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1.
Soc Sci Med ; 56(3): 569-72, 2003 Feb.
Article in English | MEDLINE | ID: mdl-12570974

ABSTRACT

Several studies have demonstrated that the nuclear power plant accident at Chernobyl in 1986 had a strong impact on the subjective health of the inhabitants in the surrounding regions and that the majority of these health complaints appear to be stress-related. An epidemiological survey among the adult population of the Gomel region in Belarus near Chernobyl showed higher rates of self-reported health problems, psychological distress and medical service use in this region than in a comparable unexposed region. This paper presents an analysis of data on cognitive factors that were collected in this study. The findings support the hypothesis that cognitive variables such as risk perception and sense of control play an important role as mediating factors in the explanation of the observed health differences between the exposed and non-exposed regions. A tentative model is presented to further clarify the role of risk perception in the occurrence of non-specific health complaints after such ecological disasters.


Subject(s)
Attitude to Health , Disasters , Environmental Exposure , Explosions , Health Status Indicators , Radiation Injuries/psychology , Radioactive Hazard Release/psychology , Adult , Attitude to Health/ethnology , Cognition , Humans , Power Plants , Radiation Injuries/complications , Republic of Belarus , Risk Assessment , Russia , Social Perception , Ukraine
2.
Structure ; 9(8): 739-50, 2001 Aug.
Article in English | MEDLINE | ID: mdl-11587648

ABSTRACT

BACKGROUND: The specificity of ribonucleotide reductases (RNRs) toward their four substrates is governed by the binding of deoxyribonucleoside triphosphates (dNTPs) to the allosteric specificity site. Similar patterns in the kinetics of allosteric regulation have been a strong argument for a common evolutionary origin of the three otherwise widely divergent RNR classes. Recent structural information settled the case for divergent evolution; however, the structural basis for transmission of the allosteric signal is currently poorly understood. A comparative study of the conformational effects of the binding of different effectors has not yet been possible; in addition, only one RNR class has been studied. RESULTS: Our presentation of the structures of a class III anaerobic RNR in complex with four dNTPs allows a full comparison of the protein conformations. Discrimination among the effectors is achieved by two side chains, Gln-114 and Glu-181, from separate monomers. Large conformational changes in the active site (loop 2), in particular Phe-194, are induced by effector binding. The conformational differences observed in the protein when the purine effectors are compared with the pyrimidine effectors are large, while the differences observed within the purine group itself are more subtle. CONCLUSIONS: The subtle differences in base size and hydrogen bonding pattern at the effector site are communicated to major conformational changes in the active site. We propose that the altered overlap of Phe-194 with the substrate base governs hydrogen bonding patterns with main and side chain hydrogen bonding groups in the active site. The relevance for evolution is discussed.


Subject(s)
Ribonucleotide Reductases/chemistry , Allosteric Site , Amino Acid Sequence , Binding Sites , Crystallography, X-Ray , Deoxyribonucleotides/chemistry , Evolution, Molecular , Hydrogen Bonding , Models, Molecular , Molecular Sequence Data , Polyphosphates/chemistry , Protein Binding , Protein Conformation , Sequence Homology, Amino Acid , Substrate Specificity
3.
J Biol Chem ; 276(44): 40457-63, 2001 Nov 02.
Article in English | MEDLINE | ID: mdl-11526118

ABSTRACT

Class III ribonucleotide reductase is an anaerobic enzyme that uses a glycyl radical to catalyze the reduction of ribonucleotides to deoxyribonucleotides and formate as ultimate reductant. The reaction mechanism of class III ribonucleotide reductases requires two cysteines within the active site, Cys-79 and Cys-290 in bacteriophage T4 NrdD numbering. Cys-290 is believed to form a transient thiyl radical that initiates the reaction with substrate and Cys-79 to take part as a transient thiyl radical in later steps of the reductive reaction. The recently solved three-dimensional structure of class III ribonucleotide reductase (RNR) from bacteriophage T4 shows that two highly conserved asparagines, Asn-78 and Asn-311, are positioned close to the essential Cys-79. We have investigated the function of Asn-78 and Asn-311 by site-directed mutagenesis and measured enzyme activity and glycyl radical formation in five single (N78(A/C/D) and N311(A/C)) and one double (N78A/N311A) mutant proteins. Our results suggest that both asparagines are important for the catalytic mechanism of class III RNR and that one asparagine can partially compensate for the lack of the other functional group in the single Asn --> Ala mutant proteins. A plausible role for these two asparagines could be in positioning formate in the active site to orient it toward the proposed thiyl radical of Cys-79. This would also control the highly reactive carbon dioxide radical anion form of formate within the active site before it is released as carbon dioxide. A detailed reaction scheme including the function of the two asparagines and two formate molecules is proposed for class III RNRs.


