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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, with ISFeIII–OF as the reference state) of reactant, TS andI1 and Mülliken spin populations of key atoms (Fe, the firstO denotes the oxo, the second O denotes the O of OH– bound to the iron, and C denotes the carbon of methyl group of 1-meA)for the hydrogen abstraction step for OH– pathwayin quintet (ISFeIII–OF and HSFeIII–OAF) and triplet states(LSFeIII–OF and ISFeIII–OAF).
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fig2: Relative energies (in kcal/mol, with ISFeIII–OF as the reference state) of reactant, TS andI1 and Mülliken spin populations of key atoms (Fe, the firstO denotes the oxo, the second O denotes the O of OH– bound to the iron, and C denotes the carbon of methyl group of 1-meA)for the hydrogen abstraction step for OH– pathwayin quintet (ISFeIII–OF and HSFeIII–OAF) and triplet states(LSFeIII–OF and ISFeIII–OAF).

Mentions: Our previous study on thehydrogen abstraction step of the H2O pathway shows thereare two substates for each spin state as FeIV–oxotends to be FeIII–oxyl where one electron is transferredfrom Fe to oxo. For the total quintet spin state, there are two substates:The first corresponds to HSFeIII–OAF, where s = 5/2 (high spin, HS) Fe is antiferromagnetically(AF) coupled with s = −1/2 O. The second state is ISFeIII–OF where s = 3/2 (intermediatespin, IS) Fe is ferromagnetically coupled with s = 1/2 O. Similarly,for the total triplet spin state, there are also two substates: ISFeIII–OAF where s = 3/2 (intermediatespin, IS) Fe is antiferromagnetically (AF) coupled with s = −1/2O and LSFeIII–OF where s =1/2 (low spin, LS) Fe is ferromagnetically coupled with s = 1/2 O(see SI Figure S2 for the electronic configurationdiagram).9 Figure 2 depicts the relative energies for the hydrogen abstraction stepof the OH– pathway along with the Müllikenspin populations on selected atoms for each of the critical pointson the path (see SI Figure S3 for the energyprofile for the H2O pathway9).


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, with ISFeIII–OF as the reference state) of reactant, TS andI1 and Mülliken spin populations of key atoms (Fe, the firstO denotes the oxo, the second O denotes the O of OH– bound to the iron, and C denotes the carbon of methyl group of 1-meA)for the hydrogen abstraction step for OH– pathwayin quintet (ISFeIII–OF and HSFeIII–OAF) and triplet states(LSFeIII–OF and ISFeIII–OAF).
© Copyright Policy
Related In: Results  -  Collection

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

fig2: Relative energies (in kcal/mol, with ISFeIII–OF as the reference state) of reactant, TS andI1 and Mülliken spin populations of key atoms (Fe, the firstO denotes the oxo, the second O denotes the O of OH– bound to the iron, and C denotes the carbon of methyl group of 1-meA)for the hydrogen abstraction step for OH– pathwayin quintet (ISFeIII–OF and HSFeIII–OAF) and triplet states(LSFeIII–OF and ISFeIII–OAF).
Mentions: Our previous study on thehydrogen abstraction step of the H2O pathway shows thereare two substates for each spin state as FeIV–oxotends to be FeIII–oxyl where one electron is transferredfrom Fe to oxo. For the total quintet spin state, there are two substates:The first corresponds to HSFeIII–OAF, where s = 5/2 (high spin, HS) Fe is antiferromagnetically(AF) coupled with s = −1/2 O. The second state is ISFeIII–OF where s = 3/2 (intermediatespin, IS) Fe is ferromagnetically coupled with s = 1/2 O. Similarly,for the total triplet spin state, there are also two substates: ISFeIII–OAF where s = 3/2 (intermediatespin, IS) Fe is antiferromagnetically (AF) coupled with s = −1/2O and LSFeIII–OF where s =1/2 (low spin, LS) Fe is ferromagnetically coupled with s = 1/2 O(see SI Figure S2 for the electronic configurationdiagram).9 Figure 2 depicts the relative energies for the hydrogen abstraction stepof the OH– pathway along with the Müllikenspin populations on selected atoms for each of the critical pointson the path (see SI Figure S3 for the energyprofile for the H2O pathway9).

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