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Alternative Pathway for the Reaction Catalyzed by DNA Dealkylase AlkB from Ab Initio QM/MM Calculations.

Fang D, Cisneros GA - J Chem Theory Comput (2014)

Bottom Line: The new OH rebound step is coupled with a proton transfer to the OH(-) ligand and results in a novel zwitterion intermediate.The consistency between our theoretical results and experimental findings is discussed.This study provides new insights into the oxidative repair mechanism of DNA repair by nonheme Fe(II) and α-ketoglutarate (α-KG) dependent dioxygenases and a possible explanation for the substrate preference of AlkB.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States.

ABSTRACT
AlkB is the title enzyme of a family of DNA dealkylases that catalyze the direct oxidative dealkylation of nucleobases. The conventional mechanism for the dealkylation of N(1)-methyl adenine (1-meA) catalyzed by AlkB after the formation of Fe(IV)-oxo is comprised by a reorientation of the oxo moiety, hydrogen abstraction, OH rebound from the Fe atom to the methyl adduct, and the dissociation of the resulting methoxide to obtain the repaired adenine base and formaldehyde. An alternative pathway with hydroxide as a ligand bound to the iron atom is proposed and investigated by QM/MM simulations. The results show OH(-) has a small impact on the barriers for the hydrogen abstraction and OH rebound steps. The effects of the enzyme and the OH(-) ligand on the hydrogen abstraction by the Fe(IV)-oxo moiety are discussed in detail. The new OH rebound step is coupled with a proton transfer to the OH(-) ligand and results in a novel zwitterion intermediate. This zwitterion structure can also be characterized as Fe-O-C complex and facilitates the formation of formaldehyde. In contrast, for the pathway with H2O bound to iron, the hydroxyl product of the OH rebound step first needs to unbind from the metal center before transferring a proton to Glu136 or other residue/substrate. The consistency between our theoretical results and experimental findings is discussed. This study provides new insights into the oxidative repair mechanism of DNA repair by nonheme Fe(II) and α-ketoglutarate (α-KG) dependent dioxygenases and a possible explanation for the substrate preference of AlkB.

No MeSH data available.


Related in: MedlinePlus

Relative energies (in kcal/mol) for the structures alongthe minimumenergy path (MEP) for the detachment of the DNA base from Fe and theformation of formaldehyde in the quintet state for the H2O pathway (a) and OH– pathway (b). The numbersin the parentheses are reaction barriers, which are the energy differencesbetween intermediates and their corresponding TSs. The ISFeIII–OF reactant (Figure 2) is taken as the reference for each pathway. Carbon atomsare colored in gray, hydrogen in white, nitrogen in blue, oxygen inred, iron in purple, and boundary carbon atoms for pseudo-bond incyan.
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fig8: Relative energies (in kcal/mol) for the structures alongthe minimumenergy path (MEP) for the detachment of the DNA base from Fe and theformation of formaldehyde in the quintet state for the H2O pathway (a) and OH– pathway (b). The numbersin the parentheses are reaction barriers, which are the energy differencesbetween intermediates and their corresponding TSs. The ISFeIII–OF reactant (Figure 2) is taken as the reference for each pathway. Carbon atomsare colored in gray, hydrogen in white, nitrogen in blue, oxygen inred, iron in purple, and boundary carbon atoms for pseudo-bond incyan.

Mentions: To study whether the unbinding of the methoxide moiety from themetal (Figure 8; from I2 to I3 for the H2O pathway; from I2OH to I5OH for theOH– pathway) is a necessary step, we investigatedthe formation of the formaldehyde with −CH3OH (forthe H2O pathway) or −CH3O– (for the OH– pathway) being coordinated or unboundto the iron. In the case of the H2O pathway with iron-coordinated−CH3OH, the reaction happens in a concerted manner,where the proton transfer to Asp133 and the bond breaking betweenthe C and N1 of 1-meA (C–N bond breaking, I2–P pathwayin Scheme 2) leads to the product with theformaldehyde bound to the iron (P). The calculated barrier for thisstep is 25.9 kcal/mol, which is higher than the hydrogen abstractionstep. This result suggests that this step may become the rate-determiningstep under certain circumstances, such as if no better proton acceptorsare available.


