How Metal Coordination in the Ca-, Ce-,
and Eu-Containing Methanol
Dehydrogenase Enzymes Can Influence
the Catalysis: A Theoretical Point of View
Tiziana Marino, Mario Prejanò and Nino Russo
Abstract Methanol dehydrogenase (MDH) enzymes are quinoproteins that require
calcium or magnesium ion as well as pyrroloquinoline quinone as a cofactor for
activity in the oxidation of methanol to formaldehyde. