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Narváez AJ, Voevodskaya N, Thelander L, Gräslund A. The Involvement of Arg265 of Mouse Ribonucleotide Reductase R2 Protein in Proton Transfer and Catalysis. J Biol Chem 2006; 281:26022-8. [PMID: 16829694 DOI: 10.1074/jbc.m604598200] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ribonucleotide reductase class I enzymes consist of two non-identical subunits, R1 and R2, the latter containing a diiron carboxylate center and a stable tyrosyl radical (Tyr*), both essential for catalysis. Catalysis is known to involve highly conserved amino acid residues covering a range of approximately 35 A and a concerted mechanism involving long range electron transfer, probably coupled to proton transfer. A number of residues involved in electron transfer in both the R1 and R2 proteins have been identified, but no direct model has been presented regarding the proton transfer side of the process. Arg265 is conserved in all known sequences of class Ia R2. In this study we have used site-directed mutagenesis to gain insight into the role of this residue, which lies close to the catalytically essential Asp266 and Trp103. Mutants to Arg265 included replacement by Ala, Glu, Gln, and Tyr. All mutants of Arg265 were found to have no or low catalytic activity with the exception of Arg265 to Glu, which shows approximately 40% of the activity of native R2. We also found that the Arg mutants were capable of stable tyrosyl radical generation, with similar kinetics of radical formation and R1 binding as native R2. Our results, supported by molecular modeling, strongly suggest that Arg265 is involved in the proton-coupled electron transfer pathway and may act as a proton mediator during catalysis.
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Affiliation(s)
- Ana J Narváez
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
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2
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Bassan A, Blomberg MRA, Borowski T, Siegbahn PEM. Theoretical studies of enzyme mechanisms involving high-valent iron intermediates. J Inorg Biochem 2006; 100:727-43. [PMID: 16513176 DOI: 10.1016/j.jinorgbio.2006.01.015] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2005] [Revised: 01/12/2006] [Accepted: 01/16/2006] [Indexed: 01/21/2023]
Abstract
Recent theoretical contributions to the elucidation of mechanisms for iron containing enzymes are reviewed. The method used in most of these studies is hybrid density functional theory with the B3LYP functional. Three classes of enzymes are considered, the mononuclear non-heme enzymes, enzymes containing iron dimers, and heme-containing enzymes. Mechanisms for both dioxygen and substrate activations are discussed. The reactions usually go through two half-cycles, where a high-valent intermediate Fe(IV)O species is created in the first half-cycle, and the substrate reactions involving this intermediate occur in the second half-cycle. Similarities between the three classes of enzymes dominate, but significant differences also exist.
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Affiliation(s)
- Arianna Bassan
- Department of Physics, Stockholm University, AlbaNova University Center, Stockholm Center for Physics, Astronomy and Biotechnology, SE-106 91, Stockholm, Sweden
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3
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Adrait A, Ohrström M, Barra AL, Thelander L, Gräslund A. EPR studies on a stable sulfinyl radical observed in the iron-oxygen-reconstituted Y177F/I263C protein R2 double mutant of ribonucleotide reductase from mouse. Biochemistry 2002; 41:6510-6. [PMID: 12009915 DOI: 10.1021/bi012043d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribonucleotide reductase (RNR) catalyzes the biosynthesis of deoxyribonucleotides. The active enzyme contains a diiron center and a tyrosyl free radical required for enzyme activity. The radical is located at Y177 in the R2 protein of mouse RNR. The radical is formed concomitantly with the mu-oxo-bridged diferric center in a reconstitution reaction between ferrous iron and molecular oxygen in the protein. EPR at 9.6 and 285 GHz was used to investigate the reconstitution reaction in the double-mutant Y177F/I263C of mouse protein R2. The aim was to produce a protein-linked radical derived from the Cys residue in the mutant protein to investigate its formation and characteristics. The mutation Y177F hinders normal radical formation at Y177, and the I263C mutation places a Cys residue at the same distance from the iron center as Y177 in the native protein. In the reconstitution reaction, we observed small amounts of a transient radical with a probable assignment to a peroxy radical, followed by a stable sulfinyl radical, most likely located on C263. The unusual radical stability may be explained by the hydrophobic surroundings of C263, which resemble the hydrophobic pocket surrounding Y177 in native protein R2. The observation of a sulfinyl radical in RNR strengthens the relationship between RNR and another free radical enzyme, pyruvate formate-lyase, where a similar relatively stable sulfinyl radical has been observed in a mutant. Sulfinyl radicals may possibly be considered as stabilized forms of very short-lived thiyl radicals, proposed to be important intermediates in the radical chemistry of RNR.
