Enzymatic Free Radical Reactions

Abstract

Nature has evolved an array of cofactors to aid in the initiation of enzymatic reactions that take place via mechanisms involving unpaired electrons centred on carbon atoms. A unifying theme among many of these cofactors is that they contain metal atoms that participate intimately in the radical‐generation process.

Keywords: radicals; S‐adenosylmethionine; adenosylcobalamin; ribonucleotide reductase; quinones; monooxygenases; eicasanoids; leukotrienes; iron–sulfur clusters

Figure 1.

Structures of representative cofactors that are used to initiate enzymatic reactions that proceed via radical intermediates. (a) Diferric iron centre–tyrosyl radical cofactor of the Class I ribonucleotide reductases. Glutamate and histidine amino acids in EXXH motif are labelled in red. (b) 5′‐Deoxyadenosylcobalamin: 5′‐hydrogens are labelled in red. (c) S‐Adenosyl‐l‐methionine and [4Fe–4S] cluster, which are used in the radical SAM superfamily of enzymes. (d) Haem cofactor of cytochromes P‐450 and prostaglandin synthase. A molecule of dioxygen is drawn above the haem, where it binds to the high‐spin ferrous form of the cofactor. (e) Nonhaem iron centre in soyabean lipoxygenases. In the case of the rabbit lipoxygenase, the asparagine ligand is replaced by another histidine ligand.

Figure 2.

Two types of reaction in which coenzyme B12 is known to participate. (a) Mutase reactions. X represents the migrating group in diol dehydrase, ethanolamine ammonia‐lyase, glutamate mutase, methylmalonyl‐CoA mutase and methylene glutarate mutase, respectively. (b) Ribonucleotide reductase reaction. Depending on the source of the enzyme, the substrate is either the nucleoside diphosphate or the nucleoside triphosphate.

Figure 3.

The role of coenzyme B12 in 1,2‐rearrangement reactions. The corrin macrocycle of coenzyme B12 is depicted by the oval.

Figure 4.

The role of coenzyme B12 in the ribonucleotide reductase reaction, and the mechanism of exchange of the 5′‐hydrogens of the cofactor with solvent. The corrin macrocycle of coenzyme B12 is depicted by the oval.

Figure 5.

Prototypical radical SAM reactions.

Figure 6.

The reaction cycle of cytochrome P‐450cam. The substrate is represented by RH and the product is represented by ROH.

Figure 7.

Structures of some quinone‐containing cofactors. (a) 2,4,5‐Trihydroxyphenylalanine quinone (TPQ). (b) Lysine tyrosyl quinone (LTQ). (c) Pyrroloquinoline quinone (PQQ). (d) Tryptophan tryptophyl quinone.

Figure 8.

First half‐reaction of copper amine oxidase. BH and B represent general base and general acid catalysts, respectively.

Figure 9.

Proposed mechanism for second half‐reaction of copper amine oxidase. Species that are not in red are considered to be bound at the active site of the enzyme. The aminosemiquinone cation is drawn as a circle inside of the six‐membered ring to indicate the resonance associated with this species.

Figure 10.

Pathway for cyclooxygenase activity of prostaglandin synthase. Blue arrows represent general electron flow, and blue numbers represent carbon numbering on arachidonic acid. The carboxyl carbon is C1. The red label represents the pro‐S hydrogen, which is abstracted by the tyrosine (Tyr) radical that is generated by the peroxidase activity.

Figure 11.

Proposed reaction mechanism for the soyabean lipoxygenase‐catalysed insertion of dioxygen into linoleic acid. The pro‐R hydrogen of the substrate is indicated in red. The numbering of the carbon atoms of the substrate begins at the carboxylate group, and the relevant carbons are indicated in blue. The bracketed intermediate represents the two most relevant resonance forms of the intermediate formed upon hydrogen atom abstraction.

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References

Babior BM (1975) Mechanism of cobalamin‐dependent rearrangements. Accounts of Chemical Research 8: 376–384.

