Title

Authors

Affiliation

¹Internal Medicine-Endocrinology Department, University of Texas Medical Branch, Galveston, TX 77555-1060, USA; ²Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-1079, USA; ³Stanley S. Scott Cancer Center and Department of Otolaryngology, 533 Bolivar St., University Health Sciences Center, New Orleans, LA 70112, USA;

Email

nuoezgue@utmb.edu; *Corresponding author

Phone

+1-409-772-2843

Fax

+1-409-772-8709

Article Type

Hypothesis

Date

Received September 03, 2011; Accepted October 03, 2011; Published October 14, 2011

Apurinic/apyrimidinic endonuclease 1 (APE1), a central enzyme in the base excision repair pathway, cleaves damaged DNA in Mg²⁺ dependent reaction. Despite characterization of nine X-ray crystallographic structures of human APE1, in some cases, bound to various metal ions and substrate/product, the position of the metal ion and its stoichiometry for the cleavage reaction are still being debated. While a mutation of the active site E96Q was proposed to eliminate Mg²⁺ binding at the A-site, we show experimentally that this mutant still requires Mg²⁺ at concentration similar to that for the wild type enzyme to cleave the AP site in DNA. Molecular dynamics simulations of the wild type APE1, E96Q and a double missense mutant E96Q + D210N indicate that Mg²⁺ placed at the A-site destabilizes the bound AP site-containing DNA. In these simulations, the H-bond chain D238-H309-AP site oxygen is broken and the substrate DNA is shifted away from its crystal structure position (1DE9). In contrast, simulations with the Mg²⁺ at site B or A+B sites leave the substrate DNA at the position shown in the crystal structure (1DE9). Taken together our MD simulations and biochemical analysis suggests that Mg²⁺ binding at the B site is involved in the reaction mechanism associated with endonuclease function of APE1.

Keywords

Ref-1, Base excision repair, DNA binding, Phosphodiester

Citation

Oezguen et al. Bioinformation 7(4): 184-198 (2011)
 

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.