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Montoya A, Wisniewski M, Goodsell JL, Angerhofer A. Bidentate Substrate Binding Mode in Oxalate Decarboxylase. Molecules 2024; 29:4414. [PMID: 39339409 PMCID: PMC11433825 DOI: 10.3390/molecules29184414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2024] [Revised: 09/09/2024] [Accepted: 09/13/2024] [Indexed: 09/30/2024] Open
Abstract
Oxalate decarboxylase is an Mn- and O2-dependent enzyme in the bicupin superfamily that catalyzes the redox-neutral disproportionation of the oxalate monoanion to form carbon dioxide and formate. Its best-studied isozyme is from Bacillus subtilis where it is stress-induced under low pH conditions. Current mechanistic schemes assume a monodentate binding mode of the substrate to the N-terminal active site Mn ion to make space for a presumed O2 molecule, despite the fact that oxalate generally prefers to bind bidentate to Mn. We report on X-band 13C-electron nuclear double resonance (ENDOR) experiments on 13C-labeled oxalate bound to the active-site Mn(II) in wild-type oxalate decarboxylase at high pH, the catalytically impaired W96F mutant enzyme at low pH, and Mn(II) in aqueous solution. The ENDOR spectra of these samples are practically identical, which shows that the substrate binds bidentate (κO, κO') to the active site Mn(II) ion. Domain-based local pair natural orbital coupled cluster singles and doubles (DLPNO-CCSD) calculations of the expected 13C hyperfine coupling constants for bidentate bound oxalate predict ENDOR spectra in good agreement with the experiment, supporting bidentate bound substrate. Geometry optimization of a substrate-bound minimal active site model by density functional theory shows two possible substrate coordination geometries, bidentate and monodentate. The bidentate structure is energetically preferred by ~4.7 kcal/mol. Our results revise a long-standing hypothesis regarding substrate binding in the enzyme and suggest that dioxygen does not bind to the active site Mn ion after substrate binds. The results are in agreement with our recent mechanistic hypothesis of substrate activation via a long-range electron transfer process involving the C-terminal Mn ion.
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Affiliation(s)
| | | | | | - Alexander Angerhofer
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL 32611, USA
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2
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Paramagnetic resonance investigation of mono- and di-manganese-containing systems in biochemistry. Methods Enzymol 2022; 666:315-372. [DOI: 10.1016/bs.mie.2022.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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3
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Gagnon DM, Hadley RC, Ozarowski A, Nolan EM, Britt RD. High-Field EPR Spectroscopic Characterization of Mn(II) Bound to the Bacterial Solute-Binding Proteins MntC and PsaA. J Phys Chem B 2019; 123:4929-4934. [PMID: 31117618 DOI: 10.1021/acs.jpcb.9b03633] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
During infection, the bacterial pathogens Staphylococcus aureus and Streptococcus pneumoniae employ ATP-binding cassette (ABC) transporters to acquire Mn(II), an essential nutrient, from the host environment. Staphylococcal MntABC and streptococcal PsaABC attract the attention of the biophysical and bacterial pathogenesis communities because of their established importance during infection. Previous biophysical examination of Mn(II)-MntC and Mn(II)-PsaA using continuous-wave (≈9 GHz) electron paramagnetic resonance (EPR) spectroscopy revealed broad, difficult-to-interpret spectra (Hadley et al. J. Am. Chem. Soc. 2018, 140, 110-113). Herein, we employ high-frequency (>90 GHz), high-field (>3 T) EPR spectroscopy to investigate the Mn(II)-binding sites of these proteins and determine the spin Hamiltonian parameters. Our analyses demonstrate that the zero-field splitting (ZFS) is large for Mn(II)-MntC and Mn(II)-PsaA at +2.72 and +2.87 GHz, respectively. The measured 55Mn hyperfine coupling values for Mn(II)-MntC and Mn(II)-PsaA of 241 and 236 MHz, respectively, demonstrate a more covalent interaction between Mn(II) and the protein compared to Mn(II) in aqueous solution (≈265 MHz). These studies indicate that MntC and PsaA bind Mn(II) in a similar coordination geometry. Comparison of the ZFS values determined herein with those ascertained for other Mn(II) proteins suggests that the Mn(II)-MntC and Mn(II)-PsaA coordination spheres are not five-coordinate in solution.