Cosper NJ, Booker SJ, Ruzicka F, Frey PA and Scott RA (2000) Direct FeS cluster involvement in generation of a radical in lysine 2,3‐aminomutase. Biochemistry 39(51): 15668–15673.

Davidson VL (2001) Pyrroloquinoline quinone (PQQ) from methanol dehydrogenase and tryptophan tryptophylquinone (TTQ) from methylamine dehydrogenase. Advances in Protein Chemistry 58: 95–140.

Frey PA (1990) Importance of organic radicals in enzymatic cleavage of unactivated C–H bonds. Chemical Reviews 90: 1343–1357.

Frey PA (1993) Lysine 2,3‐aminomutase: is adenosylmethionine a poor man's adenosylcobalamin? FASEB Journal 7: 662–670.

Licht S, Gerfen GJ and Stubbe J (1996) Thiyl radicals in ribonucleotide reductases. Science 271: 477–481.

Merkx M, Kopp DA, Sazinsky MH et al. (2001) Dioxygen activation and methane hydroxylation by soluble methane monooxygenase: a tale of two irons and three proteins. Angewandte Chemie International Edition 40: 2782–2807.

Mure M, Mills SA and Klinman JP (2002) Catalytic mechanism of the topa quinone containing copper amine oxidases. Biochemistry 41(30): 9269–9278.

Nordland P and Eklund H (1995) Di‐iron–carboxylate proteins. Current Opinion in Structural Biology 5: 758–766.

Que L Jr and Ho RYN (1996) Dioxygen activation by enzymes with mononuclear non‐heme iron active sites. Chemical Reviews 96: 2607–2624.

Sofia HJ, Chen G, Hetzler BG, Reyes‐Spindola JF and Miller NE (2001) Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods. Nucleic Acids Research 29(5): 1097–1106.

Sono M, Roach MP, Coulter ED and Dawson JH (1996) Heme‐containing oxygenases. Chemical Reviews 96: 2841–2887.

Walsby CJ, Ortillo D, Broderick WE, Broderick JB and Hoffman BM (2002) An anchoring role for FeS clusters: chelation of the amino acid moiety of S‐adenosylmethionine to the unique iron site of the [4Fe–4S] cluster of pyruvate formate‐lyase activating enzyme. Journal of the American Chemical Society 124(38): 11270–11271.

Further Reading

Dove JE and Klinman JP (2001) Trihydroxyphenylalanine quinone (TPQ) from copper amine oxidases and lysyl tyrosylquinone (LTQ) from lysyl oxidase. Advances in Protein Chemistry 58: 141–214.

Frey PA and Booker SJ (2001) Radical mechanisms of S‐adenosylmethionine‐dependent enzymes? Advances in Protein Chemistry 58: 1–45.

Kurumbail RG, Kierfer JR and Marnett LJ (2001) Cyclooxygenase enzymes: catalysis and inhibition. Currrent Opinion in Structural Biology 11: 752–760.

Ludwig ML and Matthews RG (1997) Structure‐based perspectives on B12‐dependent enzymes. Annual Reviews of Biochemistry 66: 269–313.

Ochiai E‐I (1994) Free radicals and metalloenzymes: general considerations. In: Sigel H and Sigel A (eds) Metal Ions in Biological Systems, vol.30 pp. 1–24. New York: Marcel Dekker.

Ortiz de Montellano PR (ed.) (1995) Cytochrome P450: Structure, Mechanism, and Biochemistry, 2nd edn. New York: Plenum Press.

Schlichting I, Berendzen J, Chu K et al. (2000) The catalytic pathway of cytochrome P450cam at atomic resolution. Science 287: 1615–1622.

Stubbe JA and van der Donk WA (1998) Protein radicals in enzyme catalysis. Chemical Reviews 98: 705–762.

Waller BJ and Lipscomb JD (1996) Dioxygen activation by enzymes containing binuclear non‐heme iron clusters. Chemical Reviews 96: 2625–2657.

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How to Cite close
Booker, Squire J(May 2005) Enzymatic Free Radical Reactions. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0000620]