organisms were larger than those of anaerobic organisms. Prokaryotic cuproproteomes were small and dominated by a single protein, cytochrome c oxidase. The data are consistent with the idea that proteins evolved to utilize copper following the oxygenation of the Earth.
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Affiliation(s)
- Perry G. Ridge
- Department of Biochemistry, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Yan Zhang
- Department of Biochemistry, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Vadim N. Gladyshev
- Department of Biochemistry, University of Nebraska, Lincoln, Nebraska, United States of America
- * To whom correspondence should be addressed. E-mail:
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103
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Xue Y, Davis AV, Balakrishnan G, Stasser JP, Staehlin BM, Focia P, Spiro TG, Penner-Hahn JE, O'Halloran TV. Cu(I) recognition via cation-pi and methionine interactions in CusF. Nat Chem Biol 2007; 4:107-9. [PMID: 18157124 DOI: 10.1038/nchembio.2007.57] [Citation(s) in RCA: 191] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Accepted: 10/24/2007] [Indexed: 11/09/2022]
Abstract
Methionine-rich motifs have an important role in copper trafficking factors, including the CusF protein. Here we show that CusF uses a new metal recognition site wherein Cu(I) is tetragonally displaced from a Met2His ligand plane toward a conserved tryptophan. Spectroscopic studies demonstrate that both thioether ligation and strong cation-pi interactions with tryptophan stabilize metal binding. This novel active site chemistry affords mechanisms for control of adventitious metal redox and substitution chemistry.
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Affiliation(s)
- Yi Xue
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
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104
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Zhang L, Koay M, Maher MJ, Xiao Z, Wedd AG. Intermolecular transfer of copper ions from the CopC protein of Pseudomonas syringae. Crystal structures of fully loaded Cu(I)Cu(II) forms. J Am Chem Soc 2007; 128:5834-50. [PMID: 16637653 DOI: 10.1021/ja058528x] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
CopC is a small soluble protein expressed in the periplasm of Pseudomonas syringae pathovar tomato as part of its copper resistance response (cop operon). Equilibrium competition reactions confirmed two separated binding sites with high affinities for Cu(I) (10(-7) > or = K(D) > or = 10(-13) M) and Cu(II) (K(D) = 10(-13(1)) M), respectively. While Cu(I)-CopC was converted cleanly by O2 to Cu(II)-CopC, the fully loaded form Cu(I)Cu(II)-CopC was stable in air. Variant forms H1F and H91F exhibited a lower affinity for Cu(II) than does the wild-type protein while variant E27G exhibited a higher affinity. Cation exchange chromatography detected each of the four different types of intermolecular copper transfer reactions possible between wild type and variant forms: Cu(I) site to Cu(II) site; Cu(II) site to Cu(I) site; Cu(I) site to Cu(I) site; Cu(II) site to Cu(II) site. The availability of an unoccupied site of higher affinity induced intermolecular transfer of either Cu(I) or Cu(II) in the presence of O2 while buffering concentrations of cupric ion at sub-picomolar levels. Crystal structures of two crystal forms of wild-type Cu(I)Cu(II)-CopC and of the apo-H91F variant demonstrate that the core structures of the molecules in the three crystal forms are conserved. However, the conformations of the amino terminus (a Cu(II) ligand) and the two copper-binding loops (at each end of the molecule) differ significantly, providing the structural lability needed to allow transfer of copper between partners, with or without change of oxidation state. CopC has the potential to interact directly with each of the four cop proteins coexpressed to the periplasm.
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Affiliation(s)
- Lianyi Zhang
- School of Chemistry and Bio21 Institute, University of Melbourne, Parkville, VIC 3010, Australia
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105
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Loftin IR, Franke S, Blackburn NJ, McEvoy MM. Unusual Cu(I)/Ag(I) coordination of Escherichia coli CusF as revealed by atomic resolution crystallography and X-ray absorption spectroscopy. Protein Sci 2007; 16:2287-93. [PMID: 17893365 PMCID: PMC2204137 DOI: 10.1110/ps.073021307] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Elevated levels of copper or silver ions in the environment are an immediate threat to many organisms. Escherichia coli is able to resist the toxic effects of these ions through strictly limiting intracellular levels of Cu(I) and Ag(I). The CusCFBA system is one system in E. coli responsible for copper/silver tolerance. A key component of this system is the periplasmic copper/silver-binding protein, CusF. Here the X-ray structure and XAS data on the CusF-Ag(I) and CusF-Cu(I) complexes, respectively, are reported. In the CusF-Ag(I) structure, Ag(I) is coordinated by two methionines and a histidine, with a nearby tryptophan capping the metal site. EXAFS measurements on the CusF-Cu(I) complex show a similar environment for Cu(I). The arrangement of ligands effectively sequesters the metal from its periplasmic environment and thus may play a role in protecting the cell from the toxic ion.
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Affiliation(s)
- Isabell R Loftin
- Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, Arizona 85721, USA
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106
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Rodionov VO, Presolski SI, Díaz DD, Fokin VV, Finn MG. Ligand-accelerated Cu-catalyzed azide-alkyne cycloaddition: a mechanistic report. J Am Chem Soc 2007; 129:12705-12. [PMID: 17914817 DOI: 10.1021/ja072679d] [Citation(s) in RCA: 337] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The experimental rate law for the Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction was found to vary in complex ways with concentration, the presence of chloride ion, and the presence of accelerating ligands. Several examples of discontinuous ("threshold behavior") kinetics were observed, along with a decidedly nonlinear correlation of electronic substituent parameter with the rate of CuAAC reaction with p-substituted arylazides. The previously observed tendency of the CuAAC reaction to provide ditriazoles from a conformationally constrained 1,3-diazide was found to be affected by a class of polybenzimidazole ligands introduced in the accompanying article. Various lines of evidence suggest that the standard tris(triazolylmethyl)amine ligand binds less strongly to Cu(I) than its benzimidazole analogues. On the basis of these observations, it is proposed that (a) a central nitrogen donor provides electron density at Cu(I) that assists the cycloaddition reaction, (b) the three-armed motif bearing relatively weakly coordinating heterocyclic ligands serves to bind the metal with sufficient strength while providing access to necessary coordination site(s), (c) at least two active catalysts or mechanisms are operative under the conditions studied, and (d) pendant acid or ester arms in the proper position can assist the reaction by speeding the protiolysis step that cleaves the Cu-C bond of a Cu.triazolyl intermediate.
