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Title

MD simulation and experimental evidence for Mg2+ binding at the b site in human AP endonuclease 1

 

Authors

Numan Oezguen1*, Anil K. Mantha2, Tadahide Izumi3, Catherine H. Schein2, Sankar Mitra2, Werner Braun2

 

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

 

Abstract

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

 

Copyright

Publisher

 

Copyright Transfer Agreement

The authors of published articles in Bioinformation automatically transfer the copyright to the publisher upon formal acceptance. However, the authors reserve right to use the information contained in the article for non commercial purposes.

 

License

This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.