Iron Cofactors: Nonhaem

Abstract

Proteins and enzymes with nonhaem iron centres display many functions: metal centres with primarily sulfur ligation are involved in electron transfer, electrophilic activation of hydroxyl groups, fixation of N2 and regulation of gene expression; mononuclear and diiron centres with oxygen and nitrogen ligation have roles in various reactions with O2 and in hydrolysis. The principles of their mechanisms of action have emerged from considerable experimentation. Ongoing research is refining understanding of their mechanisms of action and attempting to test and extend their already substantial catalytic capabilities.

Key Concepts

  • Nonhaem iron‐containing enzymes carry out a myriad of catalytic reactions.
  • Iron–sulfur centres participate in electron transfer, electrophilic catalysis, nitrogenase and hydrogenase reactions.
  • Mononuclear and diiron monooxygenases, dioxygenases and oxidases provide nonhaem counterparts to catalysis carried out by haem‐containing enzymes.
  • Rearrangements of protein ligands in nonhaem iron active sites provide a unique aspect to control catalysis.
  • Nonhaem oxidative enzymes access high‐valent states of iron during catalysis.
  • The electrophilic nature of nonhaem iron also supports effective hydrolytic catalysis in reactions where O2 activation is not required.

Keywords: iron; enzyme mechanism; enzyme structure; enzyme specificity; metalloproteins; iron–sulfur clusters; nitrogenase; hydrogenase; S‐adenosylmethionine; radical SAM; hydrogenase; monooxygenase; dioxygenase; lipoxygenase; transferrin; diiron; haemerythrin; ferritin; ribonucleotide reductase; desaturase

Figure 1. (a) Rubredoxin of Pyrococcus furiosus (PDB 1CAA). (b) Heterocyst [2Fe–2S] of Anabaena strain 7120 (PDB 1FRD). (c) [4Fe–4S] of aconitase complexed with 4‐hydroxy‐trans‐aconitate shown in purple (PDB 1FGH).
Figure 2. Spatial orientation of MoFe (a) and P cluster (b) in dinitrogenase (PDB 3U7Q). Molybdenum is shown in cyan and homocitrate is shown in purple. The inset (c) shows that the two cofactors are separated by ∼8 Å.
Figure 3. Initial step in the reaction mechanism of radical SAM enzymes. Coordination of the sulfur atom concomitant with electron transfer from the [4Fe–4S] cluster leads to formation of the adenosyl radical (•H2C–Ado).
Figure 4. Structures of the iron‐containing cofactors in different hydrogenase enzymes. (a) NiFe hydrogenase (PDB 2FRV) with nickel shown in green and two CN and one CO ligated to iron. (b) [Fe–Fe] hydrogenase (PDB 1FEH) with a [4Fe–4S] cluster and a [2Fe–2S] cluster bridged by CO and with three additional CO and two water bound to the iron in the [2Fe–2S] cluster. (c) Iron‐only hydrogenase (PDB 3DAG) active site consisting of iron bound by two CO, water and methanopterin.
Figure 5. Reaction intermediates in the extradiol dioxygenase reaction shown by X‐ray crystallography (PDB 2IGA). (a) Oxy adduct consisting of O2 and catecholic substrate (4‐nitrobenzene, purple) bound to iron. (b) Peroxy intermediate formed by reaction of oxygen at the C‐3 position of the bound catechol. (c) Aromatic ring has been opened. (d) Mechanism of reaction for extradiol cleavage of catechol.
Figure 6. Diiron centres in proteins. (a) Oxyhaemerythrin (PDB 1MHO). The μ‐oxo bridge is shown in green and bound peroxide is shown in purple. (b) Diferric state of ribonucleotide reductase R2 component (PDB 1RIB) showing the proximity of the diiron centre and Ty122 (purple), which is converted to a tyrosyl radical by reaction of the diferrous centre with O2. (c) Diferrous state of stearoyl‐ACP Δ9 (desaturase showing two carboxylate bridges and bidentate coordination of each iron (PDB 1AFR).
Figure 7. Positioning of diiron active sites in toluene‐4‐monooxygenase. (a) Diferric state of toluene 4‐monooxygenase in the absence of acetate (PDB 3IJ5). (b) Diferric state of toluene 4‐monooxygenase in complex with Rieske‐type [2Fe–2S] ferredoxin (PDB 4PIB). (c) Diferrous state of toluene 4‐monoxygenase in complex with effector protein (PDB 3DHI).
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Further Reading

Beinert H, Holm RC and Münck E (1997) Iron–sulfur clusters: nature's modular, multipurpose structures. Science 277: 653–659.

Bertini I, Gray HB, Lippard SJ and Valentine JS (1994) Bioinorganic Chemistry. Mill Valley, CA: University Science Books.

Fraústo da Silva JJR and Williams RJP (1993) The Biological Chemistry of the Elements, 2nd edn. Oxford: Clarendon Press.

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

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

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Fox, Brian G(Oct 2015) Iron Cofactors: Nonhaem. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0000668.pub3]