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Chakraborty S, Mukherjee P, Sengupta R. Ribonucleotide reductase: Implications of thiol S-nitrosylation and tyrosine nitration for different subunits. Nitric Oxide 2022; 127:26-43. [PMID: 35850377 DOI: 10.1016/j.niox.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/20/2022] [Accepted: 07/08/2022] [Indexed: 11/20/2022]
Abstract
Ribonucleotide reductase (RNR) is a multi-subunit enzyme responsible for catalyzing the rate-limiting step in the production of deoxyribonucleotides essential for DNA synthesis and repair. The active RNR complex is composed of multimeric R1 and R2 subunits. The RNR catalysis involves the formation of tyrosyl radicals in R2 subunits and thiyl radicals in R1 subunits. Despite the quaternary structure and cofactor diversity, all the three classes of RNR have a conserved cysteine residue at the active site which is converted into a thiyl radical that initiates the substrate turnover, suggesting that the catalytic mechanism is somewhat similar for all three classes of the RNR enzyme. Increased RNR activity has been associated with malignant transformation, cancer cell growth, and tumorigenesis. Efforts concerning the understanding of RNR inhibition in designing potent RNR inhibitors/drugs as well as developing novel approaches for antibacterial, antiviral treatments, and cancer therapeutics with improved radiosensitization have been made in clinical research. This review highlights the precise and potent roles of NO in RNR inhibition by targeting both the subunits. Under nitrosative stress, the thiols of the R1 subunits have been found to be modified by S-nitrosylation and the tyrosyl radicals of the R2 subunits have been modified by nitration. In view of the recent advances and progresses in the field of nitrosative modifications and its fundamental role in signaling with implications in health and diseases, the present article focuses on the regulations of RNR activity by S-nitrosylation of thiols (R1 subunits) and nitration of tyrosyl residues (R2 subunits) which will further help in designing new drugs and therapies.
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Affiliation(s)
- Surupa Chakraborty
- Amity Institute of Biotechnology, Amity University, Kolkata, 700135, West Bengal, India
| | - Prerona Mukherjee
- Amity Institute of Biotechnology, Amity University, Kolkata, 700135, West Bengal, India
| | - Rajib Sengupta
- Amity Institute of Biotechnology, Amity University, Kolkata, 700135, West Bengal, India.
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The Cell Killing Mechanisms of Hydroxyurea. Genes (Basel) 2016; 7:genes7110099. [PMID: 27869662 PMCID: PMC5126785 DOI: 10.3390/genes7110099] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/03/2016] [Accepted: 11/09/2016] [Indexed: 11/23/2022] Open
Abstract
Hydroxyurea is a well-established inhibitor of ribonucleotide reductase that has a long history of scientific interest and clinical use for the treatment of neoplastic and non-neoplastic diseases. It is currently the staple drug for the management of sickle cell anemia and chronic myeloproliferative disorders. Due to its reversible inhibitory effect on DNA replication in various organisms, hydroxyurea is also commonly used in laboratories for cell cycle synchronization or generating replication stress. However, incubation with high concentrations or prolonged treatment with low doses of hydroxyurea can result in cell death and the DNA damage generated at arrested replication forks is generally believed to be the direct cause. Recent studies in multiple model organisms have shown that oxidative stress and several other mechanisms may contribute to the majority of the cytotoxic effect of hydroxyurea. This review aims to summarize the progress in our understanding of the cell-killing mechanisms of hydroxyurea, which may provide new insights towards the improvement of chemotherapies that employ this agent.