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Affiliation(s)
- Annie Adrait
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
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4
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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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5
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Dormeyer M, Reckenfelderbäumer N, Ludemann H, Krauth-Siegel RL. Trypanothione-dependent synthesis of deoxyribonucleotides by Trypanosoma brucei ribonucleotide reductase. J Biol Chem 2001; 276:10602-6. [PMID: 11150302 DOI: 10.1074/jbc.m010352200] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Trypanosoma brucei, the causative agent of African sleeping sickness, synthesizes deoxyribonucleotides via a classical eukaryotic class I ribonucleotide reductase. The unique thiol metabolism of trypanosomatids in which the nearly ubiquitous glutathione reductase is replaced by a trypanothione reductase prompted us to study the nature of thiols providing reducing equivalents for the parasite synthesis of DNA precursors. Here we show that the dithiol trypanothione (bis(glutathionyl)spermidine), in contrast to glutathione, is a direct reductant of T. brucei ribonucleotide reductase with a K(m) value of 2 mm. This is the first example of a natural low molecular mass thiol directly delivering reducing equivalents for ribonucleotide reduction. At submillimolar concentrations, the reaction is strongly accelerated by tryparedoxin, a 16-kDa parasite protein with a WCPPC active site motif. The K(m) value of T. brucei ribonucleotide reductase for T. brucei tryparedoxin is about 4 micrometer. The disulfide form of trypanothione is a powerful inhibitor of the tryparedoxin-mediated reaction that may represent a physiological regulation of deoxyribonucleotide synthesis by the redox state of the cell. The trypanothione/tryparedoxin system is a new system providing electrons for a class I ribonucleotide reductase, in addition to the well known thioredoxin and glutaredoxin systems described in other organisms.
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Affiliation(s)
- M Dormeyer
- Biochemie-Zentrum Heidelberg, Universität Heidelberg, 69120 Heidelberg, Germany
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6
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Solomon EI, Brunold TC, Davis MI, Kemsley JN, Lee SK, Lehnert N, Neese F, Skulan AJ, Yang YS, Zhou J. Geometric and electronic structure/function correlations in non-heme iron enzymes. Chem Rev 2000; 100:235-350. [PMID: 11749238 DOI: 10.1021/cr9900275] [Citation(s) in RCA: 1351] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- E I Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305-5080
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7
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Siedow A, Cramm R, Siddiqui RA, Friedrich B. A megaplasmid-borne anaerobic ribonucleotide reductase in Alcaligenes eutrophus H16. J Bacteriol 1999; 181:4919-28. [PMID: 10438763 PMCID: PMC93980 DOI: 10.1128/jb.181.16.4919-4928.1999] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The conjugative 450-kb megaplasmid pHG1 is essential for the anaerobic growth of Alcaligenes eutrophus H16 in the presence of nitrate as the terminal electron acceptor. We identified two megaplasmid-borne genes (nrdD and nrdG) which are indispensable under these conditions. Sequence alignment identified significant similarity of the 76.2-kDa gene product NrdD and the 30.9-kDa gene product NrdG with anaerobic class III ribonucleotide reductases and their corresponding activases. Deletion of nrdD and nrdG in A. eutrophus abolished anaerobic growth and led to the formation of nondividing filamentous cells, a typical feature of bacteria whose DNA synthesis is blocked. Enzyme activity of NrdD-like ribonucleotide reductases is dependent on a stable radical at a glycine residue in a conserved C-terminal motif. A mutant of A. eutrophus with a G650A exchange in NrdD showed the DNA-deficient phenotype as the deletion strain, suggesting that G650 forms the glycyl radical. Analysis of transcriptional and translational fusions indicate that nrdD and nrdG are cotranscribed and that the translation efficiency of nrdD is 40-fold higher than that of nrdG. Thus, the two proteins NrdD and NrdG are not synthesized at a stoichiometric level.