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Affiliation(s)
- Valentin O Rodionov
- Department of Chemistry and The Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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107
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Hussain F, Sedlak E, Wittung-Stafshede P. Role of copper in folding and stability of cupredoxin-like copper-carrier protein CopC. Arch Biochem Biophys 2007; 467:58-66. [PMID: 17889826 DOI: 10.1016/j.abb.2007.08.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2007] [Revised: 08/06/2007] [Accepted: 08/10/2007] [Indexed: 11/29/2022]
Abstract
CopC is a periplasmic copper carrier that, in contrast to cytoplasmic copper chaperones, has a beta-barrel fold and two metal-binding sites distinct for Cu(II) and Cu(I). The copper sites are located in each end of the molecule: the Cu(I) site involves His and Met coordination whereas the Cu(II) site consists of charged residues. To reveal biophysical properties of this protein, we have explored the effects of the cofactors on CopC unfolding in vitro. We demonstrate that Cu(II) coordination affects both protein stability and unfolding pathway, whereas Cu(I) has only a small effect on stability. Apo-CopC unfolds in a two-state reaction between pH 4 and 7.5 with maximal stability at pH 6. In contrast, Cu(II)-CopC unfolds in a three-state reaction at pH6 that involves a partly folded intermediate that retains Cu(II). This intermediate exhibits high thermal and chemical stability. Unique energetic and structural properties of different metalated CopC forms may help facilitate metal transport to many partners in vivo.
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Affiliation(s)
- Faiza Hussain
- Department of Biochemistry and Cell Biology, Rice University, 6100 Main Street, Houston, TX 77251, USA
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108
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Djoko KY, Xiao Z, Huffman DL, Wedd AG. Conserved mechanism of copper binding and transfer. A comparison of the copper-resistance proteins PcoC from Escherichia coli and CopC from Pseudomonas syringae. Inorg Chem 2007; 46:4560-8. [PMID: 17477524 DOI: 10.1021/ic070107o] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The copper-resistance proteins PcoC from Escherichia coli and CopC from Pseudomonas syringae exhibit 67% sequence identity, but the chemistry reported for PcoC (Peariso, K.; Huffman, D. L.; Penner-Hahn, J. E.; O'Halloran, T. V. J. Am. Chem. Soc. 2003, 125, 342-343) was distinctly different from that reported for CopC (Zhang, L.; Koay, M.; Maher, M. J.; Xiao, Z.; Wedd, A. G. J. Am. Chem. Soc. 2006, 128, 5834-5850). The source of the inconsistency has been identified, and His1 is confirmed as an unprecedented bidentate ligand in each protein. Access to a bona fide wild-type PcoC protein allowed unequivocal observation of intermediates involved in intermolecular redox copper transfer reactions.
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Affiliation(s)
- Karrera Y Djoko
- School of Chemistry, University of Melbourne, Parkville, Victoria 3052, Australia
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109
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Zheng XY, Pang EG, Li HQ, Zhao YQ, Yang BS. Spectral Studies on the Interaction between Mercuric Ion and ApoCopC. CHINESE J CHEM 2007. [DOI: 10.1002/cjoc.200790117] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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110
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Rensing C, Franke S. Copper Homeostasis in Escherichia coli and Other Enterobacteriaceae. EcoSal Plus 2007; 2. [PMID: 26443582 DOI: 10.1128/ecosalplus.5.4.4.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2006] [Indexed: 06/05/2023]
Abstract
An interesting model for studying environmental influences shaping microbial evolution is provided by a multitude of copper resistance and copper homeostasis determinants in enteric bacteria. This review describes these determinants and tries to relate their presence to the habitat of the respective organism, as a current hypothesis predicts that the environment should determine an organism's genetic makeup. In Escherichia coli there are four regulons that are induced in the presence of copper. Two, the CueR and the CusR regulons, are described in detail. A central component regulating intracellular copper levels, present in all free-living enteric bacteria whose genomes have so far been sequenced, is a Cu(I)translocating P-type ATPase. The P-type ATPase superfamily is a ubiquitous group of proteins involved in the transport of charged substrates across biological membranes. Whereas some components involved in copper homeostasis can be found in both anaerobes and aerobes, multi-copper oxidases (MCOs) implicated in copper tolerance in E. coli, such as CueO and the plasmid-based PcoA, can be found only in aerobic organisms. Several features indicate that CueO, PcoA, and other related MCOs are specifically adapted to combat copper-mediated oxidative damage. In addition to these well-characterized resistance operons, there are numerous other genes that appear to be involved in copper binding and trafficking that have not been studied in great detail. SilE and its homologue PcoE, for example, are thought to effect the periplasmic binding and sequestration of silver and copper, respectively.
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111
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Linear array of conserved sequence motifs to discriminate protein subfamilies: study on pyridine nucleotide-disulfide reductases. BMC Bioinformatics 2007; 8:96. [PMID: 17367536 PMCID: PMC1847454 DOI: 10.1186/1471-2105-8-96] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2006] [Accepted: 03/16/2007] [Indexed: 12/20/2022] Open
Abstract
Background The pyridine nucleotide disulfide reductase (PNDR) is a large and heterogeneous protein family divided into two classes (I and II), which reflect the divergent evolution of its characteristic disulfide redox active site. However, not all the PNDR members fit into these categories and this suggests the need of further studies to achieve a more comprehensive classification of this complex family. Results A workflow to improve the clusterization of protein families based on the array of linear conserved motifs is designed. The method is applied to the PNDR large family finding two main groups, which correspond to PNDR classes I and II. However, two other separate protein clusters, previously classified as class I in most databases, are outgrouped: the peroxide reductases (NAOX, NAPE) and the type II NADH dehydrogenases (NDH-2). In this way, two novel PNDR classes III and IV for NAOX/NAPE and NDH-2 respectively are proposed. By knowledge-driven biochemical and functional data analyses done on the new class IV, a linear array of motifs putatively related to Cu(II)-reductase activity is detected in a specific subset of NDH-2. Conclusion The results presented are a novel contribution to the classification of the complex and large PNDR protein family, supporting its reclusterization into four classes. The linear array of motifs detected within the class IV PNDR subfamily could be useful as a signature for a particular subgroup of NDH-2.
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112
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Zheng X, Pang E, Li H, Zhao Y, Yang B. The role of cupric in maintaining the structure of CopC. CHINESE SCIENCE BULLETIN 2007. [DOI: 10.1007/s11434-007-0089-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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113
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Dalosto SD. Computer Simulation of the Interaction of Cu(I) with Cys Residues at the Binding Site of the Yeast Metallochaperone Cu(I)−Atx1. J Phys Chem B 2007; 111:2932-40. [PMID: 17388422 DOI: 10.1021/jp066689x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The copper binding site and electronic structure of the metallochaperone protein Atx1 were investigated using the combination of quantum mechanics methods and molecular mechanics methods in the ONIOM(QM:MM) scheme at the density functional theory (DFT) B3LYP/ 6-31G(d):AMBER level. The residues in the binding site, -Met13-Thr14-Cys15-Cu(I)-Cys18-Gly17-Ser16-, were modeled with QM and the rest of the residues with MM. Our results indicate that the structure for Cu(I)-Atx1 has the copper atom coordinated to two sulfur atoms from Cys15 (2.110 A) and Cys18 (2.141 A) with an angle S-Cu(I) -S of 166 degrees . The potential energy surface of the copper atom is used to estimate its binding energy and the force field for the copper ligands. The potential surface is shallow for the bending mode S-Cu-S, which explains the origin of the disorder observed in crystallographic and nuclear magnetic resonance studies. Using molecular dynamics for Cu(I)-Atx1 in a box of water molecules and in vacuum, with the force field derived in this work, we observed a correlated motion between the side chains of Thr14 and of Lys65 which enhances distortions in the S-Cu-S geometry. The results are compared with recent experiments and the previous models. The vibrational spectra for the copper ligands and for the residues in the binding site were computed. The localized modes for the copper ligands and the amide bands were assigned. The presence of the copper atom affects the amide bands' frequencies of the residues Cys15 and Cys18, giving resolved bands that can be used to sense changes in the binding site upon translocation of copper atom or interaction with target proteins. Furthermore, the EXAFS (extended X-ray absorption fine structure) spectrum of the proposed structure for Cu(I)-Atx1 was calculated and reproduced the experiments fairly well.
