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Biophysical investigations of ribonucleotide reductase: Activation and inhibition mechanisms
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. (Astrid Gräslund)
2010 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Ribonucleotide reductase (RNR) is the enzyme responsible for de novo synthesis of deoxyribonucleotides, needed for both synthesis and repair of cellular DNA. The RNRs known so far are divided into three distinct classes; I, II and III. The conventional class I enzyme is composed of two separate subunits. The larger R1 subunit contains the active site, whereas the smaller R2 subunit contains a system specialized in forming, transporting and stabilizing a tyrosyl free radical.

Recently a new class Ic RNR was discovered in the bacterium Chlamydia trachomatis. It differs from the conventional class Ia and b RNRs in that it has a phenylalanine at the otherwise conserved tyrosyl radical harboring residue in its R2 subunit. Additionally the metal cluster shows some unusual aspects, of which the most striking perhaps is that the most red-ox active form is a mixed Mn-Fe cluster, instead of the normal Fe-Fe counterpart.

In this work several biochemical and biophysical methods were used to study activation and inhibition mechanisms in RNR from various class I species. The results from studying the oxygen activation confirm the role of the iron ligand E238 as a key residue for controlling the outcome of the reaction in E. coli protein R2. The finding of a stable sulfinyl radical after reconstitution of the R2 Y177F/I263C variant from mouse indicates that sulfinyl radicals may possibly be considered as stabilized forms of very short-lived thiyl radicals, proposed to be important in the radical chemistry of RNR. The investigation of the role of the proposed radical transfer pathway during chemical reduction of the iron/radical center shows that no specific pathway is required for the reduction of protein R2 from mouse. The results from inhibition studies of C. trachomatis demonstrate that the same mechanism of inhibition functions on this new class Ic RNR, however less efficiently than in class Ia and b.

 

Place, publisher, year, edition, pages
Stockholm: Department of Biochemistry and Biophysics, Stockholm University , 2010. , 52 p.
National Category
Biophysics
Research subject
Biophysics
Identifiers
URN: urn:nbn:se:su:diva-39043ISBN: 978-91-7447-088-8 (print)OAI: oai:DiVA.org:su-39043DiVA: diva2:318270
Public defence
2010-06-10, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 10:00 (English)
Opponent
Supervisors
Note
At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 3: Manuscript.Available from: 2010-05-19 Created: 2010-05-06 Last updated: 2010-05-07Bibliographically approved
List of papers
1. Restoring proper radical generation by azide binding to the iron site of the E238A mutant R2 protein of ribonucleotide reductase from Escherichia coli.
Open this publication in new window or tab >>Restoring proper radical generation by azide binding to the iron site of the E238A mutant R2 protein of ribonucleotide reductase from Escherichia coli.
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2001 (English)In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 276, no 29, 26852-26859 p.Article in journal (Refereed) Published
Abstract [en]

The enzyme activity of Escherichia coli ribonucleotide reductase requires the presence of a stable tyrosyl free radical and diiron center in its smaller R2 component. The iron/radical site is formed in a reconstitution reaction between ferrous iron and molecular oxygen in the protein. The reaction is known to proceed via a paramagnetic intermediate X, formally a Fe(III)-Fe(IV) state. We have used 9.6 GHz and 285 GHz EPR to investigate intermediates in the reconstitution reaction in the iron ligand mutant R2 E238A with or without azide, formate, or acetate present. Paramagnetic intermediates, i.e. a long-living X-like intermediate and a transient tyrosyl radical, were observed only with azide and under none of the other conditions. A crystal structure of the mutant protein R2 E238A/Y122F with a diferrous iron site complexed with azide was determined. Azide was found to be a bridging ligand and the absent Glu-238 ligand was compensated for by azide and an extra coordination from Glu-204. A general scheme for the reconstitution reaction is presented based on EPR and structure results. This indicates that tyrosyl radical generation requires a specific ligand coordination with 4-coordinate Fe1 and 6-coordinate Fe2 after oxygen binding to the diferrous site.

