Metal-Dependent Enzymes

Metal-dependent enzymes, or metalloenzymes, are catalysts that require a metal ion at their active site to work. Roughly a third of all enzymes are thought to use a metal, and the chemistry the metal provides defines what the enzyme can do - from the zinc of carbonic anhydrase to the iron of cytochrome P450 oxygenases.

Definition

Metal-dependent enzymes (metalloenzymes) are enzymes whose catalytic activity requires one or more metal ions bound at or near the active site, where the metal participates in the reaction as a Lewis acid, a redox centre, or an organiser of substrate and intermediate geometry.

Scope

The topic covers how enzymes deploy bound metal ions for catalysis: zinc enzymes acting as Lewis acids, magnesium-dependent phosphoryl-transfer enzymes, iron-containing oxygenases and iron-sulfur enzymes, and copper and manganese enzymes. It is a reference overview of metalloenzyme chemistry, not clinical guidance. The metals themselves and how cells supply them are treated in the companion topic on metal-ion cofactors.

Core questions

• How does a bound metal lower the activation energy of a reaction?
• Why is zinc so widely used in hydrolytic and group-transfer enzymes?
• How do iron centres enable difficult oxidations such as C-H hydroxylation?
• What distinguishes a tightly bound metalloenzyme from a loosely metal-activated enzyme?

Key concepts

• Zinc as an active-site Lewis acid
• Magnesium in phosphoryl transfer (kinases, polymerases)
• Heme-iron oxygenases (cytochrome P450)
• Non-heme iron and iron-sulfur enzymes
• Copper enzymes in oxygen handling
• Manganese in oxidoreductases
• Catalytic versus structural metal sites

Mechanisms

Metalloenzymes exploit the chemistry their metals make available. A zinc ion at an active site polarises a bound water molecule or substrate carbonyl, generating a nucleophile or stabilising a developing negative charge, the strategy used by many hydrolases and carbonic anhydrase (Maret, 2013; Holm et al., 1996). Magnesium ions coordinate phosphate groups and align them for in-line attack in kinases and nucleic-acid polymerases (Cowan, 2002). Heme-iron enzymes such as cytochrome P450 activate molecular oxygen to a high-valent iron-oxo species capable of hydroxylating unreactive C-H bonds (Denisov et al., 2005). Iron-sulfur and non-heme iron centres carry out electron transfer and additional redox transformations (Beinert et al., 1997). In each case the protein tunes the metal's reactivity through the geometry and identity of its coordinating ligands.

Clinical relevance

Metalloenzymes carry out reactions central to metabolism, oxygen handling, and the processing of xenobiotics (for example the cytochrome P450 oxygenases), so their biochemistry informs pharmacology and toxicology. This entry explains catalytic mechanisms; it describes biochemistry and is not a basis for individual diagnosis or treatment.

History

The study of metalloenzymes grew from early work on zinc in carbonic anhydrase and the structural characterisation of metal sites, which showed how coordinating ligands tune a metal's catalytic behaviour. Subsequent mechanistic studies of magnesium-dependent phosphoryl transfer, heme-iron oxygenation, and iron-sulfur chemistry built a general picture of how bound metals enable otherwise difficult reactions (Holm et al., 1996; Cowan, 2002; Denisov et al., 2005; Beinert et al., 1997).

Seminal works

• holm-1996
• denisov-2005
• cowan-2002
• beinert-1997

Frequently asked questions

What makes an enzyme a metalloenzyme?

It requires one or more metal ions bound at or near its active site to catalyse its reaction; remove the metal and the enzyme loses activity, because the metal supplies chemistry the protein cannot provide on its own.

Why is zinc such a common enzyme metal?

Zinc is a strong Lewis acid that does not undergo redox chemistry, so it can reliably polarise water and substrates and stabilise charged intermediates, making it well suited to the many hydrolytic and group-transfer enzymes that use it.