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Affiliation(s)
- Derek M Gagnon
- Department of Chemistry , University of California Davis , Davis , California 95616 , United States
| | - Rose C Hadley
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Andrew Ozarowski
- National High Magnetic Field Laboratory , Florida State University , Tallahassee , Florida 32310 , United States
| | - Elizabeth M Nolan
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - R David Britt
- Department of Chemistry , University of California Davis , Davis , California 95616 , United States
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4
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Hadley RC, Gagnon DM, Brophy MB, Gu Y, Nakashige TG, Britt RD, Nolan EM. Biochemical and Spectroscopic Observation of Mn(II) Sequestration from Bacterial Mn(II) Transport Machinery by Calprotectin. J Am Chem Soc 2018; 140:110-113. [PMID: 29211955 PMCID: PMC5762273 DOI: 10.1021/jacs.7b11207] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Human calprotectin (CP, S100A8/S100A9 oligomer) is a metal-sequestering host-defense protein that prevents bacterial acquisition of Mn(II). In this work, we investigate Mn(II) competition between CP and two solute-binding proteins that Staphylococcus aureus and Streptococcus pneumoniae, Gram-positive bacterial pathogens of significant clinical concern, use to obtain Mn(II) when infecting a host. Biochemical and electron paramagnetic resonance (EPR) spectroscopic analyses demonstrate that CP outcompetes staphylococcal MntC and streptococcal PsaA for Mn(II). This behavior requires the presence of excess Ca(II) ions, which enhance the Mn(II) affinity of CP. This report presents new spectroscopic evaluation of two Mn(II) proteins important for bacterial pathogenesis, direct observation of Mn(II) sequestration from bacterial Mn(II) acquisition proteins by CP, and molecular insight into the extracellular battle for metal nutrients that occurs during infection.
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Affiliation(s)
- Rose C. Hadley
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Derek M. Gagnon
- Department of Chemistry, University of California Davis, Davis, CA 95616, United States
| | - Megan Brunjes Brophy
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Yu Gu
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Toshiki G. Nakashige
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - R. David Britt
- Department of Chemistry, University of California Davis, Davis, CA 95616, United States
| | - Elizabeth M. Nolan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
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5
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“Scorpionate-like” complexes that are held together by hydrogen bonds: Crystallographic and spectroscopic studies of (3-NH(t-butyl)-5-methyl-pyrazole) MX2 (M = Zn, Ni, Co, Mn; n= 3, 4; X = Cl, Br). Polyhedron 2016. [DOI: 10.1016/j.poly.2015.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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6
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He M, Li X, Liu Y, Li J. Axial Mn–CCN Bonds of Cyano Manganese(II) Porphyrin Complexes: Flexible and Weak? Inorg Chem 2016; 55:5871-9. [PMID: 27228473 DOI: 10.1021/acs.inorgchem.6b00173] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mingrui He
- College
of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Yanqi Lake, Huairou District,
Beijing 101408, China
| | - Xiangjun Li
- College
of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Yanqi Lake, Huairou District,
Beijing 101408, China
| | - Yanhong Liu
- Technical
Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Jianfeng Li
- College
of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Yanqi Lake, Huairou District,
Beijing 101408, China
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7
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Un S, Bruch EM. How Bonding in Manganous Phosphates Affects their Mn(II)-(31)P Hyperfine Interactions. Inorg Chem 2015; 54:10422-8. [PMID: 26488236 DOI: 10.1021/acs.inorgchem.5b01864] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Manganous phosphates have been postulated to play an important role in cells as antioxidants. In situ Mn(II) electron-nuclear double resonance (ENDOR) spectroscopy has been used to measure their speciation in cells. The analyses of such ENDOR spectra and the quantification of cellular Mn(II) phosphates has been based on comparisons to in vitro model complexes and heuristic modeling. In order to put such analyses on a more physical and theoretical footing, the Mn(II)-(31)P hyperfine interactions of various Mn(II) phosphate complexes have been measured by 95 GHz ENDOR spectroscopy. The dipolar components of these interactions remained relatively constant as a function of pH, esterification, and phosphate chain length, while the isotropic contributions were significantly affected. Counterintuitively, although the manganese-phosphate bonds are weakened by protonation and esterification, they lead to larger isotropic values, indicating higher unpaired-electron spin densities at the phosphorus nuclei. By comparison, extending the phosphate chain with additional phosphate groups lowers the spin density. Density functional theory calculations of model complexes quantitatively reproduced the measured hyperfine couplings and provided detailed insights into how bonding in Mn(II) phosphate complexes modulates the electron-spin polarization and consequently their isotropic hyperfine couplings. These results show that various classes of phosphates can be identified by their ENDOR spectra and provide a theoretical framework for understanding the in situ (31)P ENDOR spectra of cellular Mn(II) complexes.