Keyword
Azides/*metabolism, Electron Spin Resonance Spectroscopy, Escherichia coli/*enzymology, Free Radicals, Iron/*metabolism, Mutagenesis, Protein Binding, Ribonucleotide Reductases/chemistry/genetics/*metabolism, Substrate Specificity, Tyrosine/metabolism
Identifiers
urn:nbn:se:su:diva-19867 (URN)10.1074/jbc.M008190200 (DOI)11328804 (PubMedID)
Available from: 2007-11-20 Created: 2007-11-20 Last updated: 2017-12-13Bibliographically approved
2. EPR studies on a stable sulfinyl radical observed in the iron-oxygen reconstituted Y177F/I263C protein double mutant of ribonucleotide reductase from mouse
Open this publication in new window or tab >>EPR studies on a stable sulfinyl radical observed in the iron-oxygen reconstituted Y177F/I263C protein double mutant of ribonucleotide reductase from mouse
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2002 (English)In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 41, no 20, 6510-6516 p.Article in journal (Refereed) Published
Abstract [en]

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 μ-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.

Identifiers
urn:nbn:se:su:diva-39041 (URN)10.1021/bi012043d (DOI)
Available from: 2010-05-06 Created: 2010-05-06 Last updated: 2017-12-12Bibliographically approved
3. Chemical reduction of the diferric/radical center in protein R2 from mouse ribonucleotide reductase is independent of the proposed radical transfer pathway
Open this publication in new window or tab >>Chemical reduction of the diferric/radical center in protein R2 from mouse ribonucleotide reductase is independent of the proposed radical transfer pathway
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2002 (English)In: Inorganica Chimica Acta, ISSN 0020-1693, E-ISSN 1873-3255, Vol. 331, no 1, 65-72 p.Article in journal (Refereed) Published
Abstract [en]

The rates of reduction of the diferric/radical center in mouse ribonucleotide reductase protein R2 were studied by light absorption and EPR in the native protein and in three point mutants of conserved residues involved in the proposed radical transfer pathway (D266A, W103Y) or in the unstructured C terminal domain (Y370W). The pseudo-first order rate constants for chemical reduction of the tyrosyl radical and diferric center by hydroxyurea, sodium dithionite or the dihydro form of flavin adenine dinucleotide, were comparable with or higher (particularly D266A, by dithionite) than in native R2. Molecular modeling of the D266A mutant showed that the iron/radical site should be more accessible for external reductants in the mutant than in native R2. The results indicate that no specific pathway is required for the reduction. The dihydro form of flavin adenine dinucleotide was found to be a very efficient reductant in the studied proteins compared to dithionite alone. The EPR spectra of the mixed-valent Fe(II)Fe(III) sites formed by chemical reduction in the D266A and W103Y mutants were clearly different from the spectrum observed in the native protein, indicating that the structure of the diferric site was affected by the mutations, as also suggested by the modeling study. No difference was observed between the mixed-valent EPR spectra generated by chemical reduction in Y370W mutant and native mouse R2 protein

Keyword
Ribonucleotide reductase; Tyrosyl radical reduction; Diiron–oxygen protein
Identifiers
urn:nbn:se:su:diva-39039 (URN)10.1016/S0020-1693(01)00750-2 (DOI)
Available from: 2010-05-06 Created: 2010-05-06 Last updated: 2017-12-12Bibliographically approved
4. Oligopeptide inhibition of class Ic ribonucleotide reductase from Chlamydia trachomatis
Open this publication in new window or tab >>Oligopeptide inhibition of class Ic ribonucleotide reductase from Chlamydia trachomatis
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(English)Manuscript (preprint) (Other (popular science, discussion, etc.))
Identifiers
urn:nbn:se:su:diva-39042 (URN)
Available from: 2010-05-06 Created: 2010-05-06 Last updated: 2010-05-07Bibliographically approved

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