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Affiliation(s)
- A Siedow
- Institut für Biologie der Humboldt-Universität zu Berlin, D-10115 Berlin, Germany
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8
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Basch H, Mogi K, Musaev DG, Morokuma K. Mechanism of the Methane → Methanol Conversion Reaction Catalyzed by Methane Monooxygenase: A Density Functional Study. J Am Chem Soc 1999. [DOI: 10.1021/ja9906296] [Citation(s) in RCA: 129] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Harold Basch
- Contribution from the Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322
| | - Koichi Mogi
- Contribution from the Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322
| | - Djamaladdin G. Musaev
- Contribution from the Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322
| | - Keiji Morokuma
- Contribution from the Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322
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9
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Robins MJ. Mechanism-based inhibition of ribonucleotide reductases: new mechanistic considerations and promising biological applications. NUCLEOSIDES & NUCLEOTIDES 1999; 18:779-93. [PMID: 10432680 DOI: 10.1080/15257779908041565] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Ribonucleotide reductases (RNRs) perform the de novo biosynthesis of 2'-deoxynucleoside 5'-(di or tri)phosphates. Inhibition of RNRs removes a crucial source of genetic components and enhances the probability of salvage incorporation of analogues into DNA. Several laboratories have clarified aspects of the reaction cascades initiated by generation of substrate nucleotide C3' free radicals by RNRs. New considerations for radical-mediated mechanism-based inhibition and biological applications are discussed.
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Affiliation(s)
- M J Robins
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602-5700, USA
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10
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Lassmann G, Eriksson LA, Himo F, Lendzian F, Lubitz W. Electronic Structure of a Transient Histidine Radical in Liquid Aqueous Solution: EPR Continuous-Flow Studies and Density Functional Calculations. J Phys Chem A 1999. [DOI: 10.1021/jp9843454] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Günter Lassmann
- Max-Volmer-Institut fur Biophysikalische Chemie und Biochemie, Technische Universität Berlin, D-10623 Berlin, Germany, Department of Quantum Chemistry, Uppsala University, Box 518, S-75120 Uppsala, Sweden, and Department of Physics, Box 6730, Stockholm University, S-11385 Stockholm, Sweden
| | - Leif A. Eriksson
- Max-Volmer-Institut fur Biophysikalische Chemie und Biochemie, Technische Universität Berlin, D-10623 Berlin, Germany, Department of Quantum Chemistry, Uppsala University, Box 518, S-75120 Uppsala, Sweden, and Department of Physics, Box 6730, Stockholm University, S-11385 Stockholm, Sweden
| | - Fahmi Himo
- Max-Volmer-Institut fur Biophysikalische Chemie und Biochemie, Technische Universität Berlin, D-10623 Berlin, Germany, Department of Quantum Chemistry, Uppsala University, Box 518, S-75120 Uppsala, Sweden, and Department of Physics, Box 6730, Stockholm University, S-11385 Stockholm, Sweden
| | - Friedhelm Lendzian
- Max-Volmer-Institut fur Biophysikalische Chemie und Biochemie, Technische Universität Berlin, D-10623 Berlin, Germany, Department of Quantum Chemistry, Uppsala University, Box 518, S-75120 Uppsala, Sweden, and Department of Physics, Box 6730, Stockholm University, S-11385 Stockholm, Sweden
| | - Wolfgang Lubitz
- Max-Volmer-Institut fur Biophysikalische Chemie und Biochemie, Technische Universität Berlin, D-10623 Berlin, Germany, Department of Quantum Chemistry, Uppsala University, Box 518, S-75120 Uppsala, Sweden, and Department of Physics, Box 6730, Stockholm University, S-11385 Stockholm, Sweden
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11
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Robins MJ, Guo Z, Samano MC, Wnuk SF. Biomimetic Simulation of Free Radical-Initiated Cascade Reactions Postulated To Occur at the Active Site of Ribonucleotide Reductases1. J Am Chem Soc 1999. [DOI: 10.1021/ja983449p] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Morris J. Robins
- Contribution from the Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602-5700
| | - Zhiqiang Guo
- Contribution from the Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602-5700
| | - Mirna C. Samano
- Contribution from the Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602-5700
| | - Stanislaw F. Wnuk
- Contribution from the Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602-5700
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12
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Abstract
Ribonucleotide reductases provide the building blocks for DNA replication in all living cells. Three different classes of enzymes use protein free radicals to activate the substrate. Aerobic class I enzymes generate a tyrosyl radical with an iron-oxygen center and dioxygen, class II enzymes employ adenosylcobalamin, and the anaerobic class III enzymes generate a glycyl radical from S-adenosylmethionine and an iron-sulfur cluster. The X-ray structure of the class I Escherichia coli enzyme, including forms that bind substrate and allosteric effectors, confirms previous models of catalytic and allosteric mechanisms. This structure suggests considerable mobility of the protein during catalysis and, together with experiments involving site-directed mutants, suggests a mechanism for radical transfer from one subunit to the other. Despite large differences between the classes, common catalytic and allosteric mechanisms, as well as retention of critical residues in the protein sequence, suggest a similar tertiary structure and a common origin during evolution. One puzzling aspect is that some organisms contain the genes for several different reductases.
