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


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.


  1. Koehntop, K. D., Emerson, J. P. & Que, L. Jr. The 2-His-1-carboxylate facial triad: a versatile platform for dioxygen activation by mononuclear non-heme iron(ii) enzymes. J. Biol. Inorg. Chem. 10, 87–93 (2005)

    Article  CAS  Google Scholar 

  2. Hausinger, R. P. Fe(ii)/α-ketoglutarate-dependent hydroxylases and related enzymes. Crit. Rev. Biochem. Mol. Biol. 39, 21–68 (2004)

    Article  CAS  Google Scholar 

  3. Price, J. C., Barr, E. W., Hoffart, L. M., Krebs, C. & Bollinger, J. M. Jr. Kinetic dissection of the catalytic mechanism of taurine:α-ketoglutarate dioxygenase (TauD) from Escherichia coli. Biochemistry 44, 8138–8147 (2005)

    Article  CAS  Google Scholar 

  4. Price, J. C., Barr, E. W., Tirupati, B., Bollinger, J. M. Jr & Krebs, C. The first direct characterization of a high-valent iron intermediate in the reaction of an α-ketoglutarate-dependent dioxygenase: a high-spin FeIV complex in taurine/α-ketoglutarate dioxygenase (TauD) from Escherichia coli. Biochemistry 42, 7497–7508 (2003)

    Article  CAS  Google Scholar 

  5. Vaillancourt, F. H., Yin, J. & Walsh, C. T. SyrB2 in syringomycin E biosynthesis is a non-heme Feii α-ketoglutarate and O2 dependent halogenase. Proc. Natl Acad. Sci. USA 102, 10111–10116 (2005)

    Article  ADS  CAS  Google Scholar 

  6. Vaillancourt, F. H., Yeh, E., Vosburg, D. A., O'Connor, S. E. & Walsh, C. T. Cryptic chlorination by a non-haem iron enzyme during cyclopropyl amino acid biosynthesis. Nature 436, 1191–1194 (2005)

    Article  ADS  CAS  Google Scholar 

  7. Guenzi, E., Galli, G., Grgurina, I., Gross, D. C. & Grandi, G. Characterization of the syringomycin synthetase gene cluster. A link between prokaryotic and eukaryotic peptide synthetases. J. Biol. Chem. 273, 32857–32863 (1998)

    Article  CAS  Google Scholar 

  8. Grgurina, I. et al. Relevance of chlorine-substituent for the antifungal activity of syringomycin and syringotoxin, metabolites of the phytopathogenic bacterium Pseudomonas syringae pv. syringae. Experientia 50, 130–133 (1994)

    Article  CAS  Google Scholar 

  9. Dong, C. et al. Tryptophan 7-halogenase (PrnA) structure suggests a mechanism for regioselective chlorination. Science 309, 2216–2219 (2005)

    Article  ADS  CAS  Google Scholar 

  10. Chang, Z. et al. The barbamide biosynthetic gene cluster: a novel marine cyanobacterial system of mixed polyketide synthase (PKS)–non-ribosomal peptide synthetase (NRPS) origin involving an unusual trichloroleucyl starter unit. Gene 296, 235–247 (2002)

    Article  CAS  Google Scholar 

  11. Walton, J. D. Host-selective toxins: agents of compatibility. Plant Cell 8, 1723–1733 (1996)

    Article  CAS  Google Scholar 

  12. Holm, L. & Sander, C. Mapping the protein universe. Science 273, 595–603 (1996)

    Article  ADS  CAS  Google Scholar 

  13. Dann, C. E., Bruick, R. K. & Deisenhofer, J. Structure of factor-inhibiting hypoxia-inducible factor 1: an asparaginyl hydroxylase involved in the hypoxic response pathway. Proc. Natl Acad. Sci. USA 99, 15351–15356 (2002)

    Article  ADS  CAS  Google Scholar 

  14. Vaillancourt, F. H., Vosburg, D. A. & Walsh, C. T. Dichlorination and bromination of a threonyl-S-carrier protein by the nonheme Feii halogenase SyrB2. ChemBioChem (in the press)

  15. Allen, F. H. The Cambridge Structural Database: a quarter of a million crystal structures and rising. Acta Crystallogr. B 58, 380–388 (2002)

    Article  Google Scholar 

  16. Goldsmith, C. R., Jonas, R. T., Cole, A. P. & Stack, D. P. A spectrochemical walk: single-site perturbation within a series of six-coordinate ferrous complexes. Inorg. Chem. 41, 4642–4652 (2002)

    Article  CAS  Google Scholar 

  17. Grzyska, P. K. et al. Steady-state and transient kinetic analyses of taurine/α-ketoglutarate dioxygenase: effects of oxygen concentration, alternative sulfonates, and active-site variants on the FeIV-oxo intermediate. Biochemistry 44, 3845–3855 (2005)

    Article  CAS  Google Scholar 

  18. Kojima, T., Leising, R. A., Yan, S. & Que, L. Jr . Alkane functionalization at nonheme iron center. Stoichiometric transfer of metal-bound ligands to alkane. J. Am. Chem. Soc. 115, 11328–11335 (1993)

    Article  CAS  Google Scholar 

  19. Terwilliger, T. C. & Berendzen, J. Automated MAD and MIR structure solution. Acta Crystallogr. D 55, 849–861 (1999)

    Article  CAS  Google Scholar 

  20. La Fortelle, E. & Bricogne, G. Maximum-likelihood heavy-atom parameter refinement in MIR and MAD methods. Methods Enzymol. 276, 472–494 (1997)

    Article  Google Scholar 

  21. Cowtan, K. DM: an automated procedure for phase improvement by density modification. CCP4/ESF-EACBM Newslett. Protein Crystallogr. 31, 34–38 (1994)

    Google Scholar 

  22. McRee, D. E. XtalView/Xfit—a versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125, 156–165 (1999)

    Article  CAS  Google Scholar 

  23. Brunger, A. T. et al. Crystallography and NMR system (CNS): a new software system for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998)

    Article  CAS  Google Scholar 

  24. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D 53, 240–255 (1997)

    Article  CAS  Google Scholar 

  25. Potterton, E., Briggs, P., Turkenburg, M. & Dodson, E. A graphical user interface to the CCP4 program suite. Acta Crystallogr. D 59, 1131–1137 (2003)

    Article  Google Scholar 

  26. Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. PROCHECK—a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283–291 (1993)

    Article  CAS  Google Scholar 

  27. Kabsch, W. & Sander, C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577–2637 (1983)

    Article  CAS  Google Scholar 

  28. Delano, W. L. The PyMOL Molecular Graphics System (2002).

  29. Kleywegt, G. J. & Jones, T. A. A super position. CCP4/ESF-EACBM Newslett. Protein Crystallogr. 31, 9–14 (1994)

    Google Scholar 

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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 The authors declare no competing financial interests.

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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).

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