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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

α-LUMO and β-LUMO(canonical orbitals, isovalue forthe surface is 0.05 au) of the quintet reactants, TOH (Table 1) and TS structures along the OH– pathway. Carbon atoms are colored in gray, hydrogen in white, nitrogenin blue, oxygen in red, iron in purple, and boundary carbon atomsfor pseudo-bond in cyan.
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fig4: α-LUMO and β-LUMO(canonical orbitals, isovalue forthe surface is 0.05 au) of the quintet reactants, TOH (Table 1) and TS structures along the OH– pathway. Carbon atoms are colored in gray, hydrogen in white, nitrogenin blue, oxygen in red, iron in purple, and boundary carbon atomsfor pseudo-bond in cyan.

Mentions: Regarding the two quintet reactantsfor the OH– pathway (see Figure 4 for their LUMOs), the α-LUMO of the ISFeIII–OF reactant contains a large componentfrom 1-meA, and the orbital of Fe–oxo is not in a good orientationfor overlapping with the orbitals of the methyl group of 1-meA. Incontrast, the α-LUMO of HSFeIII–OAF is still mainly comprised of oxygen’s p orbital andshould be more likely to accept an α electron from the substrate.It was expected that the elongation of d(Fe–O)would lead to more electrons being transferred from the oxo to theiron for both substates and complete the state transition via a MECPlike the H2O pathway. However, the change of Müllikenspin population in Table 1 shows the elongationof d(Fe–oxo) leads to a β electron beingtransferred from the iron to the oxo for ISFeIII–OF, and smoothly change into HSFeIII–OAF. In practice, the optimization afterthe structure (TOH, in Table 1d(Fe–oxo) = 1.79 Å) that has a small energydifference for HSFeIII–OAF (and ISFeIII–OF) gives theresult that both states converge to HSFeIII–OAF. In terms of d(Fe–O), the valueis 1.62 Å in ISFeIII–OF reactant and 1.88 Å in HSFeIII–OAF reactant and TS, which suggests that the HSFeIII–OAF TS resembles the HSFeIII–OAF reactant.


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)

α-LUMO and β-LUMO(canonical orbitals, isovalue forthe surface is 0.05 au) of the quintet reactants, TOH (Table 1) and TS structures along the OH– pathway. Carbon atoms are colored in gray, hydrogen in white, nitrogenin blue, oxygen in red, iron in purple, and boundary carbon atomsfor pseudo-bond in cyan.
© Copyright Policy
Related In: Results  -  Collection

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

fig4: α-LUMO and β-LUMO(canonical orbitals, isovalue forthe surface is 0.05 au) of the quintet reactants, TOH (Table 1) and TS structures along the OH– pathway. Carbon atoms are colored in gray, hydrogen in white, nitrogenin blue, oxygen in red, iron in purple, and boundary carbon atomsfor pseudo-bond in cyan.
Mentions: Regarding the two quintet reactantsfor the OH– pathway (see Figure 4 for their LUMOs), the α-LUMO of the ISFeIII–OF reactant contains a large componentfrom 1-meA, and the orbital of Fe–oxo is not in a good orientationfor overlapping with the orbitals of the methyl group of 1-meA. Incontrast, the α-LUMO of HSFeIII–OAF is still mainly comprised of oxygen’s p orbital andshould be more likely to accept an α electron from the substrate.It was expected that the elongation of d(Fe–O)would lead to more electrons being transferred from the oxo to theiron for both substates and complete the state transition via a MECPlike the H2O pathway. However, the change of Müllikenspin population in Table 1 shows the elongationof d(Fe–oxo) leads to a β electron beingtransferred from the iron to the oxo for ISFeIII–OF, and smoothly change into HSFeIII–OAF. In practice, the optimization afterthe structure (TOH, in Table 1d(Fe–oxo) = 1.79 Å) that has a small energydifference for HSFeIII–OAF (and ISFeIII–OF) gives theresult that both states converge to HSFeIII–OAF. In terms of d(Fe–O), the valueis 1.62 Å in ISFeIII–OF reactant and 1.88 Å in HSFeIII–OAF reactant and TS, which suggests that the HSFeIII–OAF TS resembles the HSFeIII–OAF reactant.

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