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Affiliation(s)
- A Jordan
- Department of Genetics and Microbiology, Faculty of Sciences, Autonomous University of Barcelona, Bellaterra, Spain
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13
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Gerfen GJ, van der Donk WA, Yu G, McCarthy JR, Jarvi ET, Matthews DP, Farrar C, Griffin RG, Stubbe J. Characterization of a Substrate-Derived Radical Detected during the Inactivation of Ribonucleotide Reductase from Escherichia coli by 2‘-Fluoromethylene-2‘-deoxycytidine 5‘-Diphosphate. J Am Chem Soc 1998. [DOI: 10.1021/ja972166e] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gary J. Gerfen
- Contribution from the Departments of Chemistry and Biology and the Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Marion Merrell Dow Research Institute, 2110 East Galbraith Road, Cincinnati, Ohio 45215
| | - Wilfred A. van der Donk
- Contribution from the Departments of Chemistry and Biology and the Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Marion Merrell Dow Research Institute, 2110 East Galbraith Road, Cincinnati, Ohio 45215
| | - Guixue Yu
- Contribution from the Departments of Chemistry and Biology and the Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Marion Merrell Dow Research Institute, 2110 East Galbraith Road, Cincinnati, Ohio 45215
| | - James R. McCarthy
- Contribution from the Departments of Chemistry and Biology and the Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Marion Merrell Dow Research Institute, 2110 East Galbraith Road, Cincinnati, Ohio 45215
| | - Esa T. Jarvi
- Contribution from the Departments of Chemistry and Biology and the Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Marion Merrell Dow Research Institute, 2110 East Galbraith Road, Cincinnati, Ohio 45215
| | - Donald P. Matthews
- Contribution from the Departments of Chemistry and Biology and the Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Marion Merrell Dow Research Institute, 2110 East Galbraith Road, Cincinnati, Ohio 45215
| | - Christian Farrar
- Contribution from the Departments of Chemistry and Biology and the Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Marion Merrell Dow Research Institute, 2110 East Galbraith Road, Cincinnati, Ohio 45215
| | - Robert G. Griffin
- Contribution from the Departments of Chemistry and Biology and the Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Marion Merrell Dow Research Institute, 2110 East Galbraith Road, Cincinnati, Ohio 45215
| | - JoAnne Stubbe
- Contribution from the Departments of Chemistry and Biology and the Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Marion Merrell Dow Research Institute, 2110 East Galbraith Road, Cincinnati, Ohio 45215
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14
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Affiliation(s)
- JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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15
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Dormeyer M, Schöneck R, Dittmar GA, Krauth-Siegel RL. Cloning, sequencing and expression of ribonucleotide reductase R2 from Trypanosoma brucei. FEBS Lett 1997; 414:449-53. [PMID: 9315738 DOI: 10.1016/s0014-5793(97)01036-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Ribonucleotide reductase (RR) is an attractive drug target molecule. The gene of the R2 protein of Trypanosoma brucei RR (nrd B) has been cloned. It encodes a protein of 337 residues which shows about 60% identity with other eukaryotic R2 proteins. All residues which bind the iron center, the tyrosyl radical or are supposed to participate in the radical transfer are conserved in the trypanosomal protein sequence. Overexpression of the gene in E. coli resulted in 2-5 mg pure R2 protein from 100 ml bacterial cell culture. Northern blot analysis revealed a transcript of 1.85 kb in bloodstream and procyclic forms of the parasite.
