Title

Structure modeling of novel DNA glycosylase enzyme from oral pathogen Streptococcus sanguinis

Authors

Ashwani Sharma*, Anshul Nigam

Affiliation

Dept. of Bioscience & Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076 Maharashtra, India; 

E-mail*

ashwansharma@gmail.com; * Corresponding author

Article Type

Hypothesis

Date

Received June 16, 2010; accepted August 26, 2010; published September 20, 2010

The novel 3-methyladenine DNA glycosylase enzyme from oral pathogen Streptococcus sanguinisin involves in DNA repair mechanisms and participates in base excision repair. Its 3D structure is still unknown which may be a potential drug target, therefore here we proposed its putative 3D structure by
homology modeling approach. EsyPred3d software produced more précised modeled structure as compare to Swiss model software. The modeled structure was further verified by PROCHECK analysis and subjected to functional site prediction servers for active site residues prediction. The functional site was further validated by molecular docking approach with ligand EDA (3- [2- Deoxyribofuranosyl] - 3H- 1, 3, 4, 5A, 8-Pentaaza- Asindacene-5- monophosphate) from 1F4R. The EDR docked at the cavity of modeled structure of 3-methyladenine DNA glycosylase enzyme with highest Patchdock score of 3966 and lowest Autodock 4 docking energy of -10.30 Kcal/mol. The YA51, LA105, RA107 residues are surrounding the EDA and matching with ligand binding residues predicted by PROFUNC server.

Keywords

DNA glycosylase, Homology Modeling, Procheck, Patchdock, Docking, Autodock

Citation

Subramanian et al, Bioinformation 5(2): 73-76 (2010)

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

License