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Affiliation(s)
- Sergio D Dalosto
- Department of Physics, University of Washington, Seattle, Washington 98195-1560, USA.
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114
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Singleton C, Le Brun NE. Atx1-like chaperones and their cognate P-type ATPases: copper-binding and transfer. Biometals 2007; 20:275-89. [PMID: 17225061 DOI: 10.1007/s10534-006-9068-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2006] [Accepted: 11/28/2006] [Indexed: 01/05/2023]
Abstract
Copper is an essential yet toxic metal ion. To satisfy cellular requirements, while, at the same time, minimizing toxicity, complex systems of copper trafficking have evolved in all cell types. The best conserved and most widely distributed of these involve Atx1-like chaperones and P(1B)-type ATPase transporters. Here, we discuss current understanding of how these chaperones bind Cu(I) and transfer it to the Atx1-like N-terminal domains of their cognate transporter.
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Affiliation(s)
- Chloe Singleton
- Centre for Metalloprotein Spectroscopy and Biology, School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich, NR4 7TJ, UK
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115
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del Pino P, Weiss A, Bertsch U, Renner C, Mentler M, Grantner K, Fiorino F, Meyer-Klaucke W, Moroder L, Kretzschmar HA, Parak FG. The configuration of the Cu2+ binding region in full-length human prion protein. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 36:239-52. [PMID: 17225136 DOI: 10.1007/s00249-006-0124-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2006] [Revised: 12/11/2006] [Accepted: 12/18/2006] [Indexed: 11/28/2022]
Abstract
The cellular prion protein (PrP(C)) is a Cu(2+) binding protein connected to the outer cell membrane. The molecular features of the Cu(2+) binding sites have been investigated and characterized by spectroscopic experiments on PrP(C)-derived peptides and the recombinant human full-length PrP(C )(hPrP-[23-231]). The hPrP-[23-231] was loaded with (63)Cu under slightly acidic (pH 6.0) or neutral conditions. The PrP(C)/Cu(2+)-complexes were investigated by extended X-ray absorption fine structure (EXAFS), electron paramagnetic resonance (EPR), and electron nuclear double resonance (ENDOR). For comparison, peptides from the copper-binding octarepeat domain were investigated in different environments. Molecular mechanics computations were used to select sterically possible peptide/Cu(2+) structures. The simulated EPR, ENDOR, and EXAFS spectra of these structures were compared with our experimental data. For a stoichiometry of two octarepeats per copper the resulting model has a square planar four nitrogen Cu(2+) coordination. Two nitrogens belong to imidazole rings of histidine residues. Further ligands are two deprotonated backbone amide nitrogens of the adjacent glycine residues and an axial oxygen of a water molecule. Our complex model differs significantly from those previously obtained for shorter peptides. Sequence context, buffer conditions and stoichiometry of copper show marked influence on the configuration of copper binding to PrP(C).
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Affiliation(s)
- Pablo del Pino
- Physics Department E17, Technical University Munich, 85747 Garching, Germany
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116
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Hirano Y, Hossain MM, Takeda K, Tokuda H, Miki K. Purification, crystallization and preliminary X-ray crystallographic analysis of the outer membrane lipoprotein NlpE from Escherichia coli. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:1227-30. [PMID: 17142903 PMCID: PMC2225377 DOI: 10.1107/s1744309106045313] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2006] [Accepted: 10/30/2006] [Indexed: 11/10/2022]
Abstract
The outer membrane lipoprotein NlpE functions in stress response by activating the Cpx signal transduction pathway. The nonlipidated Cys1Ala mutant of NlpE with a C-terminal His tag from Escherichia coli was constructed, overexpressed and purified. Crystals of NlpE were grown in two distinct forms by the sitting-drop vapour-diffusion method at 298 K. The tetragonal crystals diffracted to 2.8 A resolution and belong to space group P4(3)2(1)2. The monoclinic crystals diffracted to 3.0 A resolution and belong to space group C2. Initial phases were obtained from a tetragonal crystal of selenomethionylated protein by the MAD method.
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Affiliation(s)
- Yu Hirano
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Md. Motarab Hossain
- Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Kazuki Takeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
- RIKEN SPring-8 Center at Harima Institute, 1-1-1 Koto, Sayo, Hyogo 679-5198, Japan
| | - Hajime Tokuda
- Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
- RIKEN SPring-8 Center at Harima Institute, 1-1-1 Koto, Sayo, Hyogo 679-5198, Japan
- Correspondence e-mail:
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117
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Monchy S, Benotmane MA, Wattiez R, van Aelst S, Auquier V, Borremans B, Mergeay M, Taghavi S, van der Lelie D, Vallaeys T. Transcriptomic and proteomic analyses of the pMOL30-encoded copper resistance in Cupriavidus metallidurans strain CH34. MICROBIOLOGY-SGM 2006; 152:1765-1776. [PMID: 16735739 DOI: 10.1099/mic.0.28593-0] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The four replicons of Cupriavidus metallidurans CH34 (the genome sequence was provided by the US Department of Energy-University of California Joint Genome Institute) contain two gene clusters putatively encoding periplasmic resistance to copper, with an arrangement of genes resembling that of the copSRABCD locus on the 2.1 Mb megaplasmid (MPL) of Ralstonia solanacearum, a closely related plant pathogen. One of the copSRABCD clusters was located on the 2.6 Mb MPL, while the second was found on the pMOL30 (234 kb) plasmid as part of a larger group of genes involved in copper resistance, spanning 17 857 bp in total. In this region, 19 ORFs (copVTMKNSRABCDIJGFLQHE) were identified based on the sequencing of a fragment cloned in an IncW vector, on the preliminary annotation by the Joint Genome Institute, and by using transcriptomic and proteomic data. When introduced into plasmid-cured derivatives of C. metallidurans CH34, the cop locus was able to restore the wild-type MIC, albeit with a biphasic survival curve, with respect to applied Cu(II) concentration. Quantitative-PCR data showed that the 19 ORFs were induced from 2- to 1159-fold when cells were challenged with elevated Cu(II) concentrations. Microarray data showed that the genes that were most induced after a Cu(II) challenge of 0.1 mM belonged to the pMOL30 cop cluster. Megaplasmidic cop genes were also induced, but at a much lower level, with the exception of the highly expressed MPL copD. Proteomic data allowed direct observation on two-dimensional gel electrophoresis, and via mass spectrometry, of pMOL30 CopK, CopR, CopS, CopA, CopB and CopC proteins. Individual cop gene expression depended on both the Cu(II) concentration and the exposure time, suggesting a sequential scheme in the resistance process, involving genes such as copK and copT in an initial phase, while other genes, such as copH, seem to be involved in a late response phase. A concentration of 0.4 mM Cu(II) was the highest to induce maximal expression of most cop genes.
