Computational protocol: Functional characterization and stability improvement of a ‘thermophilic like’ ene reductase from Rhodococcus opacus 1CP

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Protocol publication

[…] The genome of the actinobacterium R. opacus 1CP was investigated for OYE family members through similarity searches applying BLASTp (, ). Pairwise sequence analysis was performed with EMBOSS Needle (). The maximum likelihood distance tree was computed by Mega 6.06-mac applying Clustal W for multiple sequence alignment (500 bootstrap replications). The gene sequences of oyeRo2 and oyeRo2a have been deposited at GenBank under the accession numbers KR349311 and KR349312. [...] An alignment was made of the sequences of OYERo2 and OYERo2a from R. opacus 1CP and of TsER from Thermus scotoductus (50% amino acid sequence identity). Using this alignment and the available dimeric structure of TsER (PDB-id: 3hf3) as template, dimeric structural models including FMN were obtained for OYERo2 and OYERo2a using the MODELLER program version 9.15 (). One hundred comparative models were generated, after which the models with lowest corresponding DOPE scores () were selected. Tetrameric structure models were obtained by applying symmetry operators provided in the pdb file of TsER (Supplementary Figure ). Pymol (PyMOL Molecular Graphics System, Version 1.5.0.4) was used to generate images. […]

Pipeline specifications

Software tools BLASTP, EMBOSS, MEGA, Clustal W, MODELLER, PyMOL
Applications Phylogenetics, Protein structure analysis
Organisms Rhodococcus opacus, Escherichia coli
Chemicals Alkenes, Maleimides, NADP, Succinimides