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Affiliation(s)
- M Dormeyer
- Biochemie-Zentrum Heidelberg, Ruprecht-Karls-Universität, Germany
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16
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Mulliez E, Fontecave M. Structure and Reactivity of the Metal Centers of Ribonucleotide Reductases. ACTA ACUST UNITED AC 1997. [DOI: 10.1002/cber.19971300303] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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17
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Pulver SC, Froland WA, Lipscomb JD, Solomon EI. Ligand Field Circular Dichroism and Magnetic Circular Dichroism Studies of Component B and Substrate Binding to the Hydroxylase Component of Methane Monooxygenase. J Am Chem Soc 1997. [DOI: 10.1021/ja962854i] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sabine Coates Pulver
- Contribution from the Department of Chemistry, Stanford University, Stanford, California 94305 and Department of Biochemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Wayne A. Froland
- Contribution from the Department of Chemistry, Stanford University, Stanford, California 94305 and Department of Biochemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - John D. Lipscomb
- Contribution from the Department of Chemistry, Stanford University, Stanford, California 94305 and Department of Biochemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Edward I. Solomon
- Contribution from the Department of Chemistry, Stanford University, Stanford, California 94305 and Department of Biochemistry, University of Minnesota, Minneapolis, Minnesota 55455
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18
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Ribonucleotide reductases — a group of enzymes with different metallosites and a similar reaction mechanism. METAL SITES IN PROTEINS AND MODELS 1997. [DOI: 10.1007/3-540-62870-3_5] [Citation(s) in RCA: 128] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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19
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Wallar BJ, Lipscomb JD. Dioxygen Activation by Enzymes Containing Binuclear Non-Heme Iron Clusters. Chem Rev 1996; 96:2625-2658. [PMID: 11848839 DOI: 10.1021/cr9500489] [Citation(s) in RCA: 977] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bradley J. Wallar
- Department of Biochemistry, Medical School, 4-225 Millard Hall, University of Minnesota, Minneapolis, Minnesota 55455
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20
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Ormö M, Sjöberg BM. The Cys292-->Ala substitution in protein R1 of class I ribonucleotide reductase from Escherichia coli has a global effect on nucleotide binding at the specificity-determining allosteric site. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 241:363-7. [PMID: 8917431 DOI: 10.1111/j.1432-1033.1996.00363.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Ribonucleotide reductase from aerobically grown Escherichia coli is allosterically regulated, both with respect to general activity and substrate specificity. Protein R1, the homodimeric enzyme component which harbours binding sites for allosteric effectors (nucleoside triphosphates) as well as substrates (ribonucleoside diphosphates), has been engineered at Cys292 close to the dimer interaction area. This residue was earlier shown to be specifically photoaffinity labelled with the allosteric nucleotide dTTP. In this study the effect of the Cys292-->Ala substitution is shown to be an overall diminished nucleotide binding at the specificity site reflected in Kd values for dTTP, dGTP and dATP higher by more than one order of magnitude with respect to wild type. The mutant protein's interaction with other protein components of the ribonucleotide reductase system was unaffected by the mutation. These results show that Cys292 in protein R1 of class I ribonucleotide reductase from E. coli is located in the allosteric specificity site.
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Affiliation(s)
- M Ormö
- Department of Molecular Biology, Stockholm University, Sweden
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21
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Logan DT, Su XD, Aberg A, Regnström K, Hajdu J, Eklund H, Nordlund P. Crystal structure of reduced protein R2 of ribonucleotide reductase: the structural basis for oxygen activation at a dinuclear iron site. Structure 1996; 4:1053-64. [PMID: 8805591 DOI: 10.1016/s0969-2126(96)00112-8] [Citation(s) in RCA: 210] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
BACKGROUND Ribonucleotide reductases (RNRs) catalyze the formation of the deoxyribonucleotides that are essential for DNA synthesis. The R2 subunit of Escherichia coli RNR is a homodimer containing one dinuclear iron centre per monomer. A tyrosyl radical is essential for catalysis, and is formed via a reaction in which the reduced, diferrous form of the iron centre activates dioxygen. To help understand the mechanism of oxygen activation, we examined the structure of the diferrous form of R2. RESULTS The crystal structures of reduced forms of both wild type R2 and a mutant of R2 (Ser211--> Ala) have been determined at 1.7 A and 2.2 A resolution, respectively. The diferrous iron centre was compared to the previously determined structure of the oxidized, diferric form of R2. In both forms of R2 the iron centre is coordinated by the same carboxylate dominated ligand sphere, but in the reduced form there are clear conformational changes in three of the carboxylate ligands and the bridging mu-oxo group and two water molecules are lost. In the reduced form of R2 the coordination number decreases from six to four for both ferrous ions, explaining their high reactivity towards dioxygen. The structure of the mutant Ser211--> Ala, known to have impaired reduction kinetics, shows a large conformational change in one of the neighbouring helices although the iron coordination is very similar to the wild type protein. CONCLUSIONS Carboxylate shifts are often important for carboxylate coordinated metal clusters; they allow the metals to achieve different coordination modes in redox reactions. In the case of reduced R2 these carboxylate shifts allow the formation of accessible reaction sites for dioxygen. The Ser211--> Ala mutant displays a conformational change in the helix containing the mutation, explaining its altered reduction kinetics.