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Affiliation(s)
- Sébastien Monchy
- Service de Confirmation des Macromolécules Biologiques et de Bioinformatique, Université Libre de Bruxelles, Belgium
- Laboratories for Microbiology and Radiobiology, SCK.CEN, Boeretang 200, B-2400 Mol, Belgium
| | - Mohammed A Benotmane
- Laboratories for Microbiology and Radiobiology, SCK.CEN, Boeretang 200, B-2400 Mol, Belgium
| | - Ruddy Wattiez
- Département de Protéomique et de Biochimie des Protéines, University of Mons-Hainaut, B-7000 Mons, Belgium
| | - Sébastien van Aelst
- Laboratoire de Microbiologie de l'Université Libre de Bruxelles, campus CERIA, 1 av. E. Gryzon, 1070 Brussels, Belgium
- Laboratories for Microbiology and Radiobiology, SCK.CEN, Boeretang 200, B-2400 Mol, Belgium
| | - Vanessa Auquier
- Centre de Biologie Structurale et de Bioinformatique: Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, Belgium
| | | | - Max Mergeay
- Laboratories for Microbiology and Radiobiology, SCK.CEN, Boeretang 200, B-2400 Mol, Belgium
| | - Safiyh Taghavi
- Brookhaven National Laboratory, Biology Department, Upton, NY 11973-5000, USA
- Environmental Technology, Vito, B-2400 Mol, Belgium
| | | | - Tatiana Vallaeys
- INRA, Département de Microbiologie, F-78850 Thiverval Grignon, France
- Laboratories for Microbiology and Radiobiology, SCK.CEN, Boeretang 200, B-2400 Mol, Belgium
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Arnesano F, Banci L, Bertini I, Capozzi F, Ciofi-Baffoni S, Ciurli S, Luchinat C, Mangani S, Rosato A, Turano P, Viezzoli MS. An Italian contribution to structural genomics: Understanding metalloproteins. Coord Chem Rev 2006. [DOI: 10.1016/j.ccr.2006.01.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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119
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Sekine M, Tanikawa S, Omata S, Saito M, Fujisawa T, Tsukatani N, Tajima T, Sekigawa T, Kosugi H, Matsuo Y, Nishiko R, Imamura K, Ito M, Narita H, Tago S, Fujita N, Harayama S. Sequence analysis of three plasmids harboured in Rhodococcus erythropolis strain PR4. Environ Microbiol 2006; 8:334-46. [PMID: 16423019 DOI: 10.1111/j.1462-2920.2005.00899.x] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Rhodococcus erythropolis strain PR4 has been isolated as an alkane-degrading bacterium. The strain harbours one linear plasmid, pREL1 (271 577 bp) and two circular plasmids, pREC1 (104 014 bp) and pREC2 (3637 bp), all with some sequence similarities to other Rhodococcus plasmids. For pREL1, pREC1 and pREC2, 298, 102 and 3 open reading frames, respectively, were predicted. Linear plasmid pREL1 has several regions homologous to plasmid pBD2 found in R. erythropolis BD2. Sequence analysis of pREL1 and pBD2 identified common metal-resistance genes on both, but pREL1 also encodes alkane-degradation genes not found on pBD2, with enzyme constituents some of which are quite different from those of other organisms. The alkane hydroxylase consisted of a cytochrome P450 monooxygenase, a 2Fe-2S ferredoxin, and a ferredoxin reductase. The ferredoxin reductase amino acid sequence resembles the AlkT (rubredoxin reductase) sequence. A zinc-containing alcohol dehydrogenase further oxydizes alkanols, alkane oxidation products catalysed by alkane hydroxylase. Of the circular plasmids, the pREC1 sequence is partially similar to the sequence of pREAT701, the virulence plasmid found in Rhodococcus equi. pREC1 has no pREAT701 virulence genes and encodes genes for beta-oxidation of fatty acids. Thus, joint actions of enzymes encoded by pREL1 and pREC1 may enable efficient mineralization of alkanes.
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Affiliation(s)
- Mitsuo Sekine
- NITE Genome Analysis Center, Department of Biotechnology, National Institute of Technology and Evaluation (NITE), Shibuya-ku, Tokyo, Japan
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120
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Jiang J, Nadas IA, Kim MA, Franz KJ. A Mets Motif Peptide Found in Copper Transport Proteins Selectively Binds Cu(I) with Methionine-Only Coordination. Inorg Chem 2005; 44:9787-94. [PMID: 16363848 DOI: 10.1021/ic051180m] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mets motifs, which refer to methionine-rich sequences found in the high-affinity copper transporter Ctr1, also appear in other proteins involved in copper trafficking and homeostasis, including other Ctrs as well as Pco and Cop proteins isolated from copper-resistant bacteria. To understand the coordination chemistry utilized by these proteins, we studied the copper binding properties of a peptide labeled Mets7-PcoC with the sequence Met-Thr-Gly-Met-Lys-Gly-Met-Ser. By comparing this sequence to a series of mutants containing noncoordinating norleucine in place of methionine, we confirm that all three methionine residues are involved in a thioether-only binding site that is selective for Cu(I). Two independent methods, one based on mass spectrometry and one based on rate differences for the copper-catalyzed oxidation of ascorbic acid, provide an effective K(D) of approximately 2.5 microM at pH 4.5 for the 1:1 complex of Mets7-PcoC with Cu(I). These results establish that a relatively simple peptide containing an MX(2)MX(2)M motif is sufficient to bind Cu(I) with an affinity that corresponds well with its proposed biological function of extracellular copper acquisition.
