Isonitrile Formation by a Non‐Heme Iron(II)‐Dependent Oxidase/Decarboxylase

Abstract

The electron-rich isonitrile is an important functionality in bioactive natural products, but its biosynthesis has been restricted to the IsnA family of isonitrile synthases. We here provide the first structural and biochemical evidence of an alternative mechanism for isonitrile formation. ScoE, a putative non-heme iron(II)-dependent enzyme from Streptomyces coeruleorubidus, was shown to catalyze the conversion of (R)-3-((carboxymethyl)amino)butanoic acid to (R)-3-isocyanobutanoic acid through an oxidative decarboxylation mechanism. This work further provides a revised scheme for the biosynthesis of a unique class of isonitrile lipopeptides, of which several members are critical for the virulence of pathogenic mycobacteria.

Pathway from N‐Alkylglycine to Alkylisonitrile Catalyzed by Iron(II) and 2‐Oxoglutarate‐Dependent Oxygenases

“…[2] The second type involves an iron(II) and 2-oxoglutarate (Fe/2OG) dependent enzyme catalyzed decarboxylation-assisted -NC group installation. [3] Analysis of the biosynthetic gene clusters responsible for the Fe/2OG enzyme catalyzed isonitrile formation revealed that the pathway involved in isonitrile-containing peptide production is conserved in pathogenic mycobacteria including Mycobac-terium tuberculosis and M. marinum. Related operons are also found in the phylum of Actinobacteria, including Streptomyces.…”

Biosynthetic Routes to Natural Isocyanides

“…A few di‐isocyanide lipopeptides from microorganisms are known. Antibiotics SF2369 ( 11 ) and SF2768 ( 12 ) are examples and constitute rare examples of diiocyanides in the microbial world , . Recent discoveries concerning their biosynthesis will be detailed (see section 6).…”

“…In the two last years, the biosynthetic pathways to lipopeptide isocyanides have been revealed. It is at the heart of the PKS‐NRPS logic that the formation of the isocyanide functional group occurs in some Actinobacteria including Mycobacterium marinum and Streptomyces coeruleorubidus , . A unique NRPS domain denominated ScoE is responsible within the PKS‐NRPS machinery for an oxidative decarboxylation of glycine (Scheme , see discussion on mechanism below).…”

“…ScoE from Mycobacterium tuberculosis shares 97 % and 61 % similarity with M. marinum and S. coeruleorubidus respectively and the final lipopeptide may act as virulence factor in M. tuberculosis . The entire biosynthetic pathway could be expressed in E. coli and even more ScoE could be crystallized: it is a non‐heme iron(II) ketoglutarate oxidase/decarboxylase that could, in vitro, be deeply studied to ascertain its mechanism of action …”

“…Catalyzed by acyl‐ACP ligase ScoC, the loading of butenoic acid ( 30 ) onto the multiproteic complex by a thioester linkage to ScoB permits a first crucial step: the ScoD‐ dependent Michael‐type addition of glycine followed by the release of adduct 31 (Scheme ) . ScoE seems to act on free 31 for the second crucial step: the formation of the isocyanide function of intermediate 32 .…”