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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 = 0.05au) of the quintet reactants, MECP and TS structures along the H2O 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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fig3: α-LUMO and β-LUMO(canonical orbitals, isovalue = 0.05au) of the quintet reactants, MECP and TS structures along the H2O 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: To understandthese differences, we turn to the analysis of thecanonical molecular orbitals for both pathways. During the H atomabstraction, an electron will be transferred to the oxo O. Figure 3 shows the α-LUMO (lowest unoccupied molecularorbital) and β-LUMO for the reactant structures for the H2O pathway. For the ISFeIII–OF, the α-LUMO (σ* orbital) only changes slightlyduring the elongation of the d(Fe–oxo) fromthe reactant (1.60 Å) to the MECP (1.78 Å). In contrast,the percentage of O in β-LUMO (π* orbital) increases andstarts to dominate.


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 = 0.05au) of the quintet reactants, MECP and TS structures along the H2O 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

fig3: α-LUMO and β-LUMO(canonical orbitals, isovalue = 0.05au) of the quintet reactants, MECP and TS structures along the H2O 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: To understandthese differences, we turn to the analysis of thecanonical molecular orbitals for both pathways. During the H atomabstraction, an electron will be transferred to the oxo O. Figure 3 shows the α-LUMO (lowest unoccupied molecularorbital) and β-LUMO for the reactant structures for the H2O pathway. For the ISFeIII–OF, the α-LUMO (σ* orbital) only changes slightlyduring the elongation of the d(Fe–oxo) fromthe reactant (1.60 Å) to the MECP (1.78 Å). In contrast,the percentage of O in β-LUMO (π* orbital) increases andstarts to dominate.

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