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Affiliation(s)
- Jianfeng Jiang
- Department of Chemistry, Duke University, P.O. Box 90346, Durham, North Carolina 27708, USA
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121
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Andruzzi L, Nakano M, Nilges MJ, Blackburn NJ. Spectroscopic Studies of Metal Binding and Metal Selectivity in Bacillus subtilis BSco, a Homologue of the Yeast Mitochondrial Protein Sco1p. J Am Chem Soc 2005; 127:16548-58. [PMID: 16305244 DOI: 10.1021/ja0529539] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sco1 is a mitochondrial membrane protein involved in the assembly of the CuA site of cytochrome c oxidase. The Bacillus subtilis genome contains a homologue of yeast Sco1, YpmQ (hereafter termed BSco), deletion of which leads to a phenotype lacking in caa3 (CuA-containing) oxidase activity but expressing normal levels of aa3 (quinol) oxidase activity. Here, we report the characterization of the metal binding site of BSco in its Cu(I)-, Cu(II)-, Zn(II)-, and Ni(II)-bound forms. Apo BSco was found to bind Cu(II), Zn(II), and Ni(II) at a 1:1 protein/metal ratio. The Cu(I) protein could be prepared by either dithionite reduction of the Cu(II) derivative or by reconstitution of the apo protein with Cu(I). X-ray absorption (XAS) spectroscopy showed that Cu(I) was coordinated by two cysteines at 2.22 +/- 0.01 A and by a weakly bound low-Z scatterer at 1.95 +/- 0.03 A. The Cu(II) derivative was reddish-orange and exhibited a strong type-2 thiolate to Cu(II) transition around 350 nm. Multifrequency electron paramagnetic resonance (EPR), electron-nuclear double resonance (ENDOR), and electron spin-echo envelope modulation (ESEEM) studies on the Cu(II) derivative provided evidence of one strongly coupled histidine residue, at least one strongly coupled cysteine, and coupling to an exchangeable proton. XAS spectroscopy indicated two cysteine ligands at 2.21 A and two O/N donor ligands at 1.95 A, at least one of which is derived from a coordinated histidine. The Zn(II) and Ni(II) derivatives were 4-coordinate with MS2N(His)X coordination. These results provide evidence that a copper chaperone can engage in redox chemistry at the metal center and may suggest interesting redox-based mechanisms for metalation of the mixed-valence CuA center of cytochrome c oxidase.
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Affiliation(s)
- Luisa Andruzzi
- Department of Environmental and Biomolecular Systems, OGI School of Science and Engineering at OHSU, Beaverton, Oregon 97006-8921, USA
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122
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Abstract
Cellular copper uptake is a prerequisite for the biosynthesis of many copper-dependent enzymes; disruption of copper uptake results in embryonic lethality. In humans, copper is transported into cells by hCTR1, a membrane protein, composed of 190 amino acids with only three trans-membrane segments. To provide insight into the mechanism of this unusual transporter, we characterized the functional properties of various hCTR1 mutants stably expressed in Sf9 cells. Most single amino acid substitutions involving charged and potential copper-coordinating residues have some influence on the V(max) and K(m) values for copper uptake but do not greatly alter hCTR1-mediated copper transport. However, there were two notable exceptions. Replacement of Tyr(156) with Ala greatly reduced the maximal transport rate without effect on the K(m) value for copper. Also, replacement of His(139) in the second trans-membrane segment with Arg caused a dramatic increase in the rate of copper uptake and a large increase in the K(m) value for copper. This effect was not seen with an Ala replacement, pointing to the role of a positive charge in modulating copper exit from the pathway. Truncated mutants demonstrated that the deletion of a large portion of the N-terminal domain only slightly decreased the apparent K(m) value for copper and decreased the rate of transport. Similar effects were observed with the removal of the last 11 C-terminal residues. The results suggested that the N and C termini, although nonessential for transport, may have an important role in facilitating the delivery of copper to and retrieving copper from, respectively, the translocation pathway. A model of how hCTR1 mediates copper entry into cells was proposed that included a rate-limiting site in the pore close to the intracellular exit.
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Affiliation(s)
- John F Eisses
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607, USA
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123
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Fluorescence study on the interaction between apoCopC and cupric. CHINESE SCIENCE BULLETIN 2005. [DOI: 10.1007/bf03183739] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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124
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Arnesano F, Banci L, Bertini I, Martinelli M. Ortholog search of proteins involved in copper delivery to cytochrome C oxidase and functional analysis of paralogs and gene neighbors by genomic context. J Proteome Res 2005; 4:63-70. [PMID: 15707358 DOI: 10.1021/pr049862f] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochrome c oxidase (COX) is a multi-subunit enzyme of the mitochondrial respiratory chain. Delivery of metal cofactors to COX is essential for assembly, which represents a long-standing puzzle. The proteins Cox17, Sco1/2, and Cox11 are necessary for copper insertion into CuA and CuB redox centers of COX in eukaryotes. A genome-wide search in all prokaryotic genomes combined with genomic context reveals that only Sco and Cox11 have orthologs in prokaryotes. However, while Cox11 function is confined to COX assembly, Sco acts as a multifunctional linker connecting a variety of biological processes. Multifunctionality is achieved by gene duplication and paralogs. Neighbor genes of Sco paralogs often encode cuproenzymes and cytochrome c domains and, in some cases, Sco is fused to cytochrome c. This led us to suggest that cytochrome c might be relevant to Sco function and the two proteins might jointly be involved in COX assembly. Sco is also related, in terms of gene neighborhood and phylogenetic occurrence, to a newly detected protein involved in copper trafficking in bacteria and archaea, but with no sequence similarity to the mitochondrial copper chaperone Cox17. By linking the assembly system to the copper uptake system, Sco allows COX to face alternative copper trafficking pathways.
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Affiliation(s)
- Fabio Arnesano
- Magnetic Resonance Center CERM and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy
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125
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Abstract
This article deals with the solution structure determination of paramagnetic metalloproteins by NMR spectroscopy. These proteins were believed not to be suitable for NMR investigations for structure determination until a decade ago, but eventually novel experiments and software protocols were developed, with the aim of making the approach suitable for the goal and as user-friendly and safe as possible. In the article, we also give hints for the optimization of experiments with respect to each particular metal ion, with the aim of also providing a handy tool for nonspecialists. Finally, a section is dedicated to the significant progress made on 13C direct detection, which reduces the negative effects of paramagnetism and may constitute a new chapter in the whole field of NMR spectroscopy.
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Affiliation(s)
- Ivano Bertini
- Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy.
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126
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Koay M, Zhang L, Yang B, Maher MJ, Xiao Z, Wedd AG. CopC Protein fromPseudomonassyringae: Intermolecular Transfer of Copper from Both the Copper(I) and Copper(II) Sites. Inorg Chem 2005; 44:5203-5. [PMID: 16022515 DOI: 10.1021/ic0506198] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The CopC protein from Pseudomonas syringae pathovar tomato is expressed as one of four proteins encoded by the operon CopABCD that is responsible for copper resistance. It is a small soluble molecule (10.5 kDa) with a beta-barrel structure and features two distinct copper binding sites, which are highly specific for Cu(I) (K(D) > or = 10(-)(13)) and Cu(II) (K(D) approximately 10(-)(15)). These dissociation constants were estimated via ligand competition experiments monitored by electronic spectral and fluorescence probes. The chemistries of the two copper sites are interdependent. When the Cu(II) site is empty, the Cu(I) ion is oxidized by air, but when both sites are occupied, the molecule is stable in air. The availability of an unoccupied site of higher affinity induces intermolecular transfer of either Cu(I) or Cu(II) while maintaining free copper ion concentrations in solution at sub-picomolar levels. This intriguing copper chemistry is consistent with the proposed role of CopC as a copper carrier in the oxidizing periplasmic space. These properties would allow it to exchange either Cu(I) or Cu(II) with its putative partners CopA, CopB, and CopD, contrasting with the role of the Cu(I) (only) chaperones found in the reducing cytoplasm.
