NDLI: AlkB dioxygenase preferentially repairs protonated substrates: specificity against exocyclic adducts and molecular mechanism of action.

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AlkB dioxygenase preferentially repairs protonated substrates: specificity against exocyclic adducts and molecular mechanism of action.

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AlkB dioxygenase preferentially repairs protonated substrates: specificity against exocyclic adducts and molecular mechanism of action.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Kaczmarska, Zuzanna Krowisz, Beata Grzesiuk, Elzbieta Nieminuszczy, Jadwiga Maciejewska, Agnieszka M. Kusmierek, Jaroslaw T. Polkowska-nowakowska, Agnieszka Poznanski, Jaroslaw
Description	Author Affiliation: Maciejewska AM ( Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland.)
Abstract	Efficient repair by Escherichia coli AlkB dioxygenase of exocyclic DNA adducts 3,N(4)-ethenocytosine, 1,N(6)-ethenoadenine, 3,N(4)- -hydroxyethanocytosine, and reported here for the first time 3,N(4)- -hydroxypropanocytosine requires higher Fe(II) concentration than the reference 3-methylcytosine. The pH optimum for the repair follows the order of pK(a) values for protonation of the adduct, suggesting that positively charged substrates favorably interact with the negatively charged carboxylic group of Asp-135 side chain in the enzyme active center. This interaction is supported by molecular modeling, indicating that 1,N(6)-ethenoadenine and 3,N(4)-ethenocytosine are bound to AlkB more favorably in their protonated cationic forms. An analysis of the pattern of intermolecular interactions that stabilize the location of the ligand points to a role of Asp-135 in recognition of the adduct in its protonated form. Moreover, ab initio calculations also underline the role of substrate protonation in lowering the free energy barrier of the transition state of epoxidation of the etheno adducts studied. The observed time courses of repair of mixtures of stereoisomers of 3,N(4)- -hydroxyethanocytosine or 3,N(4)- -hydroxypropanocytosine are unequivocally two-exponential curves, indicating that the respective isomers are repaired by AlkB with different efficiencies. Molecular modeling of these adducts bound by AlkB allowed evaluation of the participation of their possible conformational states in the enzymatic reaction.
ISSN	00219258
e-ISSN	1083351X
Journal	Journal of Biological Chemistry
Issue Number	1
Volume Number	288
Language	English
Publisher	American Society for Biochemistry and Molecular Biology (United States)
Publisher Date	2013-01-04
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Escherichia Coli Proteins Physiology Mixed Function Oxygenases Catalytic Domain DNA Chemistry DNA Adducts DNA Repair Dose-Response Relationship, Drug Escherichia Coli Enzymology Hydrogen-Ion Concentration Kinetics Ligands Lipid Peroxidation Models, Chemical Molecular Conformation Oxidative Stress Protein Binding Protons Stereoisomerism Research Support, Non-U.S. Gov't Biochemistry Molecular Biology
Content Type	Text
Resource Type	Article
Subject	Cell Biology Biochemistry Molecular Biology

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