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Affiliation(s)
- Sun Un
- Department of Biochemistry, Biophysics and Structural Biology, Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Saclay , F-91198 Gif-sur-Yvette, France
| | - Eduardo M Bruch
- Department of Biochemistry, Biophysics and Structural Biology, Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Saclay , F-91198 Gif-sur-Yvette, France
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8
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Gagnon DM, Brophy MB, Bowman SEJ, Stich TA, Drennan CL, Britt RD, Nolan EM. Manganese binding properties of human calprotectin under conditions of high and low calcium: X-ray crystallographic and advanced electron paramagnetic resonance spectroscopic analysis. J Am Chem Soc 2015; 137:3004-16. [PMID: 25597447 DOI: 10.1021/ja512204s] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The antimicrobial protein calprotectin (CP), a hetero-oligomer of the S100 family members S100A8 and S100A9, is the only identified mammalian Mn(II)-sequestering protein. Human CP uses Ca(II) ions to tune its Mn(II) affinity at a biologically unprecedented hexahistidine site that forms at the S100A8/S100A9 interface, and the molecular basis for this phenomenon requires elucidation. Herein, we investigate the remarkable Mn(II) coordination chemistry of human CP using X-ray crystallography as well as continuous-wave (CW) and pulse electron paramagnetic resonance (EPR) spectroscopies. An X-ray crystallographic structure of Mn(II)-CP containing one Mn(II), two Ca(II), and two Na(I) ions per CP heterodimer is reported. The CW EPR spectrum of Ca(II)- and Mn(II)-bound CP prepared with a 10:0.9:1 Ca(II):Mn(II):CP ratio is characterized by an unusually low zero-field splitting of 485 MHz (E/D = 0.30) for the S = 5/2 Mn(II) ion, consistent with the high symmetry of the His6 binding site observed crystallographically. Results from electron spin-echo envelope modulation and electron-nuclear double resonance experiments reveal that the six Mn(II)-coordinating histidine residues of Ca(II)- and Mn(II)-bound CP are spectroscopically equivalent. The observed (15)N (I = 1/2) hyperfine couplings (A) arise from two distinct classes of nitrogen atoms: the coordinating ε-nitrogen of the imidazole ring of each histidine ligand (A = [3.45, 3.71, 5.91] MHz) and the distal δ-nitrogen (A = [0.11, 0.18, 0.42] MHz). In the absence of Ca(II), the binding affinity of CP for Mn(II) drops by two to three orders of magnitude and coincides with Mn(II) binding at the His6 site as well as other sites. This study demonstrates the role of Ca(II) in enabling high-affinity and specific binding of Mn(II) to the His6 site of human calprotectin.
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Affiliation(s)
- Derek M Gagnon
- Department of Chemistry, University of California , Davis, California 95616, United States
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9
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Abstract
Electron-nuclear double resonance (ENDOR) is a method that probes the local structure of paramagnetic centers via their hyperfine interactions with nearby magnetic nuclei. Here we describe the use of this technique to structurally characterize the ATPase active site of the RNA helicase DbpA, where Mg(2+)-ATP binds. This is achieved by substituting the EPR (electron paramagnetic resonance) silent Mg(2+) ion with paramagnetic, EPR active, Mn(2+) ion. (31)P ENDOR provides the interaction of the Mn(2+) with the nucleotide (ADP, ATP and its analogs) through the phosphates. The ENDOR spectra clearly distinguish between ATP- and ADP-binding modes. In addition, by preparing (13)C-enriched DbpA, (13)C ENDOR is used to probe the interaction of the Mn(2+) with protein residues. This combination allows tracking structural changes in the Mn(2+) coordination shell, in the ATPase site, in different states of the protein, namely with and without RNA and with different ATP analogs. Here, a detailed description of sample preparation and the ENDOR measurement methodology is provided, focusing on measurements at W-band (95 GHz) where sensitivity is high and spectral interpretations are relatively simple.
