Discovery of new enzymes and metabolic pathways by using structure and genome context

Abstract

Assigning valid functions to proteins identified in genome projects is challenging: overprediction and database annotation errors are the principal concerns1. We and others2 are developing computation-guided strategies for functional discovery with ‘metabolite docking’ to experimentally derived3 or homology-based4 three-dimensional structures. Bacterial metabolic pathways often are encoded by ‘genome neighbourhoods’ (gene clusters and/or operons), which can provide important clues for functional assignment. We recently demonstrated the synergy of docking and pathway context by ‘predicting’ the intermediates in the glycolytic pathway in Escherichia coli5. Metabolite docking to multiple binding proteins and enzymes in the same pathway increases the reliability of in silico predictions of substrate specificities because the pathway intermediates are structurally similar. Here we report that structure-guided approaches for predicting the substrate specificities of several enzymes encoded by a bacterial gene cluster allowed the correct prediction of the in vitro activity of a structurally characterized enzyme of unknown function (PDB 2PMQ), 2-epimerization of trans-4-hydroxy-l-proline betaine (tHyp-B) and cis-4-hydroxy-d-proline betaine (cHyp-B), and also the correct identification of the catabolic pathway in which Hyp-B 2-epimerase participates. The substrate-liganded pose predicted by virtual library screening (docking) was confirmed experimentally. The enzymatic activities in the predicted pathway were confirmed by in vitro assays and genetic analyses; the intermediates were identified by metabolomics; and repression of the genes encoding the pathway by high salt concentrations was established by transcriptomics, confirming the osmolyte role of tHyp-B. This study establishes the utility of structure-guided functional predictions to enable the discovery of new metabolic pathways.

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Figure 1: Homology modelling and docking results for HpbD, HpbJ and HpbB1.
Figure 2: Genome contexts of HpbD in P. bermudensis and the orthologous genes in P. denitrificans.
Figure 3: Chemotype analysis of HpbD docking results.
Figure 4: Catabolic pathway for tHyp-B and kinetic constants for HpbD.

Accession codes

Accessions

Protein Data Bank

Data deposits

The atomic coordinates and structure factors for APO Hyp-B 2-epimerase (HpbD) and tHyp-B-liganded HpbD are deposited in the Protein Data Bank under accession numbers 2PMQ and 4H2H, respectively.

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Acknowledgements

This research was supported by cooperative agreements from the US National Institutes of Health (U54GM093342, U54GM074945 and U54GM094662). Molecular graphics and analyses were performed with the University of California, San Francisco (UCSF) Chimera package. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics at UCSF (supported by National Institutes of Health P41-GM103311). Use of the Advanced Photon Source, an Office of Science User Facility operated for the US Department of Energy (DOE) Office of Science by Argonne National Laboratory, was supported by the US DOE under contract no. DE-AC02-06CH11357. Use of the Lilly Research Laboratories Collaborative Access Team (LRL-CAT) beamline at Sector 31 of the Advanced Photon Source was provided by Eli Lilly Company, which operates the facility.

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S.Z., R.K., A.S., M.W.V., B.M.W., S.B., J.B.B., B.S.H., R.D.S., P.C.B., S.C.A., J.V.S., J.A.G., J.E.C. and M.P.J. designed the research. S.Z., R.K., A.S., M.W.V., B.M.W., J.B.B., B.S.H. and R.D.S. performed the research. S.Z., R.K., A.S., M.W.V., B.M.W., S.B., J.B.B., B.S.H., R.D.S., P.C.B., S.C.A., J.V.S., J.A.G., J.E.C. and M.P.J. analysed data. S.Z., R.K., A.S., M.W.V., B.M.W., S.B., J.B.B., B.S.H., R.D.S., P.C.B., S.C.A., J.V.S., J.A.G., J.E.C. and M.P.J. wrote the paper.

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Correspondence to Patricia C. Babbitt or Steven C. Almo or Jonathan V. Sweedler or John A. Gerlt or John E. Cronan or Matthew P. Jacobson.

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M.P.J. is a consultant to Schrödinger LLC, which developed or licensed some of the software used in this study.

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Zhao, S., Kumar, R., Sakai, A. et al. Discovery of new enzymes and metabolic pathways by using structure and genome context. Nature 502, 698–702 (2013). https://doi.org/10.1038/nature12576

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