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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 (kcal/mol) of the structuresalong the minimumenergy path (MEP) for the OH rebound step in the quintet state forH2O pathway (a) and OH– pathway (b).The numbers in the parentheses are reaction barriers, which are theenergy differences between intermediates and their corresponding TSs.The energy of the corresponding ISFeIII–OF reactant (Figure 2) is taken as zerofor each pathway. Carbon atoms are colored in gray, hydrogen in white,nitrogen in blue, oxygen in red, iron in purple, and boundary carbonatoms for pseudo-bond in cyan.
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fig5: Relative energies (kcal/mol) of the structuresalong the minimumenergy path (MEP) for the OH rebound step in the quintet state forH2O pathway (a) and OH– pathway (b).The numbers in the parentheses are reaction barriers, which are theenergy differences between intermediates and their corresponding TSs.The energy of the corresponding ISFeIII–OF reactant (Figure 2) is taken as zerofor each pathway. Carbon atoms are colored in gray, hydrogen in white,nitrogen in blue, oxygen in red, iron in purple, and boundary carbonatoms for pseudo-bond in cyan.

Mentions: Figure 5 shows the relative energy for this step for bothpathways.The lowest energy states for I1 and I1OH are both HSFeIII–OAF, and the two substatesfor the quintet and triplet merge into one after the OH rebound stepat I2 and I2OH. Therefore, only the quintet state is consideredfor the calculations of this and subsequent steps. The next step forthe H2O pathway is a typical OH rebound process. The calculatedbarrier, TSI1I2, is 12.2 kcal/mol, which is in agreementwith a previous QM/MM study.6 For the OH– pathway, the corresponding intermediate I3OH is not stable. During the optimization, the proton is transferredto the iron-bound OH– spontaneously, and the zwitterionstructure I2OH forms.


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 (kcal/mol) of the structuresalong the minimumenergy path (MEP) for the OH rebound step in the quintet state forH2O pathway (a) and OH– pathway (b).The numbers in the parentheses are reaction barriers, which are theenergy differences between intermediates and their corresponding TSs.The energy of the corresponding ISFeIII–OF reactant (Figure 2) is taken as zerofor each pathway. Carbon atoms are colored in gray, hydrogen in white,nitrogen in blue, oxygen in red, iron in purple, and boundary carbonatoms for pseudo-bond in cyan.
© Copyright Policy
Related In: Results  -  Collection

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

fig5: Relative energies (kcal/mol) of the structuresalong the minimumenergy path (MEP) for the OH rebound step in the quintet state forH2O pathway (a) and OH– pathway (b).The numbers in the parentheses are reaction barriers, which are theenergy differences between intermediates and their corresponding TSs.The energy of the corresponding ISFeIII–OF reactant (Figure 2) is taken as zerofor each pathway. Carbon atoms are colored in gray, hydrogen in white,nitrogen in blue, oxygen in red, iron in purple, and boundary carbonatoms for pseudo-bond in cyan.
Mentions: Figure 5 shows the relative energy for this step for bothpathways.The lowest energy states for I1 and I1OH are both HSFeIII–OAF, and the two substatesfor the quintet and triplet merge into one after the OH rebound stepat I2 and I2OH. Therefore, only the quintet state is consideredfor the calculations of this and subsequent steps. The next step forthe H2O pathway is a typical OH rebound process. The calculatedbarrier, TSI1I2, is 12.2 kcal/mol, which is in agreementwith a previous QM/MM study.6 For the OH– pathway, the corresponding intermediate I3OH is not stable. During the optimization, the proton is transferredto the iron-bound OH– spontaneously, and the zwitterionstructure I2OH forms.

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