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10
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Responses of Mn2+ speciation in Deinococcus radiodurans and Escherichia coli to γ-radiation by advanced paramagnetic resonance methods. Proc Natl Acad Sci U S A 2013; 110:5945-50. [PMID: 23536297 DOI: 10.1073/pnas.1303376110] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The remarkable ability of bacterium Deinococcus radiodurans to survive extreme doses of γ-rays (12,000 Gy), 20 times greater than Escherichia coli, is undiminished by loss of Mn-dependent superoxide dismutase (SodA). D. radiodurans radiation resistance is attributed to the accumulation of low-molecular-weight (LMW) "antioxidant" Mn(2+)-metabolite complexes that protect essential enzymes from oxidative damage. However, in vivo information about such complexes within D. radiodurans cells is lacking, and the idea that they can supplant reactive-oxygen-species (ROS)-scavenging enzymes remains controversial. In this report, measurements by advanced paramagnetic resonance techniques [electron-spin-echo (ESE)-EPR/electron nuclear double resonance/ESE envelope modulation (ESEEM)] reveal differential details of the in vivo Mn(2+) speciation in D. radiodurans and E. coli cells and their responses to 10 kGy γ-irradiation. The Mn(2+) of D. radiodurans exists predominantly as LMW complexes with nitrogenous metabolites and orthophosphate, with negligible EPR signal from Mn(2+) of SodA. Thus, the extreme radiation resistance of D. radiodurans cells cannot be attributed to SodA. Correspondingly, 10 kGy irradiation causes no change in D. radiodurans Mn(2+) speciation, despite the paucity of holo-SodA. In contrast, the EPR signal of E. coli is dominated by signals from low-symmetry enzyme sites such as that of SodA, with a minority pool of LMW Mn(2+) complexes that show negligible coordination by nitrogenous metabolites. Nonetheless, irradiation of E. coli majorly changes LMW Mn(2+) speciation, with extensive binding of nitrogenous ligands created by irradiation. We infer that E. coli is highly susceptible to radiation-induced ROS because it lacks an adequate supply of LMW Mn antioxidants.
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11
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Liao RZ, Thiel W. Determinants of Regioselectivity and Chemoselectivity in Fosfomycin Resistance Protein FosA from QM/MM Calculations. J Phys Chem B 2013; 117:1326-36. [DOI: 10.1021/jp4002719] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Rong-Zhen Liao
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470, Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470, Mülheim an der Ruhr, Germany
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12
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Hayden JA, Brophy MB, Cunden LS, Nolan EM. High-affinity manganese coordination by human calprotectin is calcium-dependent and requires the histidine-rich site formed at the dimer interface. J Am Chem Soc 2013; 135:775-87. [PMID: 23276281 PMCID: PMC3575579 DOI: 10.1021/ja3096416] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Calprotectin (CP) is a transition metal-chelating antimicrobial protein of the calcium-binding S100 family that is produced and released by neutrophils. It inhibits the growth of various pathogenic microorganisms by sequestering the transition metal ions manganese and zinc. In this work, we investigate the manganese-binding properties of CP. We demonstrate that the unusual His(4) motif (site 2) formed at the S100A8/S100A9 dimer interface is the site of high-affinity Mn(II) coordination. We identify a low-temperature Mn(II) spectroscopic signal for this site consistent with an octahedral Mn(II) coordination sphere with simulated zero-field splitting parameters D = 270 MHz and E/D = 0.30 (E = 81 MHz). This analysis, combined with studies of mutant proteins, suggests that four histidine residues (H17 and H27 of S100A8; H91 and H95 of S100A9) coordinate Mn(II) in addition to two as-yet unidentified ligands. The His(3)Asp motif (site 1), which is also formed at the S100A8/S100A9 dimer interface, does not provide a high-affinity Mn(II) binding site. Calcium binding to the EF-hand domains of CP increases the Mn(II) affinity of the His(4) site from the low-micromolar to the mid-nanomolar range. Metal-ion selectivity studies demonstrate that CP prefers to coordinate Zn(II) over Mn(II). Nevertheless, the specificity of Mn(II) for the His(4) site provides CP with the propensity to form mixed Zn:Mn:CP complexes where one Zn(II) ion occupies site 1 and one Mn(II) ion occupies site 2. These studies support the notion that CP responds to physiological calcium ion gradients to become a high-affinity transition metal ion chelator in the extracellular space where it inhibits microbial growth.