Alternative Pathway for the Reaction Catalyzed by DNA Dealkylase AlkB from Ab Initio QM/MM Calculations.

Fang D, Cisneros GA - J Chem Theory Comput (2014)

Relative energies (in kcal/mol) for the structures alongthe minimumenergy path (MEP) for the detachment of the DNA base from Fe and theformation of formaldehyde in the quintet state for the H2O pathway (a) and OH– pathway (b). The numbersin the parentheses are reaction barriers, which are the energy differencesbetween intermediates and their corresponding TSs. The ISFeIII–OF reactant (Figure 2) is taken as the reference for each pathway. Carbon atomsare colored in gray, hydrogen in white, nitrogen in blue, oxygen inred, iron in purple, and boundary carbon atoms for pseudo-bond incyan.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4230374&req=5

fig8: Relative energies (in kcal/mol) for the structures alongthe minimumenergy path (MEP) for the detachment of the DNA base from Fe and theformation of formaldehyde in the quintet state for the H2O pathway (a) and OH– pathway (b). The numbersin the parentheses are reaction barriers, which are the energy differencesbetween intermediates and their corresponding TSs. The ISFeIII–OF reactant (Figure 2) is taken as the reference for each pathway. Carbon atomsare colored in gray, hydrogen in white, nitrogen in blue, oxygen inred, iron in purple, and boundary carbon atoms for pseudo-bond incyan.
Mentions: To study whether the unbinding of the methoxide moiety from themetal (Figure 8; from I2 to I3 for the H2O pathway; from I2OH to I5OH for theOH– pathway) is a necessary step, we investigatedthe formation of the formaldehyde with −CH3OH (forthe H2O pathway) or −CH3O– (for the OH– pathway) being coordinated or unboundto the iron. In the case of the H2O pathway with iron-coordinated−CH3OH, the reaction happens in a concerted manner,where the proton transfer to Asp133 and the bond breaking betweenthe C and N1 of 1-meA (C–N bond breaking, I2–P pathwayin Scheme 2) leads to the product with theformaldehyde bound to the iron (P). The calculated barrier for thisstep is 25.9 kcal/mol, which is higher than the hydrogen abstractionstep. This result suggests that this step may become the rate-determiningstep under certain circumstances, such as if no better proton acceptorsare available.

Bottom Line: The new OH rebound step is coupled with a proton transfer to the OH(-) ligand and results in a novel zwitterion intermediate.The consistency between our theoretical results and experimental findings is discussed.This study provides new insights into the oxidative repair mechanism of DNA repair by nonheme Fe(II) and α-ketoglutarate (α-KG) dependent dioxygenases and a possible explanation for the substrate preference of AlkB.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States.

ABSTRACT
AlkB is the title enzyme of a family of DNA dealkylases that catalyze the direct oxidative dealkylation of nucleobases. The conventional mechanism for the dealkylation of N(1)-methyl adenine (1-meA) catalyzed by AlkB after the formation of Fe(IV)-oxo is comprised by a reorientation of the oxo moiety, hydrogen abstraction, OH rebound from the Fe atom to the methyl adduct, and the dissociation of the resulting methoxide to obtain the repaired adenine base and formaldehyde. An alternative pathway with hydroxide as a ligand bound to the iron atom is proposed and investigated by QM/MM simulations. The results show OH(-) has a small impact on the barriers for the hydrogen abstraction and OH rebound steps. The effects of the enzyme and the OH(-) ligand on the hydrogen abstraction by the Fe(IV)-oxo moiety are discussed in detail. The new OH rebound step is coupled with a proton transfer to the OH(-) ligand and results in a novel zwitterion intermediate. This zwitterion structure can also be characterized as Fe-O-C complex and facilitates the formation of formaldehyde. In contrast, for the pathway with H2O bound to iron, the hydroxyl product of the OH rebound step first needs to unbind from the metal center before transferring a proton to Glu136 or other residue/substrate. The consistency between our theoretical results and experimental findings is discussed. This study provides new insights into the oxidative repair mechanism of DNA repair by nonheme Fe(II) and α-ketoglutarate (α-KG) dependent dioxygenases and a possible explanation for the substrate preference of AlkB.

No MeSH data available.


Related in: MedlinePlus