Structural analysis of Fe(II) and 2-oxoglutarate-dependent Dioxygenases: Escherichia coli AlkBand Saccharomyces cerevisiae Tpa1

Mohan, Monisha (2015) Structural analysis of Fe(II) and 2-oxoglutarate-dependent Dioxygenases: Escherichia coli AlkBand Saccharomyces cerevisiae Tpa1. Masters thesis, Indian Institute of Technology Hyderabad.

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Abstract

Alkylating agents induce cytotoxic DNA base adducts. Alkylation damage are usually repaired by AlkB family of enzymes, which is conserved from bacteria to human. It was first discovered in our lab that Tpa1 is involved in direct alkylation repair.Tpa1 belongs to AlkB family of Fe(II) and 2-oxoglutarate (2OG)-dependent DNA demethylase. Amino acid residues involved in 2OG and Fe (II) coordination in Tpa1 were identified using the state of the art quantum polarized ligand docking (QPLD) and molecular mechanics-generalized Born surface area (MM-GBSA) approaches. In order to design a functionally inactive tpa1 mutant without affecting the protein structure, all possible amino acid mutation using PROVEAN web server were evaluated.

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