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Affiliation(s)
- Joshua A. Hayden
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Megan Brunjes Brophy
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Lisa S. Cunden
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Elizabeth M. Nolan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
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13
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Probing in vivo Mn2+ speciation and oxidative stress resistance in yeast cells with electron-nuclear double resonance spectroscopy. Proc Natl Acad Sci U S A 2010; 107:15335-9. [PMID: 20702768 DOI: 10.1073/pnas.1009648107] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Manganese is an essential transition metal that, among other functions, can act independently of proteins to either defend against or promote oxidative stress and disease. The majority of cellular manganese exists as low molecular-weight Mn(2+) complexes, and the balance between opposing "essential" and "toxic" roles is thought to be governed by the nature of the ligands coordinating Mn(2+). Until now, it has been impossible to determine manganese speciation within intact, viable cells, but we here report that this speciation can be probed through measurements of (1)H and (31)P electron-nuclear double resonance (ENDOR) signal intensities for intracellular Mn(2+). Application of this approach to yeast (Saccharomyces cerevisiae) cells, and two pairs of yeast mutants genetically engineered to enhance or suppress the accumulation of manganese or phosphates, supports an in vivo role for the orthophosphate complex of Mn(2+) in resistance to oxidative stress, thereby corroborating in vitro studies that demonstrated superoxide dismutase activity for this species.
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Hunsicker-Wang L, Vogt M, Derose VJ. EPR methods to study specific metal-ion binding sites in RNA. Methods Enzymol 2009; 468:335-67. [PMID: 20946777 DOI: 10.1016/s0076-6879(09)68016-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The properties of metal-ion interactions with RNA can be explored by spectroscopic methods. In this chapter, we describe the use of paramagnetic Mn(2+) ions and electron paramagnetic resonance (EPR)-based techniques to monitor the association of Mn(2+) with RNA and related nucleotides. Solution EPR methods are used to determine the numbers of Mn(2+) ions associating with RNA. For RNA poised with a single-bound Mn(2+), low-temperature EPR characteristics provide information about the asymmetry of the Mn(2+) coordination site. To identify the RNA groups coordinating to the Mn(2+) ion, ENDOR (electron nuclear double resonance) and ESEEM (electron spin echo envelope modulation) methods are applied. Both continuous-wave (CW) and electron spin echo (ESE)-detected ENDOR methods are described. This chapter includes practical details for RNA sample preparation, including isotope substitution and cryoprotection, and an overview of data acquisition and analysis methods used in these techniques, as well as examples from the current literature.
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Popović-Bijelić A, Voevodskaya N, Domkin V, Thelander L, Gräslund A. Metal Binding and Activity of Ribonucleotide Reductase Protein R2 Mutants: Conditions for Formation of the Mixed Manganese−Iron Cofactor. Biochemistry 2009; 48:6532-9. [DOI: 10.1021/bi900693s] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ana Popović-Bijelić
- Department of Biochemistry and Biophysics, Stockholm University, S-10691 Stockholm, Sweden
| | - Nina Voevodskaya
- Department of Biochemistry and Biophysics, Stockholm University, S-10691 Stockholm, Sweden
| | - Vladimir Domkin
- Department of Medical Biochemistry and Biophysics, Umeå University, S-90187 Umeå, Sweden
| | - Lars Thelander
- Department of Medical Biochemistry and Biophysics, Umeå University, S-90187 Umeå, Sweden
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Stockholm University, S-10691 Stockholm, Sweden
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16
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Hureau C, Groni S, Guillot R, Blondin G, Duboc C, Anxolabéhère-Mallart E. Syntheses, X-ray structures, solid state high-field electron paramagnetic resonance, and density-functional theory investigations on chloro and aqua Mn(II) mononuclear complexes with amino-pyridine pentadentate ligands. Inorg Chem 2008; 47:9238-47. [PMID: 18817370 DOI: 10.1021/ic800551u] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The two pentadentate amino-pyridine ligands L5(2) and L5(3) (L5(2) and L5(3) stand for the N-methyl-N,N',N'-tris(2-pyridylmethyl)ethane-1,2-diamine and the N-methyl-N,N',N'-tris(2-pyridylmethyl)propane-1,3-diamine, respectively) were used to synthesize four mononuclear Mn(II) complexes, namely [(L5(2))MnCl](PF6) (1(PF6)), [(L5(3))MnCl](PF6) (2(PF6)), [(L5(2))Mn(OH2)](BPh4)2 (3(BPh4)2), and [(L5(3))Mn(OH2)](BPh4)2 (4(BPh4)2). The X-ray diffraction studies revealed different configurations for the ligand L5(n) (n = 2, 3) depending on the sixth exogenous ligand and/or the counterion. Solid state high-field electron paramagnetic resonance spectra were recorded on complexes 1-4 as on previously described mononuclear Mn(II) systems with tetra- or hexadentate amino-pyridine ligands. Positive and negative axial zero-field splitting (ZFS) parameters D were determined whose absolute values ranged from 0.090 to 0.180 cm(-1). Density-functional theory calculations were performed unraveling that, in contrast with chloro systems, the spin-spin and spin-orbit coupling contributions to the D-parameter are comparable for mixed N,O-coordination sphere complexes.
