Enzymatic Systems Studied with ONIOM

Non-heme Di-Iron Enzymes Methane Monooxygenase and Ribonucleotide Reductase 

Metalloenzymes with non-heme di-iron centers in which the two irons are bridged by an oxide (or a hydroxide) and carboxylate ligands (glutamate or aspartate) constitute an important class of enzymes. Two of these enzymes, methane monooxygenase (MMO) and ribonucleotide reductase (RNR) have very similar di-iron active sites, located in the subunits MMOH and R2 respectively. Despite their structural similarity, these metal centers catalyze very different chemical reactions. We have studied the enzymatic mechanisms of these enzymes to understand what determines their catalytic activity [24, 25, 39-41]. 

Methane monooxygenase is a classic monooxygenase in which two reducing equivalents from NAD(P)H are utilized to split the O—O bond of O2. Later, one oxygen atom is reduced to water while the second oxygen atom is incorporated into the substrate to yield methanol [42-45], 

Ribonucleotide reductase is responsible for the conversion of the four biological ribonucleotides (RNA) into their corresponding deoxy forms (DNA). Although RNR is not an oxygenase during its primary catalyzed reaction (the conversion of ribonucleotides), it activates oxygen to generate a stable tyrosyl radical that is essential to the overall mechanism [46 49]. The common link between the chemistry of MMO and RNR is the activation of O2 by the di-iron active site. 

As briefly mentioned above, the reduced form of MMO reacts with oxygen to initiate substrate oxygenation. To further analyze the protein effects on this reaction, the dioxygen-binding step was treated with two-layer ONIOM (B3LYP Amber) [25], The overall setup was similar to the one used for evaluating active-site geometries. 

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