Catalytic Role of Gln202 in the Carboligation Reaction Mechanism of Yeast AHAS: A QM/MM Study

Mechanism of Radical Initiation and Transfer in Class Id Ribonucleotide Reductase Based on Density Functional Theory

Class Id ribonucleotide reductase (RNR) is a newly discovered enzyme, which employs the dimanganese cofactor in the superoxidized state (Mn^III/Mn^IV) as the radical initiator. The dimanganese cofactor of class Id RNR in the reduced state (inactive) is clearly based on the crystal structure of the Fj-β subunit. However, the state of the dimanganese cofactor of class Id RNR in the oxidized state (active) is not known. The X-band EPR spectra have shown that the activated Fj-β subunit exists in two distinct complexes, 1 and 2. In this work, quantum mechanical/molecular mechanical calculations were carried out to study class Id RNR. First, we have determined that complex 2 contains a Mn^III-(μ-oxo)₂-Mn^IV cluster, and complex 1 contains a Mn^III-(μ-hydroxo/μ-oxo)-Mn^IV cluster. Then, based on the determined dimanganese cofactors, the mechanism of radical initiation and transfer in class Id RNR is revealed. The Mn^III-(μ-oxo)₂-Mn^IV cluster in complex 2 has not enough reduction potential to initiate radical transfer directly. Instead, it needs to be monoprotonated into Mn^III-(μ-hydroxo/μ-oxo)-Mn^IV (complex 1) before the radical transfer. The protonation state of μ-oxo can be regulated by changing the protein microenvironment, which is induced by the protein aggregation and separation of β subunits with α subunits. The radical transfer between the cluster of Mn^III-(μ-hydroxo/μ-oxo)-Mn^IV and Trp30 in the radical-transfer chain of the Fj-β subunit (Mn^III/Mn^IV ↔ His100 ↔ Asp194 ↔ Trp30 ↔ Arg99) is a water-mediated tri-proton-coupled electron transfer, which transfers proton from the ε-amino group of Lys71 to the carboxyl group of Glu97 via the water molecule Wat551 and the bridging μ-hydroxo ligand through a three-step reaction. This newly discovered proton-coupled electron-transfer mechanism in class Id RNR is different from those reported in the known Ia-Ic RNRs. The ε-amino group of Lys71, which serves as a proton donor, plays an important role in the radical transfer.

Mechanism of DOPA radical generation and transfer in metal-free class Ie ribonucleotide reductase based on density functional theory

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The mechanism of DOPA radical generation, transfer and regeneration is revealed.

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The superoxide O₂^•− should be protonated to HO₂^• prior to oxidizing Tyr126 to DOPA radical.

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The protonation of Asp88 is the prerequisite for the DOPA radical generation and radical transfer.

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Lys213 is a key residue for the transfer of the DOPA radical.

Quantum mechanical/molecular mechanical (QM/MM) calculations were carried out to investigate the mechanisms of the generation, transfer, and regeneration of the DOPA radical for metal-free class Ie ribonucleotide reductase. The crystal structure of MfR2 (Nature, 2018, 563, 416–420) was adopted for the calculations. The QM/MM calculations have revealed several key points that are vital for understanding the mechanisms. The superoxide O₂^•− provided by the flavoprotein NrdI cannot directly oxidize the residue Tyr126 to the DOPA radical. It should be protonated to HO₂^•. The calculation results suggest that the covalent modification of Tyr126 and the DOPA radical generation can be carried out with no involvement of metal cofactors. This addresses the concerns of the articles (Nature, 2018, 563, 416–420; PNAS, 2018, 115, 10022–10027). Another concern from the articles is that how the DOPA radical is transferred from the radical trap. The DFT calculations have demonstrated that Lys213 is a key residue for the radical transfer from the DOPA radical. The ε-amino group of Lys213 is used not only as a bridge for the electron transfer but also as a proton donor. It can provide a proton to DOPA126 via a water molecule, and thus the radical transfer from DOPA126 to Trp52 is facilitated. It has also been revealed that the protonation of Asp88 is the prerequisite for the DOPA radical generation and the radical transfer in class Ie. Once the radical is quenched, it can be regenerated via the oxidations by superoxide O₂^•− and hydroperoxyl radical HO₂^•.