How Metal Coordination in the Ca-, Ce- and Eu-Containing …
489
dependent methanotrophic bacterium SolV with europium have been also reported
[19].
Despite the mechanism of methanol oxidation by calcium-containing enzyme has
attracted the attention in the last 40 years and different mechanistic proposals have
been suggested and discussed, today controversial opinions are present and the debate
is still open [20–28]. In the case of REE-MDH, owing to the most recent discoveries
[7, 14, 19, 29–31], the discussion is just beginning.
Furthermore, a deeper investigation on the reaction mechanism of cerium containing MDH has been performed by employing the quantum chemical cluster methodology in the framework of density functional theory (DFT).
Having in mind that the coordination chemistry of the lanthanides can generate
structural diversity depending on the progressive decrease in ionic radius, in the
present work, we present the results obtained by the comparative DFT analysis of the
catalytic behavior of the cerium- and europium-containing methanol dehydrogenase.
In particular, the step of the enzymatic mechanism where the metal ion plays a critical
role has been considered. Both cerium and europium metal ions act as good Lewis
acids in the enzyme–substrate complex (ES), and our study is focused on this step
and the analysis of the structural, electronic properties and of the charges distribution
can contribute to gain a more comprehensive knowledge of this important event.
In addition, during the discussion, the catalytic behavior of the cerium-containing
enzyme is compared with that of the more usual calcium-containing enzyme.
2 Computational Methods
2.1 Active Site Model
For the cerium enzyme, the ES starting structure has been obtained by modeling
the X-ray structure of the Xoxf-type natural cerium-dependent MDH (PDB: 4MAE,
1.6 Å) [18]. It corresponds to the precatalytic enzyme–substrate complex where the
polyethylene glycol instead of the natural substrate prevents the occurrence of the
reaction. In the case of the Eu-MDH-used structure, the achieved crystals report the
enzyme without substrate. (PDB: 6FKW, 1.4 Å) [19].
The QM cluster includes the amino acid residues of the inner coordination shell
of Ce
3+ ion (Glu172, Asn256, Asp299, Asp301) and the cofactor PQQ and Glu55,
Arg110, Ser169, Arg326, Asp388 residues of the outer coordination shell that potentially form hydrogen bonds with the cofactor. All amino acids were truncated at the
α carbons, and hydrogen atoms were added manually. The methanol substrate is
coordinated to the metal center by the hydroxyl group. The overall model consists
of 113 atoms, including the substrate, and has a total charge of zero (Fig. 1).
As usual in the cluster approach for modeling enzymatic reactions [23, 32–37],
the truncated amino acid residues at the periphery of the active site are fixed to
489
dependent methanotrophic bacterium SolV with europium have been also reported
[19].
Despite the mechanism of methanol oxidation by calcium-containing enzyme has
attracted the attention in the last 40 years and different mechanistic proposals have
been suggested and discussed, today controversial opinions are present and the debate
is still open [20–28]. In the case of REE-MDH, owing to the most recent discoveries
[7, 14, 19, 29–31], the discussion is just beginning.
Furthermore, a deeper investigation on the reaction mechanism of cerium containing MDH has been performed by employing the quantum chemical cluster methodology in the framework of density functional theory (DFT).
Having in mind that the coordination chemistry of the lanthanides can generate
structural diversity depending on the progressive decrease in ionic radius, in the
present work, we present the results obtained by the comparative DFT analysis of the
catalytic behavior of the cerium- and europium-containing methanol dehydrogenase.
In particular, the step of the enzymatic mechanism where the metal ion plays a critical
role has been considered. Both cerium and europium metal ions act as good Lewis
acids in the enzyme–substrate complex (ES), and our study is focused on this step
and the analysis of the structural, electronic properties and of the charges distribution
can contribute to gain a more comprehensive knowledge of this important event.
In addition, during the discussion, the catalytic behavior of the cerium-containing
enzyme is compared with that of the more usual calcium-containing enzyme.
2 Computational Methods
2.1 Active Site Model
For the cerium enzyme, the ES starting structure has been obtained by modeling
the X-ray structure of the Xoxf-type natural cerium-dependent MDH (PDB: 4MAE,
1.6 Å) [18]. It corresponds to the precatalytic enzyme–substrate complex where the
polyethylene glycol instead of the natural substrate prevents the occurrence of the
reaction. In the case of the Eu-MDH-used structure, the achieved crystals report the
enzyme without substrate. (PDB: 6FKW, 1.4 Å) [19].
The QM cluster includes the amino acid residues of the inner coordination shell
of Ce
3+ ion (Glu172, Asn256, Asp299, Asp301) and the cofactor PQQ and Glu55,
Arg110, Ser169, Arg326, Asp388 residues of the outer coordination shell that potentially form hydrogen bonds with the cofactor. All amino acids were truncated at the
α carbons, and hydrogen atoms were added manually. The methanol substrate is
coordinated to the metal center by the hydroxyl group. The overall model consists
of 113 atoms, including the substrate, and has a total charge of zero (Fig. 1).
As usual in the cluster approach for modeling enzymatic reactions [23, 32–37],
the truncated amino acid residues at the periphery of the active site are fixed to