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Affiliation(s)
- D T Logan
- Department of Molecular Biology University of Stockholm S-106 91 Stockholm Sweden
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22
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Lendzian F, Sahlin M, MacMillan F, Bittl R, Fiege R, Pötsch S, Sjöberg BM, Gräslund A, Lubitz W, Lassmann G. Electronic Structure of Neutral Tryptophan Radicals in Ribonucleotide Reductase Studied by EPR and ENDOR Spectroscopy. J Am Chem Soc 1996. [DOI: 10.1021/ja960917r] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Friedhelm Lendzian
- Contribution from the Max-Volmer-Institut für Biophysikalische Chemie und Biochemie, Technische Universität Berlin, D-10623-Berlin, Germany, Department of Molecular Biology and Department of Biophysics, University of Stockholm, S-10691, Stockholm, Sweden, and Max-Delbrück-Centrum für Molekulare Medizin, D-13125-Berlin, Germany
| | - Margareta Sahlin
- Contribution from the Max-Volmer-Institut für Biophysikalische Chemie und Biochemie, Technische Universität Berlin, D-10623-Berlin, Germany, Department of Molecular Biology and Department of Biophysics, University of Stockholm, S-10691, Stockholm, Sweden, and Max-Delbrück-Centrum für Molekulare Medizin, D-13125-Berlin, Germany
| | - Fraser MacMillan
- Contribution from the Max-Volmer-Institut für Biophysikalische Chemie und Biochemie, Technische Universität Berlin, D-10623-Berlin, Germany, Department of Molecular Biology and Department of Biophysics, University of Stockholm, S-10691, Stockholm, Sweden, and Max-Delbrück-Centrum für Molekulare Medizin, D-13125-Berlin, Germany
| | - Robert Bittl
- Contribution from the Max-Volmer-Institut für Biophysikalische Chemie und Biochemie, Technische Universität Berlin, D-10623-Berlin, Germany, Department of Molecular Biology and Department of Biophysics, University of Stockholm, S-10691, Stockholm, Sweden, and Max-Delbrück-Centrum für Molekulare Medizin, D-13125-Berlin, Germany
| | - Robert Fiege
- Contribution from the Max-Volmer-Institut für Biophysikalische Chemie und Biochemie, Technische Universität Berlin, D-10623-Berlin, Germany, Department of Molecular Biology and Department of Biophysics, University of Stockholm, S-10691, Stockholm, Sweden, and Max-Delbrück-Centrum für Molekulare Medizin, D-13125-Berlin, Germany
| | - Stephan Pötsch
- Contribution from the Max-Volmer-Institut für Biophysikalische Chemie und Biochemie, Technische Universität Berlin, D-10623-Berlin, Germany, Department of Molecular Biology and Department of Biophysics, University of Stockholm, S-10691, Stockholm, Sweden, and Max-Delbrück-Centrum für Molekulare Medizin, D-13125-Berlin, Germany
| | - Britt-Marie Sjöberg
- Contribution from the Max-Volmer-Institut für Biophysikalische Chemie und Biochemie, Technische Universität Berlin, D-10623-Berlin, Germany, Department of Molecular Biology and Department of Biophysics, University of Stockholm, S-10691, Stockholm, Sweden, and Max-Delbrück-Centrum für Molekulare Medizin, D-13125-Berlin, Germany
| | - Astrid Gräslund
- Contribution from the Max-Volmer-Institut für Biophysikalische Chemie und Biochemie, Technische Universität Berlin, D-10623-Berlin, Germany, Department of Molecular Biology and Department of Biophysics, University of Stockholm, S-10691, Stockholm, Sweden, and Max-Delbrück-Centrum für Molekulare Medizin, D-13125-Berlin, Germany
| | - Wolfgang Lubitz
- Contribution from the Max-Volmer-Institut für Biophysikalische Chemie und Biochemie, Technische Universität Berlin, D-10623-Berlin, Germany, Department of Molecular Biology and Department of Biophysics, University of Stockholm, S-10691, Stockholm, Sweden, and Max-Delbrück-Centrum für Molekulare Medizin, D-13125-Berlin, Germany
| | - Günter Lassmann
- Contribution from the Max-Volmer-Institut für Biophysikalische Chemie und Biochemie, Technische Universität Berlin, D-10623-Berlin, Germany, Department of Molecular Biology and Department of Biophysics, University of Stockholm, S-10691, Stockholm, Sweden, and Max-Delbrück-Centrum für Molekulare Medizin, D-13125-Berlin, Germany
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23
