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Crystal structure of the non-haem iron halogenase SyrB2 in syringomycin biosynthesis

Abstract

Non-haem Fe(ii)/α-ketoglutarate (αKG)-dependent enzymes harness the reducing power of αKG to catalyse oxidative reactions, usually the hydroxylation of unactivated carbons, and are involved in processes such as natural product biosynthesis, the mammalian hypoxic response, and DNA repair1,2. These enzymes couple the decarboxylation of αKG with the formation of a high-energy ferryl-oxo intermediate that acts as a hydrogen-abstracting species2,3,4. All previously structurally characterized mononuclear iron enzymes contain a 2-His, 1-carboxylate motif that coordinates the iron1,2. The two histidines and one carboxylate, known as the ‘facial triad’, form one triangular side of an octahedral iron coordination geometry. A subclass of mononuclear iron enzymes has been shown to catalyse halogenation reactions, rather than the more typical hydroxylation reaction5,6. SyrB2, a member of this subclass, is a non-haem Fe(ii)/αKG-dependent halogenase that catalyses the chlorination of threonine in syringomycin E biosynthesis5. Here we report the structure of SyrB2 with both a chloride ion and αKG coordinated to the iron ion at 1.6 Å resolution. This structure reveals a previously unknown coordination of iron, in which the carboxylate ligand of the facial triad is replaced by a chloride ion.

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Figure 1: SyrB2 activity in syringomycin E biosynthesis.
Figure 2: Structure of SyrB2 with bound iron, chloride and αKG.
Figure 3: Structural comparisons.
Figure 4: Proposed mechanism for the reaction catalysed by SyrB2.

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Acknowledgements

We thank J. W. Nix and T. Doukov for help with data collection; and M. Fischbach for critically reading the manuscript. The Advanced Light Source and Stanford Synchrotron Radiation Laboratory are supported by the US Department of Energy. The SSRL Structural Molecular Biology Program is also supported by the National Institutes of Health. This work was supported in part by grants from the NIH (to C.L.D., to C.T.W. and to L.C.B.), a Merck-sponsored Fellowship of the Helen Hay Whitney Foundation (to F.H.V.) and a Natural Sciences and Engineering Research Council of Canada Postdoctoral Fellowship (to F.H.V.).

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Correspondence to Catherine L. Drennan.

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The coordinates and structure factors for αKG–SyrB2, Cl–Fe(ii)–αKG–SyrB2 and Br–Fe(ii)–αKG–SyrB2 have been deposited in the Protein Data Bank with accession codes 2FCT, 2FCU and 2FCV, respectively. Reprints and permissions information is available at npg.nature.com/reprintsandpermissions. The authors declare no competing financial interests.

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This file contains Supplementary Figures 1–4, Supplementary Methods and Supplementary Table 1. (PDF 1744 kb)

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Blasiak, L., Vaillancourt, F., Walsh, C. et al. Crystal structure of the non-haem iron halogenase SyrB2 in syringomycin biosynthesis. Nature 440, 368–371 (2006). https://doi.org/10.1038/nature04544

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