Maciejewska, Agnieszka M. and Poznański, Jarosław and Kaczmarska, Zuzanna and Krowisz, Beata and Nieminuszczy, Jadwiga and Polkowska-Nowakowska, Agnieszka and Grzesiuk, Elzbieta and Kusmierek, Jaroslaw T. (2013) AlkB dioxygenase preferentially repairs protonated substrates: specificity against exocyclic adducts and molecular mechanism of action. The Journal of biological chemistry, 288 (1). pp. 432-41. ISSN 1083-351X
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Abstract
Efficient repair by AlkB dioxygenase of exocyclic DNA adducts: 3,N(4)-ethenocytosine, 1,N(6)-ethenoadenine, 3,N(4)- α-hydroxyethanocytosine and, reported here for the first time, 3,N(4)- α-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 Asp135 side-chain in the enzyme active centre. 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 Asp135 in recognition of the adduct in its protonated form. Moreover, also ab initio calculations underline the role of substrate protonation in lowering the free energy barrier of the transition state of epoxidation of the ethenoadducts studied. The observed time-courses of repair of racemic mixtures of 3,N(4)- α-hydroxyethanocytosine or 3,N(4)- α-hydroxypropanocytosine are unequivocally two-exponential, indicating that the respective stereoisomers 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.
| Item Type: | Article |
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| Additional Information: | This research was originally published in Journal of Biological Chemistry. MACIEJEWSKA A.M., POZNAŃSKI J., KACZMARSKA Z., KROWISZ B., NIEMINUSZCZY J., POLKOWSKA-NOWAKOWSKA A., GRZESIUK E., KUŚMIEREK J.T. AlkB dioxygenase preferentially repairs protonated substrates: specificity against exocyclic adducts and molecular mechanism of action. Journal of Biological Chemistry 2013 288(1):432-41. © the American Society for Biochemistry and Molecular Biology |
| Subjects: | Q Science > QD Chemistry Q Science > QR Microbiology |
| Divisions: | Department of Biophysics Department of Molecular Biology |
| ID Code: | 643 |
| Deposited By: | dr Agnieszka M. Maciejewska |
| Deposited On: | 15 Apr 2014 12:21 |
| Last Modified: | 14 Oct 2014 11:22 |
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AlkB dioxygenase preferentially repairs protonated substrates: specificity against exocyclic adducts and molecular mechanism of action. (deposited 09 Jan 2013 09:32)
- AlkB dioxygenase preferentially repairs protonated substrates: specificity against exocyclic adducts and molecular mechanism of action. (deposited 15 Apr 2014 12:21) [Currently Displayed]
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