Cyanobacterial alkane biosynthesis further expands the catalytic repertoire of the ferritin-like 'di-iron-carboxylate' proteins

Abstract

Enzymes that activate dioxygen at carboxylate-bridged non-heme diiron clusters residing within ferritin-like, four-helix-bundle protein architectures have crucial roles in, among other processes, the global carbon cycle (e.g. soluble methane monooxygenase), fatty acid biosynthesis [plant fatty acyl-acyl carrier protein (ACP) desaturases], DNA biosynthesis [the R2 or β2 subunits of class Ia ribonucleotide reductases (RNRs)], and cellular iron trafficking (ferritins). Classic studies on class Ia RNRs showed long ago how this obligatorily oxidative di-iron/O2 chemistry can be used to activate an enzyme for even a reduction reaction, and more recent investigations of class Ib and Ic RNRs, coupled with earlier studies on dimanganese catalases, have shown that members of this protein family can also incorporate either one or two Mn ions and use them in place of iron for redox catalysis. These two strategies--oxidative activation for non-oxidative reactions and use of alternative metal ions--expand the catalytic repertoire of the family, probably to include activities that remain to be discovered. Indeed, a recent study has suggested that fatty aldehyde decarbonylases (ADs) from cyanobacteria, purported to catalyze a redox-neutral cleavage of a Cn aldehyde to the Cn-1 alkane (or alkene) and CO, also belong to this enzyme family and are most similar in structure to two other members with heterodinuclear (Mn-Fe) cofactors. Here, we first briefly review both the chemical principles underlying the O2-dependent oxidative chemistry of the 'classical' di-iron-carboxylate proteins and the two aforementioned strategies that have expanded their functional range, and then consider what metal ion(s) and what chemical mechanism(s) might be employed by the newly discovered cyanobacterial ADs.

Figure 1

Comparison of the dimetal-carboxylate sites in Pm AD (pdb code: 2OC5) and the Mn/Fe-containing putative oxidase from Mycobacterium tuberculosis (pdb code: 3EE4). Amino acid residues of Pm AD and the Mt protein are colored in green and purple, respectively. The non-protein ligands, tentatively assigned as stearate and myristate, are shown in yellow and cyan, respectively. The Fe and Mn ions are shown in orange and purple, respectively. The oxidized crosslink between Val71 and Tyr162 in the Mt protein is shown in gray. Amino acid numbers given first refer to the Pm AD, while those in parentheses refer to the Mt protein.

Scheme 1

Diverse reaction pathways of the peroxo-Fe₂(III/III) intermediates in reactions of the ferritin-like di-iron-carboxylate proteins. For simplicity, we depict the peroxo-Fe₂(III/III) intermediate as having a μ-1,2 bridging mode, although many other binding modes have been discussed. Aromatic hydroxylation is believed to proceed by a mechanism similar to that labeled as —epoxidation.

Scheme 2

Possible reaction pathways and co-products in conversion of fatty aldehydes to alk(a/e)nes by cyanobacterial aldehyde decarbonylases.

Scheme 3

Proposed organometallic mechanisms for aldehyde decarbonylation. (A) Mechanism of the Rh(I)-catalyzed aldehyde decarbonylation, adapted from [74]; (B) Possible OM-like mechanism for aldehyde decarbonylation at a hypothetical dinuclear Fe/Ni cofactor in cyanobacterial ADs.

Scheme 4

Possible mechanisms for aldehyde decarbonylation leading to generation of formate as co-product. (A) A hypothetical —RNR-like mechanism initiated by formation of a gem-diol-yl radical from the hydrated form of the fatty aldehyde. The active form of the dinuclear form of the cofactor is shown as (μ-O)-Mn(IV)/Fe(III), by analogy to the cofactor of the Ct Ic-RNR-β2 [39]. (B) A hypothetical —O₂ activation— mechanism involving nucleophilic attack of a peroxide on the substrate carbonyl group to initiate O-O and C-C fragmentation. The O₂-reactive form of the dinuclear cofactor is shown as Fe₂(II/II), due to the extensive precedent for this cofactor to form peroxo intermediates of diverse reactivity.