II Ribonucleotide Reductases

The realization of the widespread occurrence of amino acid radicals in enzyme catalysis is recent and has been documented in several reviews (52-61). Among the catalytically essential redox-active amino acids glycyl [e.g., anaerobic class III ribonucleotide reductase (62) and pyruvate formate lyase (63-65)], tryptophanyl [e.g., cytochrome peroxidase (66-68)], cysteinyl [class I and II ribonucleotide reductase (60)], tyrosyl [e.g., class I ribonucleotide reductase (69-71), photosystem II (72, 73), prostaglandin H synthase (74-78)], and modified tyrosyl [e.g., cytochrome c oxidase (79, 80), galactose oxidase (81), glyoxal oxidase (82)] are the most prevalent. The redox potentials of these protein residues are well within the realm of those achievable by biological oxidants. These redox enzymes have emerged as a distinct class of proteins of considerable interest and research activity. 

Licht, S. S., Lawrence, C. C., and Stubbe, J., 1999, Class II ribonucleotide reductases catalyze carbon-cobalt bond reformation on every turnover. J. Amer. Chem. Soc. 121 7463n7468. 

The other type of radical chemistry of importance in the carbohydrate field is one-electron reductions. A handful of these reactions (such as the metallic Zn reduction of acetobromoglucose to triacetylglucal) have been used in synthesis for decades, but, starting with the Barton-McCombie deoxygenation of sugars in the mid-1970s there has been an explosion of interest, as increasingly sophisticated cascades of elementary radical steps have been devised. Such reactions are driven by the homolysis of weak bonds such as Sn-H or N-O under conditions of photolysis or mild thermolysis. Nature uses a similar basic principle in Type II ribonucleotide reductases, where the weak bond in question is the cobalt-carbon a bond in the corrin cofactor. ... 

Figure 7.32 Propagation steps of (a) Types I and II ribonucleotide reductases, (b) Type III ribonucleotide reductase. (c) Suicide enz5une inactivation by 2 -deoxy-2 -halo- or -pseudohaloribonucleotides.

SiNTCHAK, M. D., ArJARA, G., Kellogg, B. A., Stubbe, J., Drennan, C. L. (2002) The crystal structure of class II ribonucleotide reductase reveals how an allosterically regulated monomer mimics a dimer, Nat. Struct. Biol. 9, 293-300. 

Mediation of hydrogen transfer by adenosylcobalamin is a property of all other isomerases that follow the pattern of Equation (5). The role of adenosylcobalamin in the action of class II ribonucleotide reductases is very closely related. 

Figure 19 The regulatory circuit controlling the substrate specificity of Class II ribonucleotide reductases.

Figure 20 Allosteric interactions that adjust the specificity of the T. maritima Class II ribonucleotide reductase to allow generation of balanced pools of deoxyribonucleotides. Loop 2 is shown in red. The active site is at the top, and the specificity site is at the bottom right, (a) the dTTP-GDP complex (b) the dATP-CDP complex and (c) the dGTP-ADP complex. The structure of the dATP-UDP complex is similar to the dATP-CDP complex. Reproduced with permission from P. Nordlund P. Reichard, Annu. Rev. Biochem. 2006, 75, 681-706.

Class II Ribonucleotide Reductases - Found in cyanobacteria, some bacteria, and Euglena. The enzyme acts on ribonucleoside triphosphate substrates. It uses adenosylcobalamin, a B12 coenzyme to generate a free radical. 

Fig. 10. Hydrogen donor systems for ribonucleotide reduction. Enzyme reactions are I thioredoxin reductase (EC 1.6.4.5) II ribonucleotide reductase (EC 1.17.4) III glutathione reductase (EC 1.6.4.2). GSH, GSSG reduced and oxidized glutathione NADPH, NADP reduced and oxidized nicotinamide adenine dinucleotide phosphate coenzymes. The hydrogen transfer chain is continued in Fig. II...

When induced in macrophages, iNOS produces large amounts of NO which represents a major cytotoxic principle of those cells. Due to its affinity to protein-bound iron, NO can inhibit a number of key enzymes that contain iron in their catalytic centers. These include ribonucleotide reductase (rate-limiting in DNA replication), iron-sulfur cluster-dependent enzymes (complex I and II) involved in mitochondrial electron transport and cis-aconitase in the citric acid cycle. In addition, higher concentrations of NO,... 

From these data it seems feasible that a Co(II)-species is generated during catalysis, and that homolysis of the Co—C-bond is a prerequisite for enzyme catalysis in ribonucleotide reductase. However, the kinetics of appearance of the Co(II)-signal indicates that the rate of formation of Co(II) is much slower than either the rate of ribonucleotide reduction... 

The application of ESR to the ribonucleotide reductase system indicates that the catalytic intermediate is a Co(I)-species. The appearance of Cob(Il)alamin is probably caused by partial oxidation of the Co(I)-species. In the enzyme bound Co(II)-species the benzimidazole ligand is coordinated, and the corrin ring is bound so tightly that the enzyme produces a unique highly resolved ESR spectrum. 

Un, S., M. Atta et al. (1995). g-values as a probe of the local protein environment High-field EPR of tyrosyl radicals in ribonucleotide reductase and photosystem II. J. Am. Chem. Soc. 117 10713-10719. 

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. 

Figure 13.4 A proposed mechanism for all three classes of ribonucleotide reductases. Classes I and II RNRs require an active site Glu residue and a pair of redox-active Cys. Class HI RNRs lack the Glu and one of the Cys, and use formate as the reductant. (From Stubbe etal., 2001. Copyright 2001, with permission from Elsevier.)...

To what extent are the binuclear units in the purple acid phosphatases analogous to those found in hemerythrin and ribonucleotide reductase There are similarities and differences. The oxidized form is purple and EPR silent with strong antiferromagnetic coupling between the two Fe(III) centers the reduced form is pink and EPR active (gav = 1.7-1.8) with weak antiferromagnetic coupling between the Fe(III)-Fe(II) centers (3,72,73). 

Magnesium is bound in the active site of D-xylose isomerase (Carrell et al., 1984, 1989 Farber et al., 1987 Key etal., 1988 Henrick a/., 1989). Here, the site at which two metals [from among Mg(II), Mn(ll), and Co(II)] bind is similar to that found for Fe(ll) in ribonucleotide reductase (Nordlund et al., 1990). The active site of xylose isomerase is shown in Fig. 28. Magnesium ions are preferred in ATP-utilizing enzyme reactions (Mildvan, 1987). 

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... 

Figure 6 High Field EPR spectra of radicals occurring in PS II ( Yz obtained at 245 GHz, all other spectra at 285 GHz). For comparison, the spectra of the tyrosine radical in ribonucleotide reductase (RNR) and of irradiated tyrosine hydrochloride crystals n are also shown (for details see reference 30). Note the striking differences in g values for the tyrosyl radicals. Figure reproduced from reference 30 with permission.

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