EnzymeMiner

This is a landing page of EnzymeMiner, a web application for automated and periodical mining of interesting enzyme sequences in genomic databases.

The EnzymeMiner method utilizes a number of sequence and structural bioinformatics tools for identification of protein-coding genes with conserved catalytic residues presumably catalyzing a defined enzymatic reaction. Functional diversity of mined hits selected for experimental testing is secured by prediction of protein tertiary structures, analysis of protein cavities and access tunnels, modelling of enzyme-substrate complexes and prediction of their reactivity.

The primary workflow was validated against the family of model enzymes haloalkane dehalogenases [1]. The sequence-based search identified 658 potential dehalogenases. The subsequent analysis prioritized and selected 20 candidates for exploration of protein functional diversity. The enzymes discovered originated from genetically unrelated Bacteria and Eukaryota, for the first time also from Archaea, and showed novel catalytic properties and stabilities.

The web tool EnzymeMiner is currently under development to be easily applicable on any enzyme family while offering user-friendly setup of calculation and handy tools for analysis of results. The minimal input for the calculation is a set of representative protein sequences of enzyme family of interest together with a location of their catalytic residues. The output is then a heavily annotated set of identified targets based on current version of NCBI non-redundant protein database.

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References

  1. Vanacek, P., Sebestova, E., Babkova, P., Bidmanova, S., Daniel, L., Dvorak, P., Stepankova, V., Chaloupkova, R., Brezovsky, J., Prokop, Z., Damborsky, J., 2018: Exploration of Enzyme Diversity by Integrating Bioinformatics with Expression Analysis and Biochemical Characterization. ACS Catalysis 8: 2402-2412.
  2. Hon, J., Borko, S., Bednar, D., Prokop, Z., Martinek, T., Damborsky, J., 2019: EnzymeMiner: Web Server for Automated Mining of Sequences Encoding Enzymes with Diversified Functions. Nucleic Acids Research (in preparation).