Three Dimensional Model for N-Terminal A Domain of DmpR (2-Dimethylphenol) Protein Based on Secondary Structure Prediction and Fold Recognition

Article type: Research Article

Authors: Suresh, Panneer Selvam | Kumar, Rita | Kumar, Anil

Affiliations: Lab 506, Environmental Biotechnology Division, Institute of Genomics and Integrative Biology, Mall Road, Delhi, India | National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India

Note: [] Corresponding author: Tel.: +1 91 11 27666156; 27666157 Ext-154; Fax: +1 91 11 27667471; E-mail: [email protected]

Abstract: DmpR (dimethylphenol regulatory protein) is a member of the NtrC family of transcriptional activators and controls the transcription of the dmp operons in response to aromatic effector compounds. Secondary structure and fold recognition prediction of N-terminal A domain of this protein (210 amino acid) was performed in Genesilico Metaserver and 3DJury. The consensus result from these servers suggested MJ_1460 as a template. Three dimensional structures were generated from the sequence structure alignments of the template and target protein with MODELLER. The results suggested that the N-terminal A domain of DmpR belongs to Muramoyl pentapeptide carboxypeptidase domain family. The binding interaction sites of the known effectors were predicted using protein-ligand docking. The proposed active site of N-terminal A domain of DmpR comprises of key residues such as Phe93, Glu127, Phe132, Ser160, Phe163, Met164, Arg166 and Pro189. The findings provide some direction to the experimental studies that aim to broaden the range of phenolic derivative which can be sensed by N-DmpR in order to improve the biodegradation potential.

Keywords: DmpR, fold recognition, V4R domain, MJ_1460, protein structure prediction

DOI: 10.3233/ISB-2010-0434

Journal: In Silico Biology, vol. 10, no. 5-6, pp. 223-233, 2010