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Affiliation(s)
- Christelle Hureau
- Equipe de Chimie Inorganique, Institut de Chimie Moleculaire et des Materiaux d'Orsay, UMR 8182 CNRS, Universite Paris-Sud, 91405 Orsay Cedex, France
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Duboc C, Collomb MN, Pécaut J, Deronzier A, Neese F. Definition of Magneto-Structural Correlations for the MnIIIon. Chemistry 2008; 14:6498-509. [DOI: 10.1002/chem.200800426] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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18
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Gätjens J, Sjödin M, Pecoraro VL, Un S. The Relationship between the Manganese(II) Zero-Field Interaction and Mn(II)/Mn(III) Redox Potential of Mn(4‘-X-terpy)2 Complexes. J Am Chem Soc 2007; 129:13825-7. [DOI: 10.1021/ja076024o] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jessica Gätjens
- Service de Bioénergétique Biologie Structurale et Mécanismes, CNRS URA 2096, Institut de Biologie et Technologies de Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France, and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055
| | - Martin Sjödin
- Service de Bioénergétique Biologie Structurale et Mécanismes, CNRS URA 2096, Institut de Biologie et Technologies de Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France, and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055
| | - Vincent L. Pecoraro
- Service de Bioénergétique Biologie Structurale et Mécanismes, CNRS URA 2096, Institut de Biologie et Technologies de Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France, and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055
| | - Sun Un
- Service de Bioénergétique Biologie Structurale et Mécanismes, CNRS URA 2096, Institut de Biologie et Technologies de Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France, and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055
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Rigsby RE, Brown DW, Dawson E, Lybrand TP, Armstrong RN. A model for glutathione binding and activation in the fosfomycin resistance protein, FosA. Arch Biochem Biophys 2007; 464:277-83. [PMID: 17537395 PMCID: PMC2709490 DOI: 10.1016/j.abb.2007.04.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2007] [Accepted: 04/24/2007] [Indexed: 10/23/2022]
Abstract
The genomically encoded fosfomycin resistance protein from Pseudomonas aeruginosa (FosA(PA)) utilizes Mn(II) and K(+) to catalyze the addition of glutathione (GSH) to C1 of the antibiotic rendering it inactive. Although this protein has been structurally and kinetically characterized with respect to the substrate, fosfomycin, questions remain regarding how the enzyme binds the thiol substrate, GSH. Computational studies have revealed a potential GSH binding site in FosA(PA) that involves six electrostatic or hydrogen-bonding interactions with protein side-chains as well as six additional residues that contribute van der Waals interactions. A strategically placed tyrosine residue, Y39, appears to be involved in the ionization of GSH during catalysis. The Y39F mutant exhibits a 13-fold reduction of catalytic activity (k(cat)=14+/-2s(-1)), suggesting a role in the ionization of GSH. Mutation of five other residues (W34, Q36, S50, K90, and R93) implicated in ionic of hydrogen-bonding interactions resulted in enzymes with reduced catalytic efficiency, affinity for GSH, or both. The mutant enzymes were also found to be less effective resistant proteins in the biological context of Escherichia coli. The more conservative W34H mutant has native-like catalytic efficiency suggesting that the imidazole NH group can replace the indole group of W34 that is important for GSH binding. In the absence of co-crystal structural data with the thiol substrate, these results provide important insights into the role of GSH in catalysis.