Subject(s)
Asparagine/metabolism , Bacteriophage T4/enzymology , Ribonucleotide Reductases/metabolism , Amino Acid Sequence , Base Sequence , Binding Sites , Catalysis , DNA Primers , Glycine/chemistry , Molecular Sequence Data , Mutagenesis, Site-Directed , Ribonucleotide Reductases/chemistry , Ribonucleotide Reductases/genetics , Sequence Homology, Amino Acid
4.
J Biol Chem ; 276(29): 26852-9, 2001 Jul 20.
Article in English | MEDLINE | ID: mdl-11328804

ABSTRACT

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.


Subject(s)
Azides/metabolism , Escherichia coli/enzymology , Iron/metabolism , Ribonucleotide Reductases/metabolism , Electron Spin Resonance Spectroscopy , Free Radicals , Mutagenesis , Protein Binding , Ribonucleotide Reductases/chemistry , Ribonucleotide Reductases/genetics , Substrate Specificity , Tyrosine/metabolism
5.
Nat Rev Mol Cell Biol ; 2(2): 147-51, 2001 02.
Article in English | MEDLINE | ID: mdl-11252956

ABSTRACT

Early in the history of DNA, thymine replaced uracil, thus solving a short-term problem for storing genetic information--mutation of cytosine to uracil through deamination. Any engineer would have replaced cytosine, but evolution is a tinkerer not an engineer. By keeping cytosine and replacing uracil the problem was never eliminated, returning once again with the advent of DNA methylation.


Subject(s)
Cytosine/metabolism , DNA/genetics , Evolution, Molecular
6.
J Biol Chem ; 275(33): 25365-71, 2000 Aug 18.
Article in English | MEDLINE | ID: mdl-10801858

ABSTRACT

Corynebacterium ammoniagenes contains a ribonucleotide reductase (RNR) of the class Ib type. The small subunit (R2F) of the enzyme has been proposed to contain a manganese center instead of the dinuclear iron center, which in other class I RNRs is adjacent to the essential tyrosyl radical. The nrdF gene of C. ammoniagenes, coding for the R2F component, was cloned in an inducible Escherichia coli expression vector and overproduced under three different conditions: in manganese-supplemented medium, in iron-supplemented medium, and in medium without addition of metal ions. A prominent typical tyrosyl radical EPR signal was observed in cells grown in rich medium. Iron-supplemented medium enhanced the amount of tyrosyl radical, whereas cells grown in manganese-supplemented medium had no such radical. In highly purified R2F protein, enzyme activity was found to correlate with tyrosyl radical content, which in turn correlated with iron content. Similar results were obtained for the R2F protein of Salmonella typhimurium class Ib RNR. The UV-visible spectrum of the C. ammoniagenes R2F radical has a sharp 408-nm band. Its EPR signal at g = 2.005 is identical to the signal of S. typhimurium R2F and has a doublet with a splitting of 0.9 millitesla (mT), with additional hyperfine splittings of 0.7 mT. According to X-band EPR at 77-95 K, the inactive manganese form of the C. ammoniagenes R2F has a coupled dinuclear Mn(II) center. Different attempts to chemically oxidize Mn-R2F showed no relation between oxidized manganese and tyrosyl radical formation. Collectively, these results demonstrate that enzymatically active C. ammoniagenes RNR is a generic class Ib enzyme, with a tyrosyl radical and a diferric metal cofactor.


Subject(s)
Bacterial Proteins , Corynebacterium/enzymology , Iron/chemistry , Ribonucleotide Reductases/chemistry , Ribonucleotide Reductases/genetics , Cloning, Molecular , Electron Spin Resonance Spectroscopy , Electrophoresis, Polyacrylamide Gel , Escherichia coli/metabolism , Iron/pharmacology , Ligands , Manganese/chemistry , Manganese/pharmacology , Plasmids/metabolism , Salmonella typhimurium/enzymology , Spectrophotometry , Ultraviolet Rays
7.
J Biol Chem ; 275(26): 19449-55, 2000 Jun 30.
Article in English | MEDLINE | ID: mdl-10748010