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Nicolet Y, Zeppieri L, Amara P, Fontecilla-Camps JC. Crystal Structure of Tryptophan Lyase (NosL): Evidence for Radical Formation at the Amino Group of Tryptophan. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201407320] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Nicolet Y, Zeppieri L, Amara P, Fontecilla-Camps JC. Crystal Structure of Tryptophan Lyase (NosL): Evidence for Radical Formation at the Amino Group of Tryptophan. Angew Chem Int Ed Engl 2014; 53:11840-4. [DOI: 10.1002/anie.201407320] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 08/13/2014] [Indexed: 12/23/2022]
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Rogers MS, Tyler EM, Akyumani N, Kurtis CR, Spooner RK, Deacon SE, Tamber S, Firbank SJ, Mahmoud K, Knowles PF, Phillips SEV, McPherson MJ, Dooley DM. The stacking tryptophan of galactose oxidase: a second-coordination sphere residue that has profound effects on tyrosyl radical behavior and enzyme catalysis. Biochemistry 2007; 46:4606-18. [PMID: 17385891 PMCID: PMC2532978 DOI: 10.1021/bi062139d] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The function of the stacking tryptophan, W290, a second-coordination sphere residue in galactose oxidase, has been investigated via steady-state kinetics measurements, absorption, CD and EPR spectroscopy, and X-ray crystallography of the W290F, W290G, and W290H variants. Enzymatic turnover is significantly slower in the W290 variants. The Km for D-galactose for W290H is similar to that of the wild type, whereas the Km is greatly elevated in W290G and W290F, suggesting a role for W290 in substrate binding and/or positioning via the NH group of the indole ring. Hydrogen bonding between W290 and azide in the wild type-azide crystal structure are consistent with this function. W290 modulates the properties and reactivity of the redox-active tyrosine radical; the Y272 tyrosyl radicals in both the W290G and W290H variants have elevated redox potentials and are highly unstable compared to the radical in W290F, which has properties similar to those of the wild-type tyrosyl radical. W290 restricts the accessibility of the Y272 radical site to solvent. Crystal structures show that Y272 is significantly more solvent exposed in the W290G variant but that W290F limits solvent access comparable to the wild-type indole side chain. Spectroscopic studies indicate that the Cu(II) ground states in the semireduced W290 variants are very similar to that of the wild-type protein. In addition, the electronic structures of W290X-azide complexes are also closely similar to the wild-type electronic structure. Azide binding and azide-mediated proton uptake by Y495 are perturbed in the variants, indicating that tryptophan also modulates the function of the catalytic base (Y495) in the wild-type enzyme. Thus, W290 plays multiple critical roles in enzyme catalysis, affecting substrate binding, the tyrosyl radical redox potential and stability, and the axial tyrosine function.
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Affiliation(s)
- Melanie S. Rogers
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Ejan M. Tyler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Nana Akyumani
- Astbury Centre for Structural Molecular Biology & Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Christian R. Kurtis
- Astbury Centre for Structural Molecular Biology & Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - R. Kate Spooner
- Astbury Centre for Structural Molecular Biology & Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Sarah E. Deacon
- Astbury Centre for Structural Molecular Biology & Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Sunita Tamber
- Astbury Centre for Structural Molecular Biology & Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Susan J. Firbank
- Astbury Centre for Structural Molecular Biology & Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Khaled Mahmoud
- Astbury Centre for Structural Molecular Biology & Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Peter F. Knowles
- Astbury Centre for Structural Molecular Biology & Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Simon E. V. Phillips
- Astbury Centre for Structural Molecular Biology & Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Michael J. McPherson
- Astbury Centre for Structural Molecular Biology & Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - David M. Dooley
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
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Beuning PJ, Simon SM, Godoy VG, Jarosz DF, Walker GC. Characterization of Escherichia coli translesion synthesis polymerases and their accessory factors. Methods Enzymol 2006; 408:318-40. [PMID: 16793378 DOI: 10.1016/s0076-6879(06)08020-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Members of the Y family of DNA polymerases are specialized to replicate lesion-containing DNA. However, they lack 3'-5' exonuclease activity and have reduced fidelity compared to replicative polymerases when copying undamaged templates, and thus are potentially mutagenic. Y family polymerases must be tightly regulated to prevent aberrant mutations on undamaged DNA while permitting replication only under conditions of DNA damage. These polymerases provide a mechanism of DNA damage tolerance, confer cellular resistance to a variety of DNA-damaging agents, and have been implicated in bacterial persistence. The Y family polymerases are represented in all domains of life. Escherichia coli possesses two members of the Y family, DNA pol IV (DinB) and DNA pol V (UmuD'(2)C), and several regulatory factors, including those encoded by the umuD gene that influence the activity of UmuC. This chapter outlines procedures for in vivo and in vitro analysis of these proteins. Study of the E. coli Y family polymerases and their accessory factors is important for understanding the broad principles of DNA damage tolerance and mechanisms of mutagenesis throughout evolution. Furthermore, study of these enzymes and their role in stress-induced mutagenesis may also give insight into a variety of phenomena, including the growing problem of bacterial antibiotic resistance.
