Journal Article

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

Kumar, Ritesh, Vetting, Matthew W., Sakai, Ayano, Hillerich, Brandan S., Bonanno, Jeffery B., Babbitt, Patricia C., Brown, Shoshana, Gerlt, John A., Zhao, Suwen, Almo, Steven C., Wood, B. McKay, Seidel, Ronald D., Cronan, John E., Jacobson, Matthew P., Sweedler, Jonathan V.

2013

Overview

Pathway docking ( in silico docking of metabolites to several enzymes and binding proteins in a metabolic pathway) enables the discovery of a catabolic pathway for the osmolyte trans -4-hydroxy- l -proline betaine. Structural key to predicting enzyme function Overprediction and database annotation errors in genome-sequencing projects have caused much confusion because of the difficulty of assigning valid functions to the proteins identified. These authors use structure-guided approaches for predicting the substrate specificities of several enzymes encoded by a bacterial gene cluster to correctly predict the in vitro activity of an enzyme of unknown function and identify the catabolic pathway in which it participates in cells. The substrate-liganded pose predicted by virtual library screening was confirmed experimentally, enzyme 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. This study establishes the utility of structure-guided functional predictions for the discovery of new metabolic pathways. Assigning valid functions to proteins identified in genome projects is challenging: overprediction and database annotation errors are the principal concerns 1 . We and others 2 are developing computation-guided strategies for functional discovery with ‘metabolite docking’ to experimentally derived 3 or homology-based 4 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 coli 5 . 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.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 631/114/2410 / 631/92/607 / ABC transporters / Amino acids / Bacteria - enzymology / Bacteria - genetics / Bacteria - metabolism / Bacterial Proteins - chemistry / Bacterial Proteins - genetics / Bacterial Proteins - metabolism / Binding sites / Carbon / Cell metabolism / E coli / Enzymatic activity / Enzyme activation / Enzyme kinetics / Enzymes / Enzymes - chemistry / Enzymes - genetics / Enzymes - metabolism / Gene expression / Gene Expression Profiling / Genes, Bacterial - genetics / Genome, Bacterial - genetics / Genomes / Glycolysis / Humanities and Social Sciences / Kinetics / letter / Ligands / Metabolic Networks and Pathways - genetics / Metabolism / Metabolites / Metabolomics / Microbiology / Models, Molecular / Molecular Sequence Annotation - methods / multidisciplinary / Multigene Family - genetics / Nitrogen / Operon / Proteins / Science / Structural Homology, Protein / Substrate Specificity