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Affiliation(s)
- Rachel E. Rigsby
- Department of Chemistry and the Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232, United States
| | - Daniel W. Brown
- Department of Chemistry and the Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232, United States
| | - Eric Dawson
- Department of Chemistry and the Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232, United States
| | - Terry P. Lybrand
- Department of Chemistry and the Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232, United States
| | - Richard N. Armstrong
- Department of Chemistry and the Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232, United States
- Department of Biochemistry and the Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, United States
- Corresponding author: FAX +1 615 343 2921, Email Address:
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Carmieli R, Larsen TM, Reed GH, Zein S, Neese F, Goldfarb D. The catalytic Mn2+ sites in the enolase-inhibitor complex: crystallography, single-crystal EPR, and DFT calculations. J Am Chem Soc 2007; 129:4240-52. [PMID: 17367133 PMCID: PMC2538446 DOI: 10.1021/ja066124e] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Crystals of Zn2+/Mn2+ yeast enolase with the inhibitor PhAH (phosphonoacetohydroxamate) were grown under conditions with a slight preference for binding of Zn2+ at the higher affinity site, site I. The structure of the Zn2+/Mn2+-PhAH complex was solved at a resolution of 1.54 A, and the two catalytic metal binding sites, I and II, show only subtle displacement compared to that of the corresponding complex with the native Mg2+ ions. Low-temperature echo-detected high-field (W-band, 95 GHz) EPR (electron paramagnetic resonance) and 1H ENDOR (electron-nuclear double resonance) were carried out on a single crystal, and rotation patterns were acquired in two perpendicular planes. Analysis of the rotation patterns resolved a total of six Mn2+ sites, four symmetry-related sites of one type and two out of the four of the other type. The observation of two chemically inequivalent Mn2+ sites shows that Mn2+ ions populate both sites I and II and the zero-field splitting (ZFS) tensors of the Mn2+ in the two sites were determined. The Mn2+ site with the larger D value was assigned to site I based on the 1H ENDOR spectra, which identified the relevant water ligands. This assignment is consistent with the seemingly larger deviation of site I from octahedral symmetry, compared to that of site II. The ENDOR results gave the coordinates of the protons of two water ligands, and adding them to the crystal structure revealed their involvement in a network of H bonds stabilizing the binding of the metal ions and PhAH. Although specific hyperfine interactions with the inhibitor were not determined, the spectroscopic properties of the Mn2+ in the two sites were consistent with the crystal structure. Density functional theory (DFT) calculations carried out on a cluster representing the catalytic site, with Mn2+ in site I and Zn2+ in site II, and vice versa, gave overestimated D values on the order of the experimental ones, although the larger D value was found for Mn2+ in site II rather than in site I. This discrepancy was attributed to the high sensitivity of the ZFS parameters to the Mn-O bond lengths and orientations, such that small, but significant, differences between the optimized and crystal structures alter the ZFS considerably, well above the difference between the two sites.
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Affiliation(s)
- Raanan Carmieli
- Department of Chemical Physics, The Weizmann Institute of Science, Rehovot, Israel
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21
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Stich TA, Lahiri S, Yeagle G, Dicus M, Brynda M, Gunn A, Aznar C, Derose VJ, Britt RD. Multifrequency Pulsed EPR Studies of Biologically Relevant Manganese(II) Complexes. APPLIED MAGNETIC RESONANCE 2007; 31:321-341. [PMID: 22190766 PMCID: PMC3242439 DOI: 10.1007/bf03166263] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Electron paramagnetic resonance studies at multiple frequencies (MF EPR) can provide detailed electronic structure descriptions of unpaired electrons in organic radicals, inorganic complexes, and metalloenzymes. Analysis of these properties aids in the assignment of the chemical environment surrounding the paramagnet and provides mechanistic insight into the chemical reactions in which these systems take part. Herein, we present results from pulsed EPR studies performed at three different frequencies (9, 31, and 130 GHz) on [Mn(II)(H(2)O)(6)](2+), Mn(II) adducts with the nucleotides ATP and GMP, and the Mn(II)-bound form of the hammerhead ribozyme (MnHH). Through line shape analysis and interpretation of the zero-field splitting values derived from successful simulations of the corresponding continuous-wave and field-swept echo-detected spectra, these data are used to exemplify the ability of the MF EPR approach in distinguishing the nature of the first ligand sphere. A survey of recent results from pulsed EPR, as well as pulsed electron-nuclear double resonance and electron spin echo envelope modulation spectroscopic studies applied to Mn(II)-dependent systems, is also presented.
