• 3D Structure Prediction of Halohydrin Dehalogenase from Mycobacterium sp. GP1 for Proceedings of the International Conference on Bioinformatics and Biomedical Engineering (iCBBE 2014)   [iCBBE 2014]
  • Author(s)
  • Xiong Wang, Lixia Tang
  • Based on sequence similarities, six known halohydrin dehalogenases so far have been divided into three different groups, namely group A, B and C. These enzymes have been cloned, sequenced, expressed and purified. HheB which belongs to group B was isolated from Mycobacterium sp. GP1 for its ability to use 1,2-dibromoethane as a sole source of carbon and energy. Strikingly, HheB can catalyze the ring-opening reaction of 1,2-epoxy-2-methylbutane with CN-, displaying a distinct substrate preference as compare with the other two groups. The crystal structures of HheC from Agrobacterium radiobacter AD1 and HheA from Arthrobacter sp. AD2 have already been solved, providing important information for their follow-up study. But the crystal structure of HheB is still unknown. In this work, three webservers were used to predict the 3D structure model of HheB. Firstly, the accuracy of these webservers in structure prediction was evaluated by predicting the structure of HheC. The merit rating of these predicted HheC structures was analyzed by using server TM-Align and CαRMSD method. Compared with the crystal structure of HheC, the ROBETTA predicts the best models. Secondly, ROBETTA was used to predict the 3D structure models of HheB and the best structure model was picked by using Rampage. Finally, Q-Site Finder was used to predict the functional sites in the modeled structure of HheB. The results showed that most of the proposed functional sites are equivalent to the important residues in HheC. This work will provide important structure information for the future research of HheB.
  • Halohydrin Dehalogenase, Structure Prediction, ROBETTA, Rampage, Q-site Finder
  • References
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