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. 2020 May 4;59(19):7367-7371.
doi: 10.1002/anie.201914896. Epub 2020 Mar 10.

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

Tzu-Yu Chen  1 , Jinfeng Chen  2 , Yijie Tang  3 , Jiahai Zhou  2 , Yisong Guo  3 , Wei-Chen Chang  1
Affiliations

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

Tzu-Yu Chen et al. Angew Chem Int Ed Engl. .

Abstract

N-alkylisonitrile, a precursor to isonitrile-containing lipopeptides, is biosynthesized by decarboxylation-assisted -N≡C group (isonitrile) formation by using N-alkylglycine as the substrate. This reaction is catalyzed by iron(II) and 2-oxoglutarate (Fe/2OG) dependent enzymes. Distinct from typical oxygenation or halogenation reactions catalyzed by this class of enzymes, installation of the isonitrile group represents a novel reaction type for Fe/2OG enzymes that involves a four-electron oxidative process. Reported here is a plausible mechanism of three Fe/2OG enzymes, Sav607, ScoE and SfaA, which catalyze isonitrile formation. The X-ray structures of iron-loaded ScoE in complex with its substrate and the intermediate, along with biochemical and biophysical data reveal that -N≡C bond formation involves two cycles of Fe/2OG enzyme catalysis. The reaction starts with an FeIV -oxo-catalyzed hydroxylation. It is likely followed by decarboxylation-assisted desaturation to complete isonitrile installation.

Keywords: catalysis; decarboxylation; enzymes; iron; reaction mechanisms.

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Figures

Figure 1.
Figure 1.
Crystal structures of ScoE. A) The overall structure of ScoE is shown in cartoon model, with the jellyroll motif colored in cyan. 2Fo-Fc (light gray mesh, contoured at 1.0 σ) electron density map for 1. Dashed lines illustrate hydrogen-bonding interactions involving 1 or bonds between the iron and its ligands. B) Active site of ScoE in the presence of 1 or 3. Putative 2OG binding sites appear to be occupied by exogenous ligands (TAR and FMT). The 2-His-1-Asp triad is shown in wheat stick format. Molecules 1 and 3 are colored in cyan, the electron density maps for 1 and 3 are shown in dark-gray mesh and contoured at 1.0 σ. Iron and waters are shown in orange and red sphere. Putative 2OG binding sites appear to be occupied by exogenous ligands (TAR or FMT) colored in forest. C) Superposition of ScoE•Fe•1 and ScoE•Fe•3.
Figure 2.
Figure 2.
13C NMR spectra of SfaA catalyzed 2 formation under C-H decoupling and C-H coupling conditions. The top, middle and bottom traces represent the 13C-NMR recorded with 5-13C-1 to 2OG ratio at 1:0, 1:1.5 and 1:2.5, respectively.
Figure 3.
Figure 3.
The Mössbauer spectra of SfaA•Fe(II)•2OG•5-2H2-1 and SfaA•Fe(II)•2OG•1 are shown in A and E; The spectra of the samples quenched at 0.03 s are shown in B and F; The difference spectra between A and B (B-A), E and F (F-E), and the spectral simulations (grey lines) are shown in C and G, which indicate the decrease of the quaternary complex (upward blue simulations), the accumulation of the ferryl intermediate (the red simulations) and the additional ferrous species (the green simulations in D and H). See Table S1–S3 for details simulation parameters.
Scheme 1
Scheme 1
A) Two different approaches used to install isonitrile. B) Fe/2OG enzyme catalyzed hydroxylation.
Scheme 2
Scheme 2
Possible pathways for isonitrile formation. Starting from C5-hydroxylation, two pathways involving either second hydroxylation (pathway i) or decarboxylation-assisted desaturation (pathway ii) are proposed.
See this image and copyright information in PMC

References

    1. Wang LJ, Zhu MY, Zhang QB, Zhang X, Yang PL, Liu ZH, Deng Y, Zhu YG, Huang XS, Han L, Li SQ, He J, ACS Chem. Biol 2017, 12, 3067–3075; - PubMed
    2. Crawford JM, Portmann C, Zhang X, Roeffaers MBJ, Clardy J, Proc. Natl. Acad. Sci. U.S.A 2012, 109, 10821–10826; - PMC - PubMed
    3. Mo SY, Krunic A, Chlipala G, Orjala J, J. Nat. Prod 2009, 72, 894–899; - PMC - PubMed
    4. Clarke-Pearson MF, Brady SF, J. Bacteriol 2008, 190, 6927–6930; - PMC - PubMed
    5. Brady SF, Clardy J, Angew. Chem. Int. Ed. Engl 2005, 44, 7063–7065; - PubMed
    6. Garson MJ, Simpson JS, Nat. Prod. Rep 2004, 21, 164–179; - PubMed
    7. Stratmann K, Moore RE, Bonjouklian R, Deeter JB, Patterson GML, Shaffer S, Smith CD, Smitka TA, J. Am. Chem. Soc 1994, 116, 9935–9942;
    8. Parker WL, Rathnum ML, Johnson JH, Wells JS, Principe PA, Sykes RB, J. Antibiot 1988, 41, 454–460; - PubMed
    9. Chang CWJ, Patra A, Roll DM, Scheuer PJ, Matsumoto GK, Clardy J, J. Am. Chem. Soc 1984, 106, 4644–4646.
    1. Chang W.-c., Sanyal D, Huang JL, Ittiamornkui K, Zhu Q, Liu X, Org. Lett 2017, 19, 1208–1211; - PubMed
    2. Brady SF, Clardy J, Angew. Chem. Int. Ed. Engl 2005, 44, 7045–7048. - PubMed
    1. Harris NC, Born DA, Cai WL, Huang YB, Martin J, Khalaf R, Drennan CL, Zhang WJ, Angew. Chem. Int. Ed. Engl 2018, 57, 9707–9710; - PMC - PubMed
    2. Harris NC, Sato M, Herman NA, Twigg F, Cai WL, Liu J, Zhu XJ, Downey J, Khalaf R, Martin J, Koshino H, Zhang WJ, Proc. Natl. Acad. Sci. U.S.A 2017, 114, 7025–7030. - PMC - PubMed
    1. Islam MS, Leissing TM, Chowdhury R, Hopkinson RJ, Schofield CJ, Annu. Rev. Biochem 2018, 87, 585–620; - PubMed
    2. Gao SS, Naowarojna N, Cheng R, Liu X, Liu, Nat. Prod. Rep 2018, 35, 792–837; - PMC - PubMed
    3. Martinez S, Hausinger RP, J. Biol. Chem 2015, 290, 20702–20711; - PMC - PubMed
    4. Bollinger JM Jr.;, Chang W.-c., Matthews ML, Martinie RJ, Boal AK, Krebs C, in 2-Oxoglutarate-Dependent Oxygenases (Eds.: Hausinger RP, Schofield CJ), Royal Society of Chemistry; 2015, pp. 95–122.
    1. Price JC, Barr EW, Tirupati B, Bollinger JM Jr., Krebs C, Biochemistry 2003, 42, 7497–7508; - PubMed
    2. Price JC, Barr EW, Glass TE, Krebs C, Bollinger JM Jr., J. Am. Chem. Soc 2003, 125, 13008–13009. - PubMed

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