Diversity of structures and functions of oxo-bridged non-heme diiron proteins

Abstract

Oxo-bridged diiron proteins are a distinct class of non-heme iron proteins. Their active sites are composed of two irons that are coordinated by amino acid side chains, and a bridging oxygen that interacts with each iron. These proteins are members of the ferritin superfamily and share the structural feature of a four α-helix bundle that provides the residues that coordinate the irons. The different proteins also display a wide range of structures and functions. A prototype of this family is hemerythrin, which functions as an oxygen transporter. Several other hemerythrin-like proteins have been described with a diversity of functions including oxygen and iron sensing, and catalytic activities. Rubrerythrins react with hydrogen peroxide and rubrerythrin-like proteins possess a rubredoxin domain, in addition to the oxo-bridged diiron center. Other redox enzymes with oxo-bridged irons include flavodiiron proteins that act as O₂ or NO reductases, ribonucleotide reductase and methane monooxygenase. Ferritins have an oxo-bridged diiron in the ferroxidase center of the protein, which plays a role in the iron storage function of these proteins. There are also bacterial ferritins that exhibit catalytic activities. The structures and functions of this broad class of oxo-bridged diiron proteins are described and compared in this review.

Keywords: Ferritin; Flavodiiron protein; Hemerythrin; Methane monooxygenase; Ribonucleotide reductase; Rubrerythrin.

Figure 1.. A

A. Structure of the octomeric hemerythrin from Phascolopsis gouldii (PDB entry 1I4Y) [14]. B. Structure of the canonical four 〈-helix bundle of the monomeric hemerythrin from M. capsulatus (Bath) (PDB entry 4XPX) [15]. The two irons shown as brown spheres. C. The oxo-bridged diiron center of M. capsulatus hemerythrin (PDB entry 4XPX) [15]. Amino acid residues that coordinate irons (brown spheres) are shown as sticks, and the bridging oxygen is shown as a red sphere. Figures were prepared using PyMOL [17].

Figure 2.

Interconversion of the deoxy, oxy, and met forms of the oxo-bridged diiron center of hemerythrin.

Figure 3.

Examples of the different combinations of amino acid residues that coordinate the irons in hemerythrin-like proteins. A. HLP from Mycobacterium kansasii with 4H/2E/1Y coordination (PDB entry 6Q09) [20]. B. Iron-sulfur center repair HLP, YtfE, from E. coli with 4H/2E coordination (PDB entry 5FNN) [21]. C. Iron sensing FBXL5 HLP from Homo sapiens with 4H/3E coordination (PDB entry 3V5X) [22]. Figures were prepared using PyMOL [17].

Figure 4.

Structural features of the rubrerythrin from D. vulgaris. A. The rubrerythrin monomer with the hemerythrin-like domain is pale cyan and the rubredoxin-like domain is light blue. B. The Fe-4Cys rubredoxin-like site. C. The hemerythrin-like diiron center. The Fe, N, O and S atoms are colored brown, blue, red and yellow, respectively. The figures were prepared with PyMOL [17] using PDB entry 1RYT [37].

Figure 5.

Dimeric structure of rubrerythrin from P. furiosus. Each monomer is colored gray or cyan. Irons are shown as brown spheres. The figure was prepared with PyMOL [17] using PDB entry 3PWF [40].

Figure 6.

The FlRd FDP from E. coli A. The oxo-bridged diiron site from PDB entry 5LMC [52]. B. Electron transfer path from NADH-reduced FlRd reductase to the oxo-bridged diiron center for reduction of NO. Two electrons are required for the reduction of NO. They are transferred one at a time via the FMN. Figure 6A was prepared using PyMOL [17].

Figure 7.. A

A. Substrate and product of the reaction catalyzed by ribonucleotide reductase. The R group represents the nitrogen base from adenine, cytosine, guanine, or uracil. B. The diiron site in the R2 subunit of the E. coli class ribonucleotide reductase from PDB entry 1MXR [59]. The Fe, N and O atoms are colored brown, blue and red, respectively. Figure7B was prepared using PyMOL [17].

Figure 8.

Structure of ribonucleotide reductase. Two orientations are presented to view α₂β₂ heterodimer. The R1 dimer subunits are colored gray and light blue. Only one of the α subunits (light blue) makes contact with the R2 dimer subunits (pale-cyan and pale-green). In this structure, the substrate GDP molecule (red) is present on this α subunit. The two diiron sites on each β subunit are shown as brown spheres. This figure was prepared in PyMOL [17] using PDB entry 6W4X [61].

Figure 9.

The soluble methane monooxygenase from M. capsulatus Bath. A. The overall structure of the enzyme with its subunits α, β and γ colored in cyan, purple, and gray, respectively. B. The oxo-bridged diiron site of MMOH subunit α. The irons colored brown, oxygen red (including a crystallographic water) and nitrogen blue. Figures were prepared with PyMOL [17] using PDB entry 1MMO [67].

Figure 10.

Proposed mechanism of soluble methane monooxygenase.

Figure 11.

Human H-type Ferritin. A. Structure of the 24-mer structure with two orientations shown to illustrate the 3-fold and 4-fold pore symmetry highlighted in pale-cyan and light blue respectively (PDB entry 6JPS) [80]. B. The 5-helix subunit with A, B and C irons as spheres (PDB entry 4OYN) [82]. C. The oxo-bridged AB diiron site and C iron site. Residues that coordinate the AB site irons are colored in pale-cyan and those that coordinate the C-site iron in light blue (PDB entry 4OYN). [82]. The Fe, N and O atoms are colored brown, blue and red, respectively. Figures were prepared using PyMOL [17].

Figure 12.

Bacterial Ftn iron centers. A. The AB diiron site of E. coli Ftn (PDB entry 4ZTT) [94]. B. The AB diiron site and C iron site of P. aeruginosa Ftn with the AB site colored in pale-cyan and C site colored in light blue (PDB entry 3R2L) [91]. The Fe, N and O atoms are colored brown, blue and red, respectively. Figures were prepared using PyMOL [17].

Figure 13.

Bacterioferritin from E. coli. A. Overall structure of the protein with the subunits of the dimer colored light blue and gray. The irons are shown as spheres and the heme is colored in red. B. Residues that coordinate the AB diiron and the C site. Figures were prepared with PyMOL [17] using PDB entry 3E1M [103].