Comparative Modeling and Structure Validation of Holliday Junction DNA Helicase RUVB in Chlamydophila pneumoniae AR39

Abstract

Chlamydophila pneumoniae is a species of Chlamydophila bacteria. C. pneumoniae is a widespread obligate intracellular gram negative bacterium that causes upper and lower respiratory infections worldwide. In addition to acute  infections, several chronic inflammatory diseases have been associated with C. pneumoniae infection. RuvB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. DNA helicases utilize the energy from ATP hydrolysis to unwind double-stranded DNA and the biological process is carried out in the cell synthesis of C. pneumoniae. The protein structural characterization is important in rational structure-based drug and vaccine design. Homology modeling can produce high-quality structural models when the target and templates are closely related. Modeller is the program used for homology modeling which provides accurate and efficient models to build loops and side chains found non-identical in sequence. The stereo chemical quality of a best model was validated by PROCHECK server with 94.2% residues under favored region from Ramachandran plot. The CASTp is used for locating, delineating and measuring concave surface regions on 3D structures of proteins. The residues are identified in surface cavity of the best model as Leu (18, 61), Phe (14, 26), Glu (25), Gly (60, 62), Tyr (27,179), Lys (63), Thr (64), Ser (65), Ile (187), Arg (190, 216), and Pro (20, 215) with hydrophobic nature. Thus present study of modeling of Holliday junction DNA helicase RuvB has brought future prospective to fight against C. pneumoniae infection and several chronic inflammatory diseases in order to design rational drugs and vaccines.