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Affiliation(s)
- Melissa Koay
- School of Chemistry, University of Melbourne, Victoria 3010, Australia
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127
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Redecke L, Meyer-Klaucke W, Koker M, Clos J, Georgieva D, Genov N, Echner H, Kalbacher H, Perbandt M, Bredehorst R, Voelter W, Betzel C. Comparative Analysis of the Human and Chicken Prion Protein Copper Binding Regions at pH 6.5. J Biol Chem 2005; 280:13987-92. [PMID: 15684434 DOI: 10.1074/jbc.m411775200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recent experimental evidence supports the hypothesis that prion proteins (PrPs) are involved in the Cu(II) metabolism. Moreover, the copper binding region has been implicated in transmissible spongiform encephalopathies, which are caused by the infectious isoform of prion proteins (PrP(Sc)). In contrast to mammalian PrP, avian prion proteins have a considerably different N-terminal copper binding region and, most interestingly, are not able to undergo the conversion process into an infectious isoform. Therefore, we applied x-ray absorption spectroscopy to analyze in detail the Cu(II) geometry of selected synthetic human PrP Cu(II) octapeptide complexes in comparison with the corresponding chicken PrP hexapeptide complexes at pH 6.5, which mimics the conditions in the endocytic compartments of neuronal cells. Our results revealed that structure and coordination of the human PrP copper binding sites are highly conserved in the pH 6.5-7.4 range, indicating that the reported pH dependence of copper binding to PrP becomes significant at lower pH values. Furthermore, the different chicken PrP hexarepeat motifs display homologous Cu(II) coordination at sub-stoichiometric copper concentrations. Regarding the fully cation-saturated prion proteins, however, a reduced copper coordination capability is supposed for the chicken prion protein based on the observation that chicken PrP is not able to form an intra-repeat Cu(II) binding site. These results provide new insights into the prion protein structure-function relationship and the conversion process of PrP.
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Affiliation(s)
- Lars Redecke
- Center of Experimental Medicine, Institute of Biochemistry and Molecular Biology I, University Hospital Hamburg-Eppendorf, c/o Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany
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128
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Banci L, Bertini I, Ciofi-Baffoni S, Katsari E, Katsaros N, Kubicek K, Mangani S. A copper(I) protein possibly involved in the assembly of CuA center of bacterial cytochrome c oxidase. Proc Natl Acad Sci U S A 2005; 102:3994-9. [PMID: 15753304 PMCID: PMC554794 DOI: 10.1073/pnas.0406150102] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2004] [Indexed: 11/18/2022] Open
Abstract
Sco1 and Cox17 are accessory proteins required for the correct assembly of eukaryotic cytochrome c oxidase. At variance with Sco1, Cox17 orthologs are found only in eukaryotes. We browsed bacterial genomes to search proteins functionally equivalent to Cox17, and we identified a class of proteins of unknown function displaying a conserved gene neighborhood to bacterial Sco1 genes, all sharing a potential metal binding motif H(M)X10MX21HXM. Two members of this group, DR1885 from Deinococcus radiodurans and CC3502 from Caulobacter crescentus, were expressed, and their interaction with copper was investigated. The solution structure and extended x-ray absorption fine structure data on the former protein reveal that the protein binds copper(I) through a histidine and three Mets in a cupredoxin-like fold. The surface location of the copper-binding site as well as the type of coordination are well poised for metal transfer chemistry, suggesting that DR1885 might transfer copper, taking the role of Cox17 in bacteria. On the basis of our results, a possible pathway for copper delivery to the Cu(A) center in bacteria is proposed.
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Affiliation(s)
- Lucia Banci
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy
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129
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Calderone V, Dolderer B, Hartmann HJ, Echner H, Luchinat C, Del Bianco C, Mangani S, Weser U. The crystal structure of yeast copper thionein: the solution of a long-lasting enigma. Proc Natl Acad Sci U S A 2005; 102:51-6. [PMID: 15613489 PMCID: PMC544076 DOI: 10.1073/pnas.0408254101] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2004] [Indexed: 11/18/2022] Open
Abstract
We report here the crystal structure of yeast copper thionein (Cu-MT), determined at 1.44-A resolution. The Cu-MT structure shows the largest known oligonuclear Cu(I) thiolate cluster in biology, consisting of six trigonally and two digonally coordinated Cu(I) ions. This is at variance with the results from previous spectroscopic determinations, which were performed on MT samples containing seven rather than eight metal ions. The protein backbone has a random coil structure with the loops enfolding the copper cluster, which is located in a cleft where it is bound to 10 cysteine residues. The protein structure is somewhat different from that of Ag(7)-MT and similar, but not identical, to that of Cu(7)-MT. Besides the different structure of the metal cluster, the main differences lie in the cysteine topology and in the conformation of some portions of the backbone. The present structure suggests that Cu-MT, in addition to its role as a safe depository for copper ions in the cell, may play an active role in the delivery of copper to metal-free chaperones.
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Affiliation(s)
- Vito Calderone
- Department of Chemistry, University of Siena, Via Aldo Moro, 53100 Siena, Italy
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130
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Delobel A, Graciet E, Andreescu S, Gontero B, Halgand F, Laprévote O. Mass spectrometric analysis of the interactions between CP12, a chloroplast protein, and metal ions: a possible regulatory role within a PRK/GAPDH/CP12 complex. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2005; 19:3379-88. [PMID: 16259044 DOI: 10.1002/rcm.2192] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The small chloroplast protein CP12 plays the role of a protein linker in the assembly process of a PRK/GAPDH/CP12 complex that is involved in CO2 assimilation in photosynthetic organisms. The redox state of CP12 regulates its role as a protein linker. Only the oxidized protein, with two disulfide bonds, is active in complex formation. Several observations indicating that CP12 might bind a metal ion led us to screen the binding of different metal ions on oxidized or reduced CP12 using non-covalent electrospray ionization mass spectrometry (ESI-MS) experiments. The oxidized protein bound specifically Cu2+ and Ni2+ (Kd of 26+/-1 microM and 11+/-1 microM, respectively); other cations such as Fe2+ and Zn2+ did not bind, while cations such as Cd2+ formed non-specific adducts to CP12. Similar results were obtained for metal ions on screening with the reduced CP12. Interestingly, the present results suggest that Cu2+ catalyzes the re-formation of the disulfide bonds of the reduced CP12, leading to recovery of the fully oxidized CP12 that is then able to bind a Cu2+ ion. Finally the high similarity between CP12 and copper chaperones from Arabidopsis thaliana, as judged by hydrophobic cluster analysis, provides additional evidence for the relevance of metal binding for the in vivo situation. The findings that CP12 is able to bind a metal ion, and that Cu2+ catalyzes the oxidation of the thiol groups of CP12, are new characteristics of this protein that may prove to be important in the regulation of the assembly process of the PRK/GAPDH/CP12 complex.
