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The structure of VibH represents nonribosomal peptide synthetase condensation, cyclization and epimerization domains

Nature Structural Biology volume 9, pages 522–526 (2002)Cite this article

Abstract

Nonribosomal peptide synthetases (NRPSs) are large, multidomain enzymes that biosynthesize medically important natural products. We report the crystal structure of the free-standing NRPS condensation (C) domain VibH, which catalyzes amide bond formation in the synthesis of vibriobactin, a Vibrio cholerae siderophore. Despite low sequence identity, NRPS condensation enzymes are structurally related to chloramphenicol acetyltransferase (CAT) and dihydrolipoamide acyltransferases. However, although the latter enzymes are homotrimers, VibH is a monomeric pseudodimer. The VibH structure is representative of both NRPS condensation and epimerization domains, as well as the condensation-variant cyclization domains, which are all expected to be monomers. Surprisingly, despite favorable positioning in the active site, a universally conserved histidine important in CAT and in other C domains is not critical for general base catalysis in VibH.

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Figure 1: NRPS condensation domains, their activity and their sequences.
Figure 2: Structure of the VibH monomer and comparison to the CAT trimer.
Figure 3: The active site of VibH and models of substrate binding.

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Acknowledgements

We thank S.D. Bruner, V.N. Malashkevich and L. Luo for suggestions and technical assistance, A.G. Leslie for providing the coordinates of CAT–CoA, and A. Saxena, R. Sweet and the NSLS beamline staff for their generous help. T.A.K. was a fellow of the Damon Runyon-Walter Winchell Foundation. C.G.M. received funding from the NSERC of Canada and the Canadian Institutes of Health Research. This work was funded by the NIH (C.T.W.) and by MIT startup funds (A.E.K.).

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Authors and Affiliations

  1. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, 02115, Massachusetts, USA

    Thomas A. Keating, C. Gary Marshall & Christopher T. Walsh

  2. Department of Biology, Massachusetts Institute of Technology, Cambridge, 02139, Massachusetts, USA

    Amy E. Keating

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  1. Thomas A. Keating
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  2. C. Gary Marshall
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Correspondence to Christopher T. Walsh or Amy E. Keating.

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Keating, T., Marshall, C., Walsh, C. et al. The structure of VibH represents nonribosomal peptide synthetase condensation, cyclization and epimerization domains. Nat Struct Mol Biol 9, 522–526 (2002). https://doi.org/10.1038/nsb810

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