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Ekberg M, Sahlin M, Eriksson M, Sjöberg BM. Two conserved tyrosine residues in protein R1 participate in an intermolecular electron transfer in ribonucleotide reductase. J Biol Chem 1996; 271:20655-9. [PMID: 8702814 DOI: 10.1074/jbc.271.34.20655] [Citation(s) in RCA: 110] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The enzyme ribonucleotide reductase consists of two nonidentical proteins, R1 and R2, which are each inactive alone. R1 contains the active site and R2 contains a stable tyrosyl radical essential for catalysis. The reduction of ribonucleotides is radical-based, and a long range electron transfer chain between the active site in R1 and the radical in R2 has been suggested. To find evidence for such an electron transfer chain in Escherichia coli ribonucleotide reductase, we converted two conserved tyrosines in R1 into phenylalanines by site-directed mutagenesis. The mutant proteins were shown to be enzymatically inactive. In addition, the mechanism-based inhibitor 2'-azido-2'-deoxy-CDP was incapable of scavenging the R2 radical, and no azido-CDP-derived radical intermediate was formed. We also show that the loss of enzymatic activity was not due to impaired R1-R2 complex formation or substrate binding. Based on these results, we predict that the two tyrosines, Tyr-730 and Tyr-731, are part of a hydrogen-bonded network that constitutes an electron transfer pathway in ribonucleotide reductase. It is demonstrated that there is no electron delocalization over these tyrosines in the resting wild-type complex.
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Affiliation(s)
- M Ekberg
- Department of Molecular Biology, University of Stockholm, S-10691 Stockholm, Sweden
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24
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Larsson A, Climent I, Nordlund P, Sahlin M, Sjöberg BM. Structural and functional characterization of two mutated R2 proteins of Escherichia coli ribonucleotide reductase. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 237:58-63. [PMID: 8620893 DOI: 10.1111/j.1432-1033.1996.0058n.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The R2 protein of ribonucleotide reductase from Escherichia coli is a homodimeric tyrosyl-radical-containing enzyme with two identical dinuclear iron centers. Two randomly generated genomic mutants, nrdB-1 and nrdB-2, that produce R2 enzymes with low enzymatic activity, have been cloned and characterized to identify functionally important residues and areas of the enzyme. The mutations were identified as Pro348 to leucine in nrdB-1 and Leu304 to phenylalanine in nrdB-2. Both mutations are the results of single amino acid replacements of non-conserved residues. The three-dimensional structures of [L348]R2 and [F304]R2 have been determined to 0.26-nm and 0.28-nm resolution, respectively. Compared with wild-type R2, [L348]R2 binds with higher affinity to R1, probably due to increased flexibility of its C-terminus. Since the three-dimensional structure, iron-center properties and radical properties of [L348]R2 are comparable to those of wild-type R2, the low catalytic activity of the holoenzyme is probably caused by a perturbed interaction between R2 and R1. The [F304]R2 enzyme has increased radical sensitivity and low catalytic activity compared with wild-type R2. In [F304]R2 the only significant change in structure is that the evolutionary conserved Ser211 forms a different hydrogen bond to a distorted helix. The results obtained with [F304]R2 indicate that structural changes in E. coli R2 in the vicinity of this helix distortion can influence the catalytic activity of the holoenzyme.
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Affiliation(s)
- A Larsson
- Department of Molecular Biology, University of Stockholm, Sweden
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25
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Sun X, Ollagnier S, Schmidt PP, Atta M, Mulliez E, Lepape L, Eliasson R, Gräslund A, Fontecave M, Reichard P, Sjöberg BM. The Free Radical of the Anaerobic Ribonucleotide Reductase from Escherichia coli Is at Glycine 681. J Biol Chem 1996. [DOI: 10.1074/jbc.271.12.6827] [Citation(s) in RCA: 117] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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