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Affiliation(s)
- Penny J Beuning
- Department of Biology, Massachusetts Institute of Technology, Cambridge, USA
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Sneeden JL, Loeb LA. Mutations in the R2 subunit of ribonucleotide reductase that confer resistance to hydroxyurea. J Biol Chem 2004; 279:40723-8. [PMID: 15262976 DOI: 10.1074/jbc.m402699200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ribonucleotide reductase is an essential enzyme that catalyzes the reduction of ribonucleotides to deoxyribonucleotides for use in DNA synthesis. Ribonucleotide reductase from Escherichia coli consists of two subunits, R1 and R2. The R2 subunit contains an unusually stable radical at tyrosine 122 that participates in catalysis. Buried deep within a hydrophobic pocket, the radical is inaccessible to solvent although subject to inactivation by radical scavengers. One such scavenger, hydroxyurea, is a highly specific inhibitor of ribonucleotide reductase and therefore of DNA synthesis; thus it is an important anticancer and antiviral agent. The mechanism of radical access remains to be established; however, small molecules may be able to access Tyr-122 directly via channels from the surface of the protein. We used random oligonucleotide mutagenesis to create a library of 200,000 R2 mutants containing random substitutions at five contiguous residues (Ile-74, Ser-75, Asn-76, Leu-77, Lys-78) that partially comprise one side of a channel where Tyr-122 is visible from the protein surface. We subjected this library to increasing concentrations of hydroxyurea and identified mutants that enhance survival more than 1000-fold over wild-type R2 at high drug concentrations. Repetitive selections yielded S75T as the predominant R2 mutant in our library. Purified S75TR2 exhibits a radical half-life that is 50% greater than wild-type R2 in the presence of hydroxyurea. These data represent the first demonstration of R2 protein mutants in E. coli that are highly resistant to hydroxyurea; elucidation of their mechanism of resistance may provide valuable insight into the development of more effective inhibitors.
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Affiliation(s)
- Jessica L Sneeden
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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Miller JE, Grădinaru C, Crane BR, Di Bilio AJ, Wehbi WA, Un S, Winkler JR, Gray HB. Spectroscopy and reactivity of a photogenerated tryptophan radical in a structurally defined protein environment. J Am Chem Soc 2004; 125:14220-1. [PMID: 14624538 DOI: 10.1021/ja037203i] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Near-UV irradiation of structurally characterized [Re(I)(CO)3(1,10-phenanthroline)(Q107H)](W48F/Y72F/H83Q/Y108W)AzM(II) [Az = Pseudomonas aeruginosa azurin, M = Cu, Zn]/[Co(NH3)5Cl]Cl2 produces a tryptophan radical (W108*) with unprecedented kinetic stability. After rapid formation (k = 2.8 x 106 s-1), the radical persists for more than 5 h at room temperature in the folded ReAzM(II) structure. The absorption spectrum of ReAz(W108*)M(II) exhibits maxima at 512 and 536 nm. Oxidation of K4[Mo(CN)8] by ReAz(W108*)Zn(II) places the W108*/W108 reduction potential in the protein above 0.8 V vs NHE.