ABSTRACT

Class III ribonucleotide reductase (RNR) is an anaerobic glycyl radical enzyme that catalyzes the reduction of ribonucleotides to deoxyribonucleotides. We have investigated the importance in the reaction mechanism of nine conserved cysteine residues in class III RNR from bacteriophage T4. By using site-directed mutagenesis, we show that two of the cysteines, Cys-79 and Cys-290, are directly involved in the reaction mechanism. Based on the positioning of these two residues in the active site region of the known three-dimensional structure of the phage T4 enzyme, and their structural equivalence to two cysteine residues in the active site region of the aerobic class I RNR, we suggest that Cys-290 participates in the reaction mechanism by forming a transient thiyl radical and that Cys-79 participates in the actual reduction of the substrate. Our results provide strong experimental evidence for a similar radical-based reaction mechanism in all classes of RNR but also identify important differences between class III RNR and the other classes of RNR as regards the reduction per se. We also identify a cluster of four cysteines (Cys-543, Cys-546, Cys-561, and Cys-564) in the C-terminal part of the class III enzyme, which are essential for formation of the glycyl radical. These cysteines make up a CX(2)C-CX(2)C motif in the vicinity of the stable radical at Gly-580. We propose that the four cysteines are involved in radical transfer between Gly-580 and the cofactor S-adenosylmethionine of the activating NrdG enzyme needed for glycyl radical generation.


Subject(s)
Bacterial Proteins , Bacteriophage T4/chemistry , Cysteine/metabolism , Glycine/metabolism , Ribonucleotide Reductases/chemistry , Ribonucleotide Reductases/metabolism , Binding Sites , Catalysis , Cysteine/chemistry , Electron Spin Resonance Spectroscopy , Electrophoresis, Polyacrylamide Gel , Free Radicals/metabolism , Kinetics , Models, Molecular , Mutagenesis, Site-Directed , Oxygen/metabolism , Plasmids , Protein Engineering , Protein Structure, Tertiary , Viral Proteins/metabolism
8.
J Biol Chem ; 275(26): 19443-8, 2000 Jun 30.
Article in English | MEDLINE | ID: mdl-10748029

ABSTRACT

Ribonucleotide reductase (RNR) is an essential enzyme in all organisms. It provides precursors for DNA synthesis by reducing all four ribonucleotides to deoxyribonucleotides. The overall activity and the substrate specificity of RNR are allosterically regulated by deoxyribonucleoside triphosphates and ATP, thereby providing balanced dNTP pools. We have characterized the allosteric regulation of the class III RNR from bacteriophage T4. Our results show that the T4 enzyme has a single type of allosteric site to which dGTP, dTTP, dATP, and ATP bind competitively. The dissociation constants are in the micromolar range, except for ATP, which has a dissociation constant in the millimolar range. ATP and dATP are positive effectors for CTP reduction, dGTP is a positive effector for ATP reduction, and dTTP is a positive effector for GTP reduction. dATP is not a general negative allosteric effector. These effects are similar to the allosteric regulation of class Ib and class II RNRs, and to the class Ia RNR of bacteriophage T4, but differ from that of the class III RNRs from the host bacterium Escherichia coli and from Lactococcus lactis. The relative rate of reduction of the four substrates was measured simultaneously in a mixed-substrate assay, which mimics the physiological situation and illustrates the interplay between the different effectors in vivo. Surprisingly, we did not observe any significant UTP reduction under the conditions used. Balancing of the pyrimidine deoxyribonucleotide pools may be achieved via the dCMP deaminase and dCMP hydroxymethylase pathways.


Subject(s)
Bacteriophage T4/chemistry , Ribonucleotide Reductases/chemistry , Ribonucleotide Reductases/metabolism , Adenosine Triphosphate/metabolism , Allosteric Regulation , Allosteric Site , Binding, Competitive , Cytidine Triphosphate/metabolism , Deoxyadenine Nucleotides/metabolism , Deoxycytosine Nucleotides/metabolism , Deoxyguanine Nucleotides/metabolism , Deoxyuracil Nucleotides/metabolism , Guanosine Triphosphate/metabolism , Kinetics , Nucleotides/metabolism , Substrate Specificity , Time Factors , Uridine Triphosphate/metabolism
10.
Science ; 283(5407): 1499-504, 1999 Mar 05.
Article in English | MEDLINE | ID: mdl-10066165

ABSTRACT

Ribonucleotide reductases catalyze the reduction of ribonucleotides to deoxyribonucleotides. Three classes have been identified, all using free-radical chemistry but based on different cofactors. Classes I and II have been shown to be evolutionarily related, whereas the origin of anaerobic class III has remained elusive. The structure of a class III enzyme suggests a common origin for the three classes but shows differences in the active site that can be understood on the basis of the radical-initiation system and source of reductive electrons, as well as a unique protein glycyl radical site. A possible evolutionary relationship between early deoxyribonucleotide metabolism and primary anaerobic metabolism is suggested.