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Affiliation(s)
- T A Stich
- Department of Chemistry, University of California-Davis, Davis, California, USA
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22
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García-Rubio I, Angerhofer A, Schweiger A. EPR and HYSCORE investigation of the electronic structure of the model complex Mn(imidazole)6: exploring Mn(II)-imidazole binding using single crystals. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2007; 184:130-42. [PMID: 17055309 DOI: 10.1016/j.jmr.2006.09.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2006] [Accepted: 09/18/2006] [Indexed: 05/12/2023]
Abstract
The electronic structure of the Mn(II)-imidazole binding was studied by EPR spectroscopy using the model complex Mn(Im)(6) diluted in a single crystal of Zn(Im)(6)Cl(2).4(H(2)O). The second rank zero-field splitting (ZFS) tensor (D tensor) of the two sites, a and b, present in the crystal was determined by measuring the orientation patterns of the echo-detected EPR spectra in three different planes at 10K (D(a)=-106, D(b)=-118, E(a)=-17, E(b)=-22x10(-4)cm(-1). Euler angles with respect to the crystal habitus: alpha(a)=13 degrees , beta(a)=76 degrees , gamma(a)=108.5 degrees , alpha(b)=14 degrees , beta(b)=73.5 degrees , gamma(b)=103.5 degrees ). The contribution of cubic ZFS terms to the spectrum allowed us to determine the orientation of the N-Mn-N directions of the complex as well (Euler angles in the D tensor reference frame alpha=100 degrees , beta=23 degrees , gamma=0 degrees , both centers having the same orientation). The hyperfine interactions with (14)N were explored by HYSCORE spectroscopy. The correlation patterns and modulation amplitudes in the 2D experiments were studied for different electron spin transitions and orientations of the crystal. Signals of three different pairs of nitrogens were found. The results were analyzed considering that the N-Mn binding directions are principal directions of the hyperfine and nuclear quadrupole tensor of (14)N. All three pairs of nitrogens were found to be almost equivalent with an isotropic contribution of A(iso) approximately 3.2MHz and an almost axial anisotropic coupling of 2T approximately 1.1MHz along the N-Mn bonding direction. The nuclear quadrupole principal values are 1.5MHz along the bonding direction, -0.6MHz in the direction perpendicular to the imidazole plane, and -0.9MHz in the direction perpendicular to both.
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Affiliation(s)
- Inés García-Rubio
- Laboratory of Physical Chemistry, ETH Zurich, CH-8093 Zürich, Switzerland.
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23
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Bennati M, Hertel MM, Fritscher J, Prisner TF, Weiden N, Hofweber R, Spörner M, Horn G, Kalbitzer HR. High-frequency 94 GHz ENDOR characterization of the metal binding site in wild-type Ras x GDP and its oncogenic mutant G12V in frozen solution. Biochemistry 2006; 45:42-50. [PMID: 16388579 DOI: 10.1021/bi051156k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The guanine nucleotide binding protein Ras plays a central role as molecular switch in cellular signal transduction. Ras cycles between a GDP-bound "off" state and a GTP-bound "on" state. Specific oncogenic mutations in the Ras protein are found in up to 30% of all human tumors. Previous 31P NMR studies had demonstrated that in liquid solution different conformational states in the GDP-bound as well as in the GTP-bound form coexist. High-field EPR spectroscopy of the GDP complexes in solution displayed differences in the ligand sphere of the wild-type complex as compared to its oncogenic mutant Ras(G12V). Only three water ligands were found in the former with respect to four in the G12V mutant [Rohrer, M. et al. (2001) Biochemistry 40, 1884-1889]. These differences were not detected in previous X-ray structures in the crystalline state. In this paper, we employ high-frequency electron nuclear double resonance (ENDOR) spectroscopy to probe the ligand sphere of the metal ion in the GDP-bound state. This technique in combination with selective isotope labeling has enabled us to detect the resonances of nuclei in the first ligand sphere of the ion with high spectral resolution. We have observed the 17O ENDOR spectra of the water ligands, and we have accurately determined the 17O hyperfine coupling with a(iso) = -0.276 mT, supporting the results of previous line shape analysis in solution. Further, the distinct resonances of the alpha-, beta-, and gamma-phosphorus of the bound nucleotides are illustrated in the 31P ENDOR spectra, and their hyperfine tensors lead to distances in agreement with the X-ray structures. Finally, 13C ENDOR spectra of uniformly 13C-labeled Ras(wt) x GDP and Ras(G12V) x GDP complexes as well as of the Ras(wt) x GppNHp and the selectively 1,4-13C-Asp labeled Ras(wt) x GDP complexes have revealed that in frozen solution only one amino acid is ligated to the ion in the GDP state, whereas two are bound in the GppNHp complex. Our results suggest that a second conformational state of the protein, if correlated with a different ligand sphere of the Mn2+ ion, is not populated in the GDP form of Ras at low temperatures in frozen solution.
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Affiliation(s)
- M Bennati
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, J. W. Goethe University of Frankfurt, D-60439 Frankfurt, Germany.
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