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Affiliation(s)
- Jeremiah E Miller
- Beckman Institute, California Institute of Technology, CA 91125, USA
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Affiliation(s)
- Marc Fontecave
- Laboratoire de Chimie ét Biochimie des Centres Redox Biologiques, DBMS-CEA/CNRS/Université Joseph Fourier, 38054 Grenoble, France
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Davydov A, Öhrström M, Liu A, Thelander L, Gräslund A. Chemical reduction of the diferric/radical center in protein R2 from mouse ribonucleotide reductase is independent of the proposed radical transfer pathway. Inorganica Chim Acta 2002. [DOI: 10.1016/s0020-1693(01)00750-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Eklund H, Uhlin U, Färnegårdh M, Logan DT, Nordlund P. Structure and function of the radical enzyme ribonucleotide reductase. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2001; 77:177-268. [PMID: 11796141 DOI: 10.1016/s0079-6107(01)00014-1] [Citation(s) in RCA: 256] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ribonucleotide reductases (RNRs) catalyze all new production in nature of deoxyribonucleotides for DNA synthesis by reducing the corresponding ribonucleotides. The reaction involves the action of a radical that is produced differently for different classes of the enzyme. Class I enzymes, which are present in eukaryotes and microorganisms, use an iron center to produce a stable tyrosyl radical that is stored in one of the subunits of the enzyme. The other classes are only present in microorganisms. Class II enzymes use cobalamin for radical generation and class III enzymes, which are found only in anaerobic organisms, use a glycyl radical. The reductase activity is in all three classes contained in enzyme subunits that have similar structures containing active site cysteines. The initiation of the reaction by removal of the 3'-hydrogen of the ribose by a transient cysteinyl radical is a common feature of the different classes of RNR. This cysteine is in all RNRs located on the tip of a finger loop inserted into the center of a special barrel structure. A wealth of structural and functional information on the class I and class III enzymes can now give detailed views on how these enzymes perform their task. The class I enzymes demonstrate a sophisticated pattern as to how the free radical is used in the reaction, in that it is only delivered to the active site at exactly the right moment. RNRs are also allosterically regulated, for which the structural molecular background is now starting to be revealed.
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Affiliation(s)
- H Eklund
- Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala Biomedical Center, Box 590, S-751 24, Uppsala, Sweden.
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Un S, Gerez C, Elleingand E, Fontecave M. Sensitivity of tyrosyl radical g-values to changes in protein structure: a high-field EPR study of mutants of ribonucleotide reductase. J Am Chem Soc 2001; 123:3048-54. [PMID: 11457015 DOI: 10.1021/ja003650b] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The local electrostatic environment plays a critical role in determining the physicochemical properties of reactive radicals in proteins. High-field electron paramagnetic resonance (HF-EPR) spectroscopy has been used to determine the sensitivity of the tyrosyl radical g-values to local electrostatic environment. Site-specific mutants of ribonucleotide reductase from Escherichia coli were used to study the effect of introducing a charge group on the HF-EPR spectrum of the stable tyrosyl (Y122) radical. The changes affected by the mutations were small, but measurable. Mutation of isoleucine-74 to an arginine (I74R) or lysine (I74K) induced disorder in the hyperfine interactions. Similar effects were observed for the mutation of valine-136 to an arginine (V136R) or asparagine (V136N). For five or six mutants studied, the g(x)() component of the g-tensor was distributed. For the isoleucine-74 to lysine (I74K) and leucine-77 to phenylalanine (L77F) mutants, a shift of 1 x 10(-)(4) in g(x)() value was also detected. For the I74K mutant, it is shown that the shift is consistent with the introduction of a charged residue, but cannot be distinguished from changes in the electrostatic effect of the nearby diiron center. For the L77F mutant, the shift is induced by the diiron center. Using existing tyrosyl radical g-tensor measurements, we have developed a simple effective charge model that allows us to rationalize the effect of the local electrostatic environments in a number of proteins.