Subject(s)
Glycine/chemistry , Ribonucleotide Reductases/chemistry , Acetyltransferases/chemistry , Acetyltransferases/metabolism , Amino Acid Sequence , Anaerobiosis , Binding Sites , Crystallography, X-Ray , Dimerization , Evolution, Molecular , Hydrogen Bonding , Models, Molecular , Molecular Sequence Data , Mutation , Protein Conformation , Protein Folding , Protein Structure, Secondary , Ribonucleotide Reductases/genetics , Ribonucleotide Reductases/metabolism , Viral Proteins/chemistry
11.
J Biol Chem ; 273(47): 31016-20, 1998 Nov 20.
Article in English | MEDLINE | ID: mdl-9812999

ABSTRACT

All classes of ribonucleotide reductase are proposed to have a common reaction mechanism involving a transient cysteine thiyl radical that initiates catalysis by abstracting the 3'-hydrogen atom of the substrate nucleotide. In the class Ia ribonucleotide reductase system of Escherichia coli, we recently trapped two kinetically coupled transient radicals in a reaction involving the engineered E441Q R1 protein, wild-type R2 protein, and substrate (Persson, A. L., Eriksson, M., Katterle, B., Pötsch, S., Sahlin, M., and Sjöberg, B.-M. (1997) J. Biol. Chem. 272, 31533-31541). Using isotopically labeled R1 protein or substrate, we now demonstrate that the early radical intermediate is a cysteinyl radical, possibly in weak magnetic interaction with the diiron site of protein R2, and that the second radical intermediate is a carbon-centered substrate radical with hyperfine coupling to two almost identical protons. This is the first report of a cysteinyl free radical in ribonucleotide reductase that is a kinetically coupled precursor of an identified substrate radical. We suggest that the cysteinyl radical is localized to the active site residue, Cys439, which is conserved in all classes of ribonucleotide reductase, and which, in the three-dimensional structure of protein R1, is positioned to abstract the 3'-hydrogen atom of the substrate. We also suggest that the substrate radical is localized to the 3'-position of the ribose moiety, the first substrate radical intermediate in the postulated reaction mechanism.


Subject(s)
Cysteine/metabolism , Cytidine Diphosphate/metabolism , Escherichia coli/enzymology , Ribonucleotide Reductases/metabolism , Catalytic Domain , Electron Spin Resonance Spectroscopy , Free Radicals/metabolism , Models, Chemical , Mutation , Ribonucleotide Reductases/genetics , Spin Trapping
12.
J Biol Chem ; 273(38): 24853-60, 1998 Sep 18.
Article in English | MEDLINE | ID: mdl-9733790

ABSTRACT

We have used 8-azidoadenosine 5'-triphosphate (8-N3ATP) to investigate the nucleotide-binding sites on the NrdD subunit of the anaerobic ribonucleotide reductase from T4 phage. Saturation studies revealed two saturable sites for this photoaffinity analog of ATP. One site exhibited half-maximal saturation at approximately 5 microM [gamma-32P]8-N3ATP, whereas the other site required 45 microM. To localize the sites of photoinsertion, photolabeled peptides from tryptic and chymotryptic digests were isolated by immobilized Al3+ affinity chromatography and high performance liquid chromatography and subjected to amino acid sequence and mass spectrometric analyses. The molecular masses of the photolabeled products of cyanogen bromide cleavage were estimated using tricine-SDS-polyacrylamide gel electrophoresis. Overlapping sequence analysis localized the higher affinity site to the region corresponding to residues 289-291 and the other site to the region corresponding to residues 147-160. Site-directed mutagenesis of Cys290, a residue conserved in all known class III reductases, resulted in a protein that exhibited less than 10% of wild type enzymatic activity. These observations indicate that Cys290 may reside in or near the active site. High performance liquid chromatography analysis revealed that photoinsertion of [gamma-32P]8-N3ATP into the site corresponding to residues 147-160 was almost completely abolished when 100 microM dATP, dGTP, or dTTP was included in the photolabeling reaction mixture, whereas 100 microM ATP, GTP, CTP, or dCTP had virtually no effect. Based on these nucleotide binding properties, we conclude that this site is an allosteric site analogous to the one that has been shown to regulate substrate specificity of other ribonucleotide reductases. There was no evidence for a second allosteric nucleotide-binding site as observed in the anaerobic ribonucleotide reductase from Escherichia coli.


