Computational protocol: A Terpene Synthase Is Involved in the Synthesis of the Volatile Organic Compound Sodorifen of Serratia plymuthica 4Rx13

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Protocol publication

[…] 3D-protein structure homology modeling of the Serratia plymuthica 4Rx13 terpene cyclase was performed with YASARA (). A search for templates in the protein database () revealed one appropriate X-ray template, the selinadiene synthase, which was complexed with dihydrofarnesyl pyrophosphate from Streptomyces pristinaespiralis (pdb-code 4OKZ) (). Based on this X-ray structure three homology models of the S. plymuthica terpene cyclase were created, two of them were based on slightly alternative sequence alignments including secondary structure predictions, and a final hybrid model joining was extracted from the best folded fragments of both initial models. The latter one was used for final refinements and docking of the product sodorifen into the active site. Since the template structure was co-crystallized with the ligand dihydrofarnesyl pyrophosphate, this information was automatically transferred into the homology model of S. plymuthica by YASARA. The ligand, however, was manually modified to farnesyl pyrophosphate using the molecular modeling environment program MOE 2014.09 and was subsequently optimized in the active site pocket using fixed coordinates of the protein. Sodorifen was docked into the active site using the program MOE as well. The quality of the homology model was evaluated using PROCHECK () and ProSA II (, ). The model is of excellent quality with 91.9% residues being in the most favored region of the Ramachandran plot and no outlier were recognized. The ProSA energy graphs are all in negative range and the calculated z-scores are in the range of natively folded proteins. […]

Pipeline specifications

Software tools YASARA, PROCHECK
Applications Drug design, Protein structure analysis
Organisms Serratia plymuthica
Chemicals Amino Acids, Carbon, Hydrogen