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Affiliation(s)
- S Un
- Département de Biologie Cellulaire et Moléculaire, Section de Bioénergétique, CNRS URA2096, CEA Saclay, F-91191 Gif-sur-Yvette, France
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Guittet O, Decottignies P, Serani L, Henry Y, Le Maréchal P, Laprévote O, Lepoivre M. Peroxynitrite-mediated nitration of the stable free radical tyrosine residue of the ribonucleotide reductase small subunit. Biochemistry 2000; 39:4640-8. [PMID: 10769119 DOI: 10.1021/bi992206m] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Ribonucleotide reductase activity is rate-limiting for DNA synthesis, and inhibition of this enzyme supports cytostatic antitumor effects of inducible NO synthase. The small R2 subunit of class I ribonucleotide reductases contains a stable free radical tyrosine residue required for activity. This radical is destroyed by peroxynitrite, which also inactivates the protein and induces nitration of tyrosine residues. In this report, nitrated residues in the E. coli R2 protein were identified by UV-visible spectroscopy, mass spectrometry (ESI-MS), and tryptic peptide sequencing. Mass analysis allowed the detection of protein R2 as a native dimer with two iron clusters per subunit. The measured mass was 87 032 Da, compared to a calculated value of 87 028 Da. Peroxynitrite treatment preserved the non-heme iron center and the dimeric form of the protein. A mean of two nitrotyrosines per E. coli protein R2 dimer were obtained at 400 microM peroxynitrite. Only 3 out of the 16 tyrosines were nitrated, including the free radical Tyr122. Despite its radical state, that should favor nitration, the buried Tyr122 was not nitrated with a high yield, probably owing to its restricted accessibility. Dose-response curves for Tyr122 nitration and loss of the free radical were superimposed. However, protein R2 inactivation was higher than nitration of Tyr122, suggesting that nitration of the nonconserved Tyr62 and Tyr289 might be also of importance for peroxynitrite-mediated inhibition of E. coli protein R2.
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Affiliation(s)
- O Guittet
- Unité 8619, Centre National de la Recherche Scientifique, Université Paris-Sud, Orsay, France
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Guittet O, Ducastel B, Salem JS, Henry Y, Rubin H, Lemaire G, Lepoivre M. Differential sensitivity of the tyrosyl radical of mouse ribonucleotide reductase to nitric oxide and peroxynitrite. J Biol Chem 1998; 273:22136-44. [PMID: 9705359 DOI: 10.1074/jbc.273.34.22136] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ribonucleotide reductase is essential for DNA synthesis in cycling cells. It has been previously shown that the catalytically competent tyrosyl free radical of its small R2 subunit (R2-Y.) is scavenged in tumor cells co-cultured with macrophages expressing a nitric oxide synthase II activity. We now demonstrate a loss of R2-Y. induced either by .NO or peroxynitrite in vitro. The .NO effect is reversible and followed by an increase in ferric iron release from mouse protein R2. A similar increased iron lability in radical-free, diferric metR2 protein suggests reciprocal stabilizing interactions between R2-Y. and the diiron center in the mouse protein. Scavenging of R2-Y. by peroxynitrite is irreversible and paralleled to an irreversible loss of R2 activity. Formation of nitrotyrosine and dihydroxyphenylalanine was also detected in peroxynitrite-modified protein R2. In R2-overexpressing tumor cells co-cultured with activated murine macrophages, scavenging of R2-Y. following NO synthase II induction was fully reversible, even when endogenous production of peroxynitrite was induced by triggering NADPH oxidase activity with a phorbol ester. Our results did not support the involvement of peroxynitrite in R2-Y. scavenging by macrophage .NO synthase II activity. They confirmed the preponderant physiological role of .NO in the process.
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Affiliation(s)
- O Guittet
- Unité 571, Centre National de la Recherche Scientifique, Bâtiment 430, Université Paris-Sud, France
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