Subject(s)
Adenosine Triphosphate/metabolism , Bacteriophage T4/enzymology , Ribonucleotide Reductases/chemistry , Ribonucleotide Reductases/metabolism , Adenosine Triphosphate/analogs & derivatives , Affinity Labels , Allosteric Site , Amino Acid Sequence , Azides/metabolism , Binding Sites , Binding, Competitive , Conserved Sequence , Cysteine , Escherichia coli/enzymology , Kinetics , Macromolecular Substances , Molecular Sequence Data , Mutagenesis, Site-Directed , Peptide Fragments/chemistry , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism , Ribonucleotides/pharmacology , Sequence Alignment , Sequence Homology, Amino Acid , Viral Proteins/chemistry , Viral Proteins/metabolism
13.
J Biol Chem ; 273(33): 21003-8, 1998 Aug 14.
Article in English | MEDLINE | ID: mdl-9694851

ABSTRACT

A hydrogen-bonded catalytic radical transfer pathway in Escherichia coli ribonucleotide reductase (RNR) is evident from the three-dimensional structures of the R1 and R2 proteins, phylogenetic studies, and site-directed mutagenesis experiments. Current knowledge of electron transfer processes is difficult to apply to the very long radical transfer pathway in RNR. To explore the importance of the hydrogen bonds between the participating residues, we converted the protein R2 residue Asp237, one of the conserved residues along the radical transfer route, to an asparagine and a glutamate residue in two separate mutant proteins. In this study, we show that the D237E mutant is catalytically active and has hydrogen bond connections similar to that of the wild type protein. This is the first reported mutant protein that affects the radical transfer pathway while catalytic activity is preserved. The D237N mutant is catalytically inactive, and its tyrosyl radical is unstable, although the mutant can form a diferric-oxo iron center and a R1-R2 complex. The data strongly support our hypothesis that an absolute requirement for radical transfer during catalysis in ribonucleotide reductase is an intact hydrogen-bonded pathway between the radical site in protein R2 and the substrate binding site in R1. Our data thus strongly favor the idea that the electron transfer mechanism in RNR is coupled with proton transfer, i.e. a radical transfer mechanism.


Subject(s)
Ribonucleotide Reductases/metabolism , Amino Acid Substitution , Asparagine/chemistry , Asparagine/metabolism , Aspartic Acid/chemistry , Aspartic Acid/metabolism , Catalysis , Escherichia coli/enzymology , Free Radicals , Glutamic Acid/chemistry , Glutamic Acid/metabolism , Hydrogen Bonding , Iron/metabolism , Protein Binding , Protein Engineering , Ribonucleotide Reductases/chemistry , Tyrosine/chemistry , Tyrosine/metabolism
14.
Biochemistry ; 37(30): 10798-807, 1998 Jul 28.
Article in English | MEDLINE | ID: mdl-9692970

ABSTRACT

The R2 protein of ribonucleotide reductase catalyzes the dioxygen-dependent one-electron oxidation of Tyr122 at a diiron-carboxylate site. Methane monooxygenase and related hydroxylases catalyze hydrocarbon hydroxylation at diiron sites structurally related to the one in R2. In protein R2, the likely reaction site for dioxygen is close to Phe208. The crystal structure of an iron ligand mutant R2, Y122F/E238A, reveals the hydroxylation of Phe208 at the meta, or epsilon-, ring position and the subsequent coordination of this residue to the diiron site. In another mutant, F208Y, the "foreign" residue Tyr208 is hydroxylated to Dopa. The structures of apo and diferrous F208Y presented here suggest that Tyr208 is coordinated to the iron site of F208Y throughout the Dopa generation cycle. Together, the structural data on these two mutants suggest two possible reaction geometries for the hydroxylation reaction catalyzed by these modified R2 diiron sites, geometries which might be relevant for the hydroxylation reaction catalyzed by other diiron sites such as methane monooxygenase. A critical role for residue Glu238 in directing the oxidative power of the reactive intermediate toward oxidation of Tyr122 is proposed.


Subject(s)
Iron/chemistry , Mutagenesis, Site-Directed , Oxygen/chemistry , Ribonucleotide Reductases/chemistry , Ribonucleotide Reductases/genetics , Alanine/genetics , Apoenzymes/chemistry , Catalysis , Crystallization , Crystallography, X-Ray , Ferrous Compounds/chemistry , Glutamic Acid/genetics , Hydroxylation , Iron/metabolism , Models, Molecular , Oxygen/metabolism , Phenylalanine/analogs & derivatives , Phenylalanine/chemistry , Phenylalanine/genetics , Ribonucleotide Reductases/metabolism , Tyrosine/genetics
15.
Biochem Biophys Res Commun ; 246(3): 740-5, 1998 May 29.
Article in English | MEDLINE | ID: mdl-9618282

ABSTRACT

The highly conserved residue F208 in protein R2 of E. coli ribonucleotide reductase is close to the binuclear iron center, and found to be involved in stabilizing the tyrosyl radical Y122. in wild type R2. Upon the reconstitution reaction of the mutant R2 F208Y with ferrous iron and molecular oxygen, we observed a new EPR singlet signal (g = 2.003) formed concomitantly with decay of the transient tyrosyl radical Y122. (g = 2.005). This new paramagnetic species (denoted Z) was stable for weeks at 4 degrees C and visible by EPR only below 50 K. The EPR singlet could not be saturated by available microwave power, suggesting that Z may be a mainly metal centered species. The maximum amount of the compound Z in the protein purified from cells grown in rich medium was about 0.18 unpaired spin/R2. An identical EPR signal of Z was found also in the double mutant R2 F208Y/Y122F. In the presence of high concentration of sodium ascorbate, the amounts of both the transient Y122. and the new species Z increased considerably in the reconstitution reaction. The results suggest that Z is most likely an oxo-ferryl species possibly in equilibrium with a Y208 ligand radical.


Subject(s)
Escherichia coli/enzymology , Mutation , Nonheme Iron Proteins/metabolism , Ribonucleotide Reductases/metabolism , Tyrosine/metabolism , Binding Sites , Dihydroxyphenylalanine , Electron Spin Resonance Spectroscopy , Free Radicals , Models, Chemical , Nonheme Iron Proteins/genetics , Phenylalanine/genetics , Phenylalanine/metabolism , Ribonucleotide Reductases/genetics , Tyrosine/genetics
16.
J Biol Chem ; 273(8): 4329-37, 1998 Feb 20.
Article in English | MEDLINE | ID: mdl-9468481

ABSTRACT

Ribonucleotide reductases (RNRs) are key enzymes in living cells that provide the precursors of DNA synthesis. The three characterized classes of RNRs differ by their metal cofactor and their stable organic radical. We have purified to near homogeneity the enzymatically active Mn-containing RNR of Corynebacterium ammoniagenes, previously claimed to represent a fourth RNR class. N-terminal and internal peptide sequence analyses clearly indicate that the C. ammoniagenes RNR is a class Ib enzyme. In parallel, we have cloned a 10-kilobase pair fragment from C. ammoniagenes genomic DNA, using primers specific for the known class Ib RNR. The cloned class Ib locus contains the nrdHIEF genes typical for class Ib RNR operon. The deduced amino acid sequences of the nrdE and nrdF genes matched the peptides from the active enzyme, demonstrating that C. ammoniagenes RNR is composed of R1E and R2F components typical of class Ib. We also show that the Mn-containing RNR has a specificity for the NrdH-redoxin and a response to allosteric effectors that are typical of class Ib RNRs. Electron paramagnetic resonance and atomic absorption analyses confirm the presence of Mn as a cofactor and show, for the first time, insignificant amounts of iron and cobalt found in the other classes of RNR. Our discovery that C. ammoniagenes RNR is a class Ib enzyme and possesses all the highly conserved amino acid side chains that are known to ligate two ferric ions in other class I RNRs evokes new, challenging questions about the control of the metal site specificity in RNR. The cloning of the entire NrdHIEF locus of C. ammoniagenes will facilitate further studies along these lines.


Subject(s)
Corynebacterium/enzymology , Manganese/metabolism , Ribonucleotide Reductases/metabolism , Amino Acid Sequence , Chromatography, Ion Exchange , Cloning, Molecular , Corynebacterium/genetics , Electrophoresis, Polyacrylamide Gel , Genes, Bacterial , Molecular Sequence Data , Polymerase Chain Reaction , Ribonucleotide Reductases/chemistry , Ribonucleotide Reductases/genetics , Sequence Homology, Amino Acid
17.
Nucleic Acids Res ; 25(17): 3543-9, 1997 Sep 01.
Article in English | MEDLINE | ID: mdl-9254717

ABSTRACT

The nrdB gene of bacteriophage T4 contains a group IA2 intron. We have investigated the kinetics of self-splicing by a shortened variant of nrdB pre-mRNA in the presence of the co-substrates guanosine and 2'-amino-2'-deoxyguanosine. The pH dependence of the first transesterification step displayed parallel linear correlations for the two different co-substrates up to pH 7, above which the reaction with guanosine levels off to become pH independent. The plot for the 30-fold slower reaction with 2'-aminoguanosine is linear up to pH 8-8.5 and then levels off. The linear correlations with slopes close to unity suggest that a deprotonation event accelerates the transesterification reaction and that a change in rate limiting step occurs at a first order rate constant of approximately 1 min-1(i.e. for our system k cat/ K m approximately 10(5) M-1 min-1). The pH dependence of observed rate constants in different divalent metal ion mixtures, where the 2'-aminoguanosine-dependent reaction is enhanced 6- and 35-fold compared with that in magnesium, strongly supports this conclusion. This is, to our knowledge, the first report on an intact self-splicing group I intron where use of different co-substrates and divalent metal ions shows that a deprotonation enhances the rate and verifies that the transitions occurring during splicing of group I introns are all part of a common reaction sequence.


Subject(s)
Bacteriophage T4/genetics , Introns , RNA Precursors/metabolism , RNA Splicing , RNA, Messenger/metabolism , Ribonucleoside Diphosphate Reductase/genetics , Deoxyguanosine/analogs & derivatives , Deoxyguanosine/metabolism , Deoxyguanosine/pharmacology , Esterification , Guanosine/metabolism , Hydrogen-Ion Concentration , Magnesium/pharmacology , Nucleic Acid Conformation , RNA, Viral/metabolism
18.
Structure ; 5(8): 1077-92, 1997 Aug 15.
Article in English | MEDLINE | ID: mdl-9309223

ABSTRACT

BACKGROUND: Ribonucleotide reductase (RNR) is an essential enzyme in DNA synthesis, catalyzing all de novo synthesis of deoxyribonucleotides. The enzyme comprises two dimers, termed R1 and R2, and contains the redox active cysteine residues, Cys462 and Cys225. The reduction of ribonucleotides to deoxyribonucleotides involves the transfer of free radicals. The pathway for the radical has previously been suggested from crystallographic results, and is supported by site-directed mutagenesis studies. Most RNRs are allosterically regulated through two different nucleotide-binding sites: one site controls general activity and the other controls substrate specificity. Our aim has been to crystallographically demonstrate substrate binding and to locate the two effector-binding sites. RESULTS: We report here the first crystal structure of RNR R1 in a reduced form. The structure shows that upon reduction of the redox active cysteines, the sulfur atom of Cys462 becomes deeply buried. The more accessible Cys225 moves to the former position of Cys462 making room for the substrate. In addition, the structures of R1 in complexes with effector, effector analog and effector plus substrate provide information about these binding sites. The substrate GDP binds in a cleft between two domains with its beta-phosphate bound to the N termini of two helices; the ribose forms hydrogen bonds to conserved residues. Binding of dTTP at the allosteric substrate specificity site stabilizes three loops close to the dimer interface and the active site, whereas the general allosteric binding site is positioned far from the active site. CONCLUSIONS: Binding of substrate at the active site of the enzyme is structurally regulated in two ways: binding of the correct substrate is regulated by the binding of allosteric effectors and binding of the actual substrate occurs primarily when the active-site cysteines are reduced. One of the loops stabilized upon binding of dTTP participates in the formation of the substrate-binding site through direct interaction with the nucleotide base. The general allosteric effector site, located far from the active site, appears to regulate subunit interactions within the holoenzyme.


Subject(s)
Cysteine/chemistry , Ribonucleotide Reductases/chemistry , Allosteric Regulation , Amino Acid Sequence , Binding Sites , Conserved Sequence/genetics , Crystallography, X-Ray , Dimerization , Guanosine Diphosphate/chemistry , Models, Chemical , Models, Molecular , Molecular Sequence Data , Oxidation-Reduction , Sequence Alignment , Substrate Specificity , Thymine Nucleotides/chemistry
19.
J Biol Chem ; 272(16): 10414-21, 1997 Apr 18.
Article in English | MEDLINE | ID: mdl-9099682

ABSTRACT

Reconstitution of the tyrosyl radical in ribonucleotide reductase protein R2 requires oxidation of a diferrous site by oxygen. The reaction involves one externally supplied electron in addition to the three electrons provided by oxidation of the Tyr-122 side chain and formation of the mu-oxo-bridged diferric site. Reconstitution of R2 protein Y122F, lacking the internal pathway involving Tyr-122, earlier identified two radical intermediates at Trp-107 and Trp-111 in the vicinity of the di-iron site, suggesting a novel internal transfer pathway (Sahlin, M., Lassmann, G., Pötsch, S., Sjöberg, B. -M., and Gräslund, A. (1995) J. Biol. Chem. 270, 12361-12372). Here, we report the construction of the double mutant W107Y/Y122F and its three-dimensional structure and demonstrate that the tyrosine Tyr-107 can harbor a transient, neutral radical (Tyr-107(.)). The Tyr-107(.) signal exhibits the hyperfine structure of a quintet with coupling constants of 1.3 mT for one beta-methylene proton and 0.75 mT for each of the 3 and 5 hydrogens of the phenyl ring. Rapid freeze quench kinetics of EPR-visible intermediates reveal a preferred radical transfer pathway via Trp-111, Glu-204, and Fe-2, followed by a proton coupled electron transfer through the pi-interaction of the aromatic rings of Trp-(Tyr-)107 and Trp-111. The kinetic pattern observed in W107Y/Y122F is considerably changed as compared with Y122F: the Trp-111(.) EPR signal has vanished, and the Tyr-107(.) has the same formation rate as does Trp-111(.) in Y122F. According to the proposed consecutive reaction, Trp-111(.) becomes very short lived and is no longer detectable because of the faster formation of Tyr-107(.). We conclude that the phenyl rings of Trp-111 and Tyr-107 form a better stacking complex so that the proton-coupled electron transfer is facilitated compared with the single mutant. Comparison with the formation kinetics of the stable tyrosyl radical in wild type R2 suggests that these protein-linked radicals are substitutes for the missing Tyr-122. However, in contrast to Tyr-122(.) these radicals lack a direct connection to the radical transfer pathway utilized during catalysis.


Subject(s)
Escherichia coli/enzymology , Point Mutation , Protein Conformation , Ribonucleotide Reductases/chemistry , Ribonucleotide Reductases/metabolism , Tyrosine , Crystallography, X-Ray , Electron Spin Resonance Spectroscopy , Free Radicals , Kinetics , Models, Molecular , Mutagenesis, Site-Directed , Oligodeoxyribonucleotides , Recombinant Proteins/chemistry , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , Ribonucleotide Reductases/isolation & purification , Spectrophotometry
20.
Nucleic Acids Res ; 25(3): 648-53, 1997 Feb 01.
Article in English | MEDLINE | ID: mdl-9016608

ABSTRACT

The catalytic mechanism for self-splicing of the group I intron in the pre-mRNA from the nrdB gene in bacteriophage T4 has been investigated using 2'-amino- 2'-deoxyguanosine or guanosine as cosubstrates in the presence of Mg2+, Mn2+and Zn2+. The results show that a divalent metal ion interacts with the cosubstrate and thereby influences the efficiency of catalysis in the first step of splicing. This suggests the existence of a metal ion that catalyses the nucleophilic attack of the cosubstrate. Of particular significance is that the transesterification reactions of the first step of splicing with 2'-amino-2'-deoxyguanosine as cosubstrate are more efficient in mixtures containing either Mn2+or Zn2+together with Mg2+than with only magnesium ions present. The experiments in metal ion mixtures show that two (or more) metal ions are crucial for the self-splicing of group I introns and suggest the possibility that more than one of these have a direct catalytic role. A working model for a two-metal-ion mechanism in the transesterification steps is suggested.


Subject(s)
Bacteriophage T4/enzymology , Introns , Magnesium/pharmacology , Manganese/pharmacology , RNA Precursors , RNA Splicing , RNA, Viral , Ribonucleotide Reductases/genetics , Viral Proteins/genetics , Zinc/pharmacology , Cations, Divalent , Deoxyguanosine/analogs & derivatives , Deoxyguanosine/metabolism , Guanosine/metabolism , Substrate Specificity
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