Journal of Proteomics & Bioinformatics
Open Access

Broad spectrum ligand binding in biphenyl dehydrogenase (BphBB356): Ternary complex structures of BphBB356 from P. pnomenusa

2^nd International Conference on Proteomics & Bioinformatics

July 2-4, 2012 Embassy Suites Las Vegas, USA

Pravindra Kumar, Sonali Dhindwal and Dipak N. Patil

Scientific Tracks Abstracts: J Proteomics Bioinform

Abstract :

Biphenyl dehydrogenase, a member of short-chain dehydrogenase/reductase enzymes, catalyses the second step of aerobic biodegradation of biphenyl/polychlorinated biphenyls. Here, we present the structural characterization of biphenyl dehydrogenase from Pandoraea pnomenusa strain B-356 (BphBB-356). The crystal structures of apo form of enzyme, its complexes with NAD+ (binary form) and with NAD+-product (2,3-dihydroxybiphenyl)/product analog (4,4?-dihydroxybiphenyl) (ternary form) were determined. An intermediate structure of product-soaked enzyme was also obtained, where the electron density of co-enzyme and product were not located but the substrate binding loop was ordered as compared to the apo and binary form and displaced significantly with respect to the ternary structure. These five structures provide snapshots of the conformational changes during the ligand binding. Comparative analyses of these structures revealed that substrate binding loop is highly mobile and a series of structural changes take place starting from the disorganized loop in apo form towards its organization in presence of ligand, then undergoes a conformational change during ligand binding forming a cavity to accommodate the large range of ligands. For the first time, combinations of structural and molecular docking studies of BphBB356 elucidate the unique ability of the enzyme to transform the cis-dihydrodiols of -meta, para- and ortho- substituted chlorobiphenyls.