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.

Scheme 1. 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.

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

Scheme 3. 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 2. Prototypical radical SAM reactions.

Scheme 4. The reaction cycle of cytochrome P-450cam. The substrate is represented by RH and the product is represented by ROH.

Figure 3. 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.

Scheme 5. First half-reaction of copper amine oxidase. BH and ^–B represent general base and general acid catalysts, respectively.

Scheme 6. 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.

Scheme 7. 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.

Scheme 8. 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.