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Affiliation(s)
- Arnaud Delobel
- Institut de Chimie des Substances Naturelles, CNRS, 1 avenue de la terrasse, 91198 Gif/Yvette, France
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131
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Mentler M, Weiss A, Grantner K, del Pino P, Deluca D, Fiori S, Renner C, Klaucke WM, Moroder L, Bertsch U, Kretzschmar HA, Tavan P, Parak FG. A new method to determine the structure of the metal environment in metalloproteins: investigation of the prion protein octapeptide repeat Cu2+ complex. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2004; 34:97-112. [PMID: 15452673 DOI: 10.1007/s00249-004-0434-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2004] [Revised: 07/02/2004] [Accepted: 07/05/2004] [Indexed: 10/26/2022]
Abstract
Since high-intensity synchrotron radiation is available, "extended X-ray absorption fine structure" spectroscopy (EXAFS) is used for detailed structural analysis of metal ion environments in proteins. However, the information acquired is often insufficient to obtain an unambiguous picture. ENDOR spectroscopy allows the determination of hydrogen positions around a metal ion. However, again the structural information is limited. In the present study, a method is proposed which combines computations with spectroscopic data from EXAFS, EPR, electron nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM). From EXAFS a first picture of the nearest coordination shell is derived which has to be compatible with EPR data. Computations are used to select sterically possible structures, from which in turn structures with correct H and N positions are selected by ENDOR and ESEEM measurements. Finally, EXAFS spectra are re-calculated and compared with the experimental data. This procedure was successfully applied for structure determination of the Cu(2+) complex of the octapeptide repeat of the human prion protein. The structure of this octarepeat complex is rather similar to a pentapeptide complex which was determined by X-ray structure analysis. However, the tryptophan residue has a different orientation: the axial water is on the other side of the Cu.
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Affiliation(s)
- Matthias Mentler
- Physik-Department E17, Technische Universität München, Garching, Germany
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132
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Bermel W, Bertini I, Felli IC, Kümmerle R, Pierattelli R. 13C direct detection experiments on the paramagnetic oxidized monomeric copper, zinc superoxide dismutase. J Am Chem Soc 2004; 125:16423-9. [PMID: 14692785 DOI: 10.1021/ja037676p] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this report, the use of 13C direct detection has been pursued in 2D experiments (13C-13C COSY, 13C-13C COCAMQ, 13C-13C NOESY) to detect broad lines in nuclear magnetic resonance spectra of paramagnetic metalloproteins. The sample is a monomeric oxidized copper, zinc superoxide dismutase. Thanks to direct detection probeheads, cryogenic technology, and implementation of 13C band-selective homodecoupling, many broadened signals were detected. Proton signals for the same residues escaped detection in 1H and 1H-15N HSQC experiments because of the broadening. Only the 13C signals which experience large contact coupling escaped detection, i.e., the 13C nuclei of the metal coordinated histidines. Otherwise, nuclei as close to copper(II) as 4 A can be detected. Paramagnetic-based restraints can in principle be used for solution structure determination of paramagnetic metalloproteins and in copper(II) proteins in particular. The present study is significant also for the study of large diamagnetic proteins for which proton relaxation makes proton-based spectroscopy not adequate.
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133
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Morante S, González-Iglesias R, Potrich C, Meneghini C, Meyer-Klaucke W, Menestrina G, Gasset M. Inter- and Intra-octarepeat Cu(II) Site Geometries in the Prion Protein. J Biol Chem 2004; 279:11753-9. [PMID: 14703517 DOI: 10.1074/jbc.m312860200] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cu(II) binding to the alpha prion protein (alphaPrP) can be both intramolecular and intermolecular. X-ray absorption spectroscopy at the copper K-edge has been used to explore the site geometry under each binding mode using both insoluble polymeric Cu(II).alphaBoPrP-(24-242) (bovine PrP) complexes and soluble Cu(II) complexes of peptides containing one, two, and four copies of the octarepeat. Analysis of the extended region of the spectra using a multiple scattering approach revealed two types of sites differing in the number of His residues in the first coordination shell of Cu(II). Peptides containing one and two-octarepeat copies in sub-stoichiometric Cu(II) complexes showed the direct binding of a single His in accord with crystallographic intra-repeat geometry. Alternatively, the polymeric Cu(II).alphaBoPrP-(24-242) complex and Cu(II) in its soluble complex with a four-octarepeat peptide at half-site-occupancy showed Cu(II) directly bound to two His residues, consistent with an inter-repeat binding mode. Increasing the Cu(II) site occupancy from 0.5 to 0.75 in the peptide containing four octarepeats resulted in spectral features that are intermediate to those of the inter- and intra-repeat modes. The transition from His-Cu-His (inter-repeat) to Cu-His (intra-repeat) on increasing Cu(II) saturation offers a structural basis for the positive cooperativity of the cation binding process and explains the capacity of alphaPrP to participate in Cu(II)-mediated intermolecular interactions.
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Affiliation(s)
- Silvia Morante
- Department of Physics, Universitá di Roma "Tor Vergata" and Istituto Nazionale per la Fisica della Materia, Via della Ricerca Scientifica 1, I-00133 Roma, Italy
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134
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Narindrasorasak S, Yao P, Sarkar B. Protein disulfide isomerase, a multifunctional protein chaperone, shows copper-binding activity. Biochem Biophys Res Commun 2004; 311:405-14. [PMID: 14592429 DOI: 10.1016/j.bbrc.2003.09.226] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Protein disulfide isomerase (PDI) is a 55 kDa multifunctional protein of the endoplasmic reticulum (ER) involved in protein folding and isomerization. In addition to the chaperone and catalytic functions, PDI is a major calcium-binding protein of the ER. Although the active site of PDI has a similar motif CXXC to the Cu-binding motif in Wilson and Menkes proteins and in other copper chaperones, there has been no report on any metal-binding capability of PDI other than calcium binding. We present evidence that PDI is a copper-binding protein. In the absence of reducing agent freshly reduced PDI can bind a maximum of 4 mol of Cu(II) and convert to Cu(I). These bound Cu(I) are surface exposed as they can be competed readily by BCS reagent, a Cu(I) specific chelator. However, when the binding is performed using the mixture of Cu(II) and 1mM DTT, the total number of Cu(I) bound increases to 10 mol/mol, and it is slower to react with BCS, indicating a more protected environment. In both cases, the copper-bound forms of PDI exist as tetramers while apo-protein is a monomer. These findings suggest that PDI plays a role in intracellular copper disposition.
