Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
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Homology Modeling and Docking Studies of Streptomyces peucetius CYP147F1 as Limonene Hydroxylase

  • Bhattarai, Saurabh (Institute of Biomolecule Reconstruction (iBR), Department of Pharmaceutical Engineering, SunMoon University) ;
  • Liou, Kwangkyoung (Institute of Biomolecule Reconstruction (iBR), Department of Pharmaceutical Engineering, SunMoon University) ;
  • Oh, Tae-Jin (Institute of Biomolecule Reconstruction (iBR), Department of Pharmaceutical Engineering, SunMoon University)
  • Received : 2011.12.21
  • Accepted : 2012.02.24
  • Published : 2012.07.28
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Abstract

Homology modeling of Streptomyces peucetius CYP147F1 was constructed using three cytochrome P450 structures, CYP107L1, CYPVdh, and CYPeryF, as templates. The lowest energy SPCYP147F1 model was then assessed for stereochemical quality and side-chain environment by Accelrys Discovery Studio 3.1 software. Further activesite optimization of the SPCYP147F1 was performed by molecular dynamics to generate the final SPCYP147F1 model. The substrate limonene was then docked into the model. The model-limonene complex was used to validate the active-site architecture, and functionally important residues within the substrate recognition site were identified by subsequent characterization of the secondary structure. The docking of limonene suggested that SPCYP147F1 would have broad specificity with the ligand based on the two different orientations of limonene within the active site facing to the heme. Limonene with C7 facing the heme with distance of $3.4{\AA}$ from the Fe was predominant.

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