Structure and reactions of the cofactors of oxidoreductases such as ferredoxin

Summary

Enzymes catalysing oxido-reductive reactions (oxidoreductases) do so with the aid of non-protein molecules (prosthetic groups or cofactors) at their active sites. The three main types of such prosthetic groups or cofactors are iron–sulphur clusters, derivatives of flavin (FAD and FMN) and nucleotide derivatives of nicotinamide (NAD and NADP). The groups of proteins incorporating these type of cofactors are often referred to by the general terms ferredoxins (also iron-sulphur proteins), flavoproteins, and NAD(P)-linked oxidoreductases, respectively.

Introduction

The vast majority of enzymes are proteins, linear polypeptide chains folded into specific but irregular spheroidal shapes. In addition to interacting with the reaction substrates, the amino acid side-chains of the polypeptide chains participate in the actual reactions catalysed by many enzymes, and in many cases are sufficient for the catalytic properties of enzymes. However for the catalysis of some sophisticated reactions, additional non-protein molecules are required — metal ions or organic molecules — known generally as ‘co-factors’, ‘co-enzymes’ or ‘prosthetic groups’. This is the case for the various enzymes termed oxidoreductases, which catalyse oxidation/reduction reactions, involving the transfer of electrons.

Nucleotide derivatives of nicotinamide in NAD(P)-linked oxidoreductases

The cofactors found most frequently in oxidoreductases are nicotinamide adenine dinucleotide (NAD) and nicotinamide adenine dinucleotide phosphate (NADP). The pyridine ring of the cofactor is the electron acceptor, and the oxidized and reduced forms are termed NAD⁺ and NADH, respectively.

[Own diagram]

Proteins with bound NAD or NADP (non-covalently) are the most common type involved in oxido-reductions, and have systematic names composed of the cofactor, substrate and ‘oxidoreductase’.
e.g.
Systematic Name: lactate:NAD⁺ oxidoreductase
Common Name: lactate dehydrogenase)

Flavin Nucleotides in Flavoproteins

The other common cofactors in oxidoreductases are flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN). The isoalloxazine ring is the electron acceptor, and the oxidized and reduced forms are termed FAD (FMN) and FADH₂ (FMNH₂), respectively.

[Adapted from section 14.3 of Berg et al.]

Proteins containing FAD or FMN are called flavoproteins, and are less abundant than NAD(P)-linked oxidoreductases, and a few of them actually perform non-redox reactions. Example of nomenclature:
Systemic name: short-chain acyl-CoA:electron-transfer flavoprotein 2,3-oxidoreductase
Common name: short-chain acyl-CoA dehydrogenase

Iron–Sulphur Clusters in Ferredoxins

Whereas the above two oxidoreductases are common in intermediary metabolism, those containing iron–sulphur clusters (some of which are known as ferredoxins) tend to be involved in more specialized and ancient reactions, such as photosynthesis, tagged in the question. The diagram shows one particular type (2Fe–2S) of iron–sulphur cluster and its covalent attachment to the ferredoxin through cysteine residues. 4Fe–4S stoichiometries are also found, as well as some others.

The electron transfer involves changes in the oxidation state — Fe(II)/Fe(III) — of the iron.

[Adapted from section 19.3.3 of Berg et al.]

The figure also provides a good illustration of the relationship between a co-factor and the protein in which it resides.

Example of nomenclature:
Systematic name: hydrogen:ferredoxin oxidoreductase
Common name: ferredoxin hydrogenase

The situation here is complicated by the fact that iron–sulphur clusters are found in other proteins besides those termed ferredoxin, including some specialized oxidoreductases involved in the electron-transport chain, and in nitrogenases. The term ferredoxin is historical rather than systematic.

Differences between these oxidoreductase cofactors

The specific roles played by these three cofactors in oxidoreductases is a topic of its own. However, it should be mentioned that an important difference is their standard reduction potentials, the biochemical background to which can be found in Section 18.2.1 of Berg et al., available online.

Ferredoxin-NADP⁺ reductase (FNR)

Electron transport occurs between the different cofactors in certain circumstances, one of which is photosynthesis where electrons are transferred from ferredoxin to NADP⁺. The enzyme catalysing this — Ferredoxin-NADP⁺ reductase — uses the third type of cofactor — FAD!