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Radical SAM enzyme QueE defines a new minimal core fold and metal-dependent mechanism

Nature Chemical Biology volume 10, pages 106–112 (2014)Cite this article

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Abstract

7-carboxy-7-deazaguanine synthase (QueE) catalyzes a key S-adenosyl-L-methionine (AdoMet)- and Mg2+-dependent radical-mediated ring contraction step, which is common to the biosynthetic pathways of all deazapurine-containing compounds. QueE is a member of the AdoMet radical superfamily, which employs the 5′-deoxyadenosyl radical from reductive cleavage of AdoMet to initiate chemistry. To provide a mechanistic rationale for this elaborate transformation, we present the crystal structure of a QueE along with structures of pre- and post-turnover states. We find that substrate binds perpendicular to the [4Fe-4S]-bound AdoMet, exposing its C6 hydrogen atom for abstraction and generating the binding site for Mg2+, which coordinates directly to the substrate. The Burkholderia multivorans structure reported here varies from all other previously characterized members of the AdoMet radical superfamily in that it contains a hypermodified (β6/α3) protein core and an expanded cluster-binding motif, CX14CX2C.

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Figure 1: Biosynthetic pathway for the common precursor of all deazapurines, preQ0.
Figure 2: Overall structure of QueE.
Figure 3: Binding of AdoMet, 6CP, CPH4 and CDG.
Figure 4: Metal ion interactions.
Figure 5: Proposed mechanism for QueE.

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Acknowledgements

This work was supported by US National Institutes of Health grant GM72623 (V.B.) with Administrative Supplement GM72623 S01 to V.B. for the collaboration between V.B. and C.L.D.; a Career Award in Biomedical Sciences from the Burroughs Wellcome Fund (V.B.); and a Biological Chemistry Training Grant (GM008804) (R.M.M.). Additionally, C.L.D. is a Howard Hughes Medical Investigator. This work is based on research conducted at beamline X25 of the National Synchrotron Light Source (NSLS) and at the Advanced Photon Source (APS) on the Northeastern Collaborative Access Team (NE-CAT) beamlines. Financial support from NSLS comes from the Offices of Biological and Environmental Research and of Basic Energy Sciences of the US Department of Energy (DOE) and from the National Center for Research Resources (P41RR012408) and the National Institute of General Medical Sciences at the National Institutes of Health (P41GM103473). NE-CAT at APS is supported by grants from the National Center for Research Resources (5P41RR015301-10) and the National Institute of General Medical Sciences at the National Institutes of Health (8 P41 GM103403-10). APS is an Office of Science User Facility operated for the US DOE Office of Science by Argonne National Laboratory and is also supported by the US DOE under contract number DE-AC02-06CH11357. We thank G.L. Holliday and P. Babbitt (University of California San Francisco) and the Enzyme Function Initiative for their analysis of sequences in the AdoMet radical enzyme superfamily, which are available from the Structure Function Linkage Database (http://sfld.rbvi.ucsf.edu/django/superfamily/29/).

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Authors and Affiliations

  1. Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    Daniel P Dowling & Catherine L Drennan

  2. Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    Daniel P Dowling & Catherine L Drennan

  3. Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA

    Nathan A Bruender, Anthony P Young, Reid M McCarty & Vahe Bandarian

  4. Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    Catherine L Drennan

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  1. Daniel P Dowling
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Contributions

D.P.D. and C.L.D. designed and performed the crystallography experiments. N.A.B., R.M.M., A.P.Y. and V.B. designed and carried out the biochemical experiments. D.P.D., N.A.B., V.B. and C.L.D. contributed to the writing of the manuscript.

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Correspondence to Catherine L Drennan.

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Dowling, D., Bruender, N., Young, A. et al. Radical SAM enzyme QueE defines a new minimal core fold and metal-dependent mechanism. Nat Chem Biol 10, 106–112 (2014). https://doi.org/10.1038/nchembio.1426

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