Ribonucleotide reductase R2 subunit

Figure 13.25 Three-dimensional structures of diiron proteins. The iron-binding subunits of (a) haemery-thrin, (b) bacterioferritin, (c) rubryerythrin (the FeS centre is on the top), (d) ribonucleotide reductase R2 subunit, (e) stearoyl-acyl carrier protein A9 desaturase, (f) methane monooxygenase hydroxylase a-subunit. (From Nordlund and Eklund, 1995. Copyright 1995, with permission from Elsevier.)...

Ask A, Persson L, Rehnholm A, Frostesjo L, Holm I, Heby O (1993) Development of resistance to hydroxyurea during treatment of human myelogenous leukemia K562 cells with alpha-difluoromethylornithine as a result of coamplification of genes for ornithine decarboxylase and ribonucleotide reductase R2 subunit. Cancer Res 53 5262-5268... 

Mann, G. J., Gr%oslund, A., Ochiai, E., Ingemarson, R., and Thelander, L., 1991, Purification and characterization of recombinant mouse and herpes simplex virus ribonucleotide reductase R2 subunit. Biochemistry 30 1939nl947. 

Figure 25.11. Ribonucleotide Reductase R2 Subunit. This subunit contains a stable free radical on a tyrosine residue. This radical is generated by the reaction of oxygen at a nearby site containing two iron atoms. Two R2 subunits come together to form a dimer.

Fig. 2. Diferric iron clusters from ribonucleotide reductase R2 subunit and methane monooxygenase hydroxylase. The drawings are based on (18, 19) for RNR-R2 and (15) for MMOH.

Fig. 1. Diferric iron clusters form hemer3fthrin, ribonucleotide reductase R2 subunit, and methane monooxygenase hydroxylase. The figure was made with the RasMol 2.0 program, and the protein coordinates as PDB files were obtained from Brookhaven Protein Data Bank. Only the amino acids (histidines, green carboxylates, black oxygen, red nitrogen, yellow acetate, blue iron, violet) coordinated to the iron cluster are shown, coordinated waters are not indicated. The first subunit containing the cluster is shown. Diferric Hr is from sipunculid worm Themiste dyscritra). The RNR-R2 is from E. coli. The MMOH is from Methvlococcus caosulatus (Bath).

Figure 15-4 Schematic diagrams comprising dinuclear metal centers in HuHF, EcFtna and EcBfr with those of ribonucleotide reductase R2 subunit (RNR R2), methane monooxygenase hydroxylase component (MMOH) and DvRr. The third metal sites in HuHF and EcFtna are also indicated.

ACP = acyl carrier protein ACPA D = ACPA desat-urase AlkB = octane 1-monooxygenase AOX = alternative oxidase DMQ hydroxylase = 5-demethoxyquinone hydroxylase EXAFS = extended X-ray absorption fine structure spectroscopy FMN = flavin mononucleotide FprA = flavoprotein A (flavo-diiron enzyme homologue) Hr = hemerythrin MCD = magnetic circular dichroism MME hydroxylase = Mg-protophorphyrin IX monomethyl ester hydroxylase MMO = methane monooxygenase MMOH = hydroxylase component of MMO NADH = reduced nicotinamide adenine dinucleotide PAPs = purple acid phosphatases PCET = proton-coupled electron transfer, PTOX = plastid terminal oxidase R2 = ribonucleotide reductase R2 subunit Rbr = rubrerythrin RFQ = rapid freeze-quench RNR = ribonucleotide reductase ROO = rubredoxin oxygen oxidoreductase XylM = xylene monooxygenase. 

The enzyme ribonucleotide reductase (RNR) catalyzes the reduction of ribonucleotides to deox5nibonucleotides, which is the first rate-limiting step in DNA biosynthesis. On the basis of their cofactor compositions, RNRs may be grouped into four different classes [7]. Class I RNR from E. coli is comprised of two homodi-meric subunits, R1 and R2. The R1 subunit (2 x 86kDa) contains the substrate binding site and redox-active cysteine residues, which are involved in the reduction of the ribonucleotides. The R2 subunit (2 x 43 kDa) contains in its active form (R2act) a stable tyrosyl radical (Y122 ), which is necessary for catalytic activity. This tyrosyl radical is located in close proximity to a //-oxo diferric cluster and is embedded about 10 A away from the protein surface [38, 39]. 