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Affiliation(s)
- Suree Narindrasorasak
- Department of Structural Biology and Biochemistry, The Research Institute of the Hospital for Sick Children, Toronto, Ont., Canada M5G 1X8
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135
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Nakamura K, Kawabata T, Yura K, Go N. Novel types of two-domain multi-copper oxidases: possible missing links in the evolution. FEBS Lett 2003; 553:239-44. [PMID: 14572631 DOI: 10.1016/s0014-5793(03)01000-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
An analysis of the genome sequence database revealed novel types of two-domain multi-copper oxidases. The two-domain proteins have the conspicuous combination of blue-copper and inter-domain trinuclear copper binding residues, which is common in ceruloplasmin and ascorbate oxidase but not in nitrite reductase, and therefore are considered to retain the characteristics of the plausible ancestral form of ceruloplasmin and ascorbate oxidase. A possible evolutionary relationship of these proteins is proposed.
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Affiliation(s)
- Kensuke Nakamura
- Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, 630-0101 Nara, Japan.
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136
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Abstract
The design of redox-active metalloproteins has been approached from two different directions. The de novo design approach has recently reached an important stage, at which structural information on several different designed metalloproteins has been obtained. This new information highlights the real challenge of this approach. The alternative approach involving re-engineering of evolved proteins has also made significant advances recently.
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Affiliation(s)
- Paul D Barker
- University of Cambridge, Chemical Laboratory and Centre for Protein Engineering, Lensfield Road, Cambridge CB2 1EW, UK.
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137
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Franke S, Grass G, Rensing C, Nies DH. Molecular analysis of the copper-transporting efflux system CusCFBA of Escherichia coli. J Bacteriol 2003; 185:3804-12. [PMID: 12813074 PMCID: PMC161567 DOI: 10.1128/jb.185.13.3804-3812.2003] [Citation(s) in RCA: 369] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The cus determinant of Escherichia coli encodes the CusCFBA proteins that mediate resistance to copper and silver by cation efflux. CusA and CusB were essential for copper resistance, and CusC and CusF were required for full resistance. Replacements of methionine residues 573, 623, and 672 with isoleucine in CusA resulted in loss of copper resistance, demonstrating their functional importance. Substitutions for several other methionine residues of this protein did not have any effect. The small 10-kDa protein CusF (previously YlcC) was shown to be a periplasmic protein. CusF bound one copper per polypeptide. The pink CusF copper protein complex exhibited an absorption maximum at around 510 nm. Methionine residues of CusF were involved in copper binding as shown by site-directed mutagenesis. CusF interacted with CusB and CusC polypeptides in a yeast two-hybrid assay. In contrast to other well-studied CBA-type heavy metal efflux systems, Cus was shown to be a tetrapartite resistance system that involves the novel periplasmic copper-binding protein CusF. These data provide additional evidence for the hypothesis that Cu(I) is directly transported from the periplasm across the outer membrane by the Cus complex.
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Affiliation(s)
- Sylvia Franke
- Molekulare Mikrobiologie, Institut für Mikrobiologie, Martin-Luther-Universität Halle-Wittenberg, 06099 Halle, Germany
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138
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Arnesano F, Banci L, Bertini I, Felli IC, Luchinat C, Thompsett AR. A strategy for the NMR characterization of type II copper(II) proteins: the case of the copper trafficking protein CopC from Pseudomonas Syringae. J Am Chem Soc 2003; 125:7200-8. [PMID: 12797793 DOI: 10.1021/ja034112c] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
CopC from Pseudomonas syringae was found to be a protein capable of binding both Cu(I) and Cu(II) at two different sites. The solution structure of the apo protein is available, and structural information has been obtained on the Cu(I) bound form. We attempt here to set the limits for the determination of the solution structure of a Cu(II) protein, such as the Cu(II) bound form of CopC, in which the Cu(II) ion takes a type II coordination. The electron relaxation time is estimated from NMRD measurements to be 3 ns which leads to a correlation time for the nuclear spin-electron spin dipolar interaction of 2 ns. This information allowed us to tailor the NMR experiments and to fully exploit purely heteronuclear spectroscopy to assign as many signals as possible. In this way, 37 (13)C and 11 (15)N signals that completely escape detection with conventional approaches were assigned. Paramagnetic based structural constraints were obtained by measuring paramagnetic longitudinal relaxation enhancements (rho(para)) which allowed us to precisely locate the copper ion within the protein frame. Pseudocontact shifts (pcs's) were also used as constraints for 83 (1)H and 18 (13)C nuclei. With them, together with other standard structural constraints, a structure is obtained (and submitted to PDB) where information is only missing in a sphere with a 6 A radius from the copper ion. If we borrow information from EXAFS data, which show evidence of two copper coordinated histidines, then His 1 and His 91 are unambiguously identified as copper ligands. EXAFS data indicate two more light donor atoms (O/N) which could be from Asp 27 and Glu 89, whereas the NMRD data indicate the presence of a semicoordinated water molecule at 2.8 A (Cu-O distance) roughly orthogonal to the plane identified by the other four ligands. This represents the most extensively characterized structure of a type II Cu(II) protein obtained employing the most advanced NMR methods and with the aid of EXAFS data. The knowledge of the location of the Cu(II) in the protein is important for the copper transfer mechanism.
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Affiliation(s)
- Fabio Arnesano
- CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
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139
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Finney LA, O'Halloran TV. Transition metal speciation in the cell: insights from the chemistry of metal ion receptors. Science 2003; 300:931-6. [PMID: 12738850 DOI: 10.1126/science.1085049] [Citation(s) in RCA: 809] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The essential transition metal ions are avidly accumulated by cells, yet they have two faces: They are put to use as required cofactors, but they also can catalyze cytotoxic reactions. Several families of proteins are emerging that control the activity of intracellular metal ions and help confine them to vital roles. These include integral transmembrane transporters, metalloregulatory sensors, and diffusible cytoplasmic metallochaperone proteins that protect and guide metal ions to targets. It is becoming clear that many of these proteins use atypical coordination chemistry to accomplish their unique goals. The different coordination numbers, types of coordinating residues, and solvent accessibilities of these sites are providing insight into the inorganic chemistry of the cytoplasm.
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Affiliation(s)
- Lydia A Finney
- Department of Chemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, IL 60208-3113, USA
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140
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Abstract
Advances in bioinorganic chemistry since the 1970s have been driven by three factors: rapid determination of high-resolution structures of proteins and other biomolecules, utilization of powerful spectroscopic tools for studies of both structures and dynamics, and the widespread use of macromolecular engineering to create new biologically relevant structures. Today, very large molecules can be manipulated at will, with the result that certain proteins and nucleic acids themselves have become versatile model systems for elucidating biological function.
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Affiliation(s)
- Harry B Gray
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA.
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