Rubrerythrin (Rr) was first isolated in 1988 from cellular extracts of D. vulgaris Hildenborough (38), and later also found in D. desulfuri-cans (39). Rr is constituted by two identical subunits of 22 kDa and it was shown that each monomer contains one Rd-like center, Fe(RS)4, and a diiron-oxo center similar to the ones found in methane monooxygenase (MMO) (40, 41) or ribonucleotide reductase (RNR-R2) (42). After aerobic purification, the UV-visible spectrum shows maxima at 492, 365, and 280 nm, and shoulders at 570 and 350 nm. This spectrum is similar to the ones observed for Rd proteins. From a simple subtraction of a typical Rd UV-vis spectrum (normalized to 492 nm) it is possible to show that the remainder of the spectrum (maxima at 365 nm and a shoulder at 460 nm) strongly resembles the spectrum of met-hemerythrin, another diiron-oxo containing protein. 

Metalloenzymes with non-heme di-iron centers in which the two irons are bridged by an oxide (or a hydroxide) and carboxylate ligands (glutamate or aspartate) constitute an important class of enzymes. Two of these enzymes, methane monooxygenase (MMO) and ribonucleotide reductase (RNR) have very similar di-iron active sites, located in the subunits MMOH and R2 respectively. Despite their structural similarity, these metal centers catalyze very different chemical reactions. We have studied the enzymatic mechanisms of these enzymes to understand what determines their catalytic activity [24, 25, 39-41]. 

Massie, B., Dionne, J., Lamarche, N. et al. (1995) Improved adenovirus vector provides herpes simplex virus ribonucleotide reductase R1 and R2 subunits very efficiently. Bio/Technology (Nature Publishing Company), 13 (6), 602-608. 

M. Bennati, A. Weber, J. Antonie, D.L. Perlstein, J. Robblee and J. Stubbe, Pulsed ELDOR spectroscopy measures the distance between the two tyrosyl radicals in the R2 subunit of the E. coli ribonucleotide reductase, J. Am. Chem. Soc., 2003, 125, 14988. 

Interest in this class of coordination compounds was sparked and fueled by the discovery that radical cofactors such as tyrosyl radicals play an important role in a rapidly growing number of metalloproteins. Thus, in 1972 Ehrenberg and Reichard (1) discovered that the R2 subunit of ribonucleotide reductase, a non-heme metal-loprotein, contains an uncoordinated, very stable tyrosyl radical in its active site. In contrast, Whittaker and Whittaker (2) showed that the active site of the copper containing enzyme galactose oxidase (GO) contains a radical cofactor where a Cu(II) ion is coordinated to a tyrosyl radical. 

In eukaryotes, ribonucleotide reductase is a tetramer consisting of two R1 and two R2 subunits. In addition to the disulfide bond mentioned, a tyrosine radical in the enzyme also participates in the reaction (2). It initially produces a substrate radical (3). This cleaves a water molecule and thereby becomes radical cation. Finally, the deoxyribose residue is produced by reduction, and the tyrosine radical is regenerated. 

Cyclic voltammetry has been also used for estimation of the rate constants for oxidation of water-soluble ferrocenes in the presence of HRP (131). There is a perfect match between the data obtained spectrophotometrically and electrochemically (Table IV), which proves that the cyclic voltammetry reveals information on the oxidation of ferrocenes by Compound II. It is interesting to note that an enzyme similar to HRP, viz. cytochrome c peroxidase, which catalyzes the reduction of H202 to water using two equivalents of ferrocytochrome c (133-136), is ca. 100 times more reactive than HRP (131,137). The second-order rate constant equals 1.4 x 106 M-1 s 1 for HOOCFc at pH 6.5 (131). There is no such rate difference in oxidation of [Fe(CN)e]4- by cytochrome c peroxidase and HRP (8). These comparisons should not however create an impression that the enzymatic oxidation of ferrocenes is always fast. The active-R2 subunit of Escherichia coli ribonucleotide reductase, which has dinuclear nonheme iron center in the active site, oxidizes ferrocene carboxylic acid and other water-soluble ferrocenes with a rate constant of... 

Dinuclear iron centres occur in several proteins. They either bind or activate dioxygen or they are hydrolases. Ribonucleotide reductase (RR) of the so-called class I type contains one such centre in the R2 protein in combination with a tyrosyl radical, both being essential for enzymatic activity which takes place in the R1 protein subunit. The diiron centre activates dioxygen to generate the tyrosyl radicals which in turn initiate the catalytic reaction in the R1 subunit. The interplay between the tyrosyl free radical in R2 and the formation of deoxyribonucleotides in R1 which also is proposed to involve a protein backbone radical is a topic of lively interest at present but is outside the scope of this review. Only a few recent references dealing with this aspect are mentioned without any further discussion.158 159 1 1,161... 

A four-pulse DEER measurement of the distance between two tyrosyl radicals on the monomers that make up the R2 subunit of E. coli ribonucleotide reductase gave a point-dipole distance of 33.1 A, which is in good agreement with the X-ray crystal structure.84 Better agreement between the calculated and observed dipolar frequency could be obtained by summing contributions from distributed... 

In subunit R2 of ribonucleotide reductase there is a tyrosyl radical (Y ) in close proximity to a di-iron cluster.100 In the protein from E. coli the EPR signal from Y can be observed up to room temperature. However, in the protein from yeast the Y signal broadens above 15 K and is not observable above about 60 K. Saturation recovery measurements at 140 GHz showed that at 60 K the spin-lattice relaxation rates for the Y signal in the yeast protein were about 2 orders of magnitude faster than for the E. coli protein. The temperature dependence of the relaxation enhancement was consistent with the activation energy for the first excited state of the di-iron cluster, so the relaxation enhancement was attributed to interaction with the di-iron cluster. Relaxation enhancements measured at 140 GHz showed little orientation dependence so the enhancement was assigned to isotropic exchange, which is different from the orientation-dependent dipolar interaction observed for the E. coli protein.100... 

Ribonucleotide reductase is notable in that its reaction mechanism provides the best-characterized example of the involvement of free radicals in biochemical transformations, once thought to be rare in biological systems. The enzyme in E. coli and most eukaryotes is a dimer, with subunits designated R1 and R2 (Fig. 22-40). The R1 subunit contains two lands of regulatory sites, as described below. The two active sites of the enzyme are formed at the interface between the R1 and R2 subunits. At each active site, R1 contributes two sulfhydryl groups required for activity and R2 contributes a stable tyrosyl radical. The R2 subunit also has a binuclear iron (Fe3+) cofactor that helps generate and stabilize the tyrosyl radicals (Fig. 22-40). The tyrosyl radical is too far from the active site to interact directly with the site, but it generates another radical at the active site that functions in catalysis. 

MECHANISM FIGURE 22-41 Proposed mechanism for ribonucleotide reductase. In the enzyme of . coli and most eukaryotes, the active thiol groups are on the R1 subunit the active-site radical (—X ) is on the R2 subunit and in . coli is probably a thiyl radical of Cys439 (see Fig. 22-40). Steps (T) through are described in the text. 

Figure 16-21 (A) Scheme showing the diiron center of the R2 subunit of E. coli ribonucleotide reductase. Included are the side chains of tyrosine 122, which loses an electron to form a radical, and of histidine 118, aspartate 237, and tryptophan 48. These side chains provide a pathway for radical transfer to the R1 subunit where the chain continues to tyrosines 738 and 737 and cysteine 429.354a c From Andersson et al.35ic (B) Schematic drawing of the active site region of the E. coli class IH ribonucleotide reductase with a plausible position for a model-built substrate molecule. Redrawn from Lenz and Giese373 with permission.

Andersson, M. E., H"gbom, M., Rinaldo-Matthis, A., Andersson, K. K., Sj berg, B.-M., and Nordlund, P., 1999, The crystal structnre of an azide complex of the diferrous R2 subunit of ribonucleotide reductase displays a novel carboxylate shift with important mechanistic implications for diiron-catalyzed oxygen activation. J. Amer. Chem. Soc. 121 2346n2352. 

Atta, M., Andersson, K. K., Ingemarson, R., Thelander, L., and Gr%oslund, A., 1994, EPR studies of mixed-valent [Fe Fe ] clusters formed in the R2 subunit of ribonucleotide reductase from mouse or herpes simplex virus Mild chemical reduction of the diferric centers. J. Am. Chem. Soc. 116 6429n6430. 

Climent, L, Sj berg, B.-M., and Huang, C. Y., 1992, Site-directed mutagenesis and deletion of the carboxyl terminus of Escherichia coli ribonucleotide reductase protein R2. Effects on catalytic activity and subunit interaction. Biochemistry 31 4801fi4807. 

Scheme 1 Reaction cycle for R2 subunit of ribonucleotide reductase...

One example of an enzyme-catalyzed reaction involving a radical intermediate is the enzyme ribonucleotide reductase, which catalyzes the conversion of ribonucleotides (used for RNA biosynthesis) to 2 -deoxyribonucleotides (used for DNA biosynthesis), as illustrated in Fig. 16. Spectroscopic studies of the R2 subunit of Escherichia coli ribonucleotide reductase have shown that it can form a stable, long-lived, tyrosyl radical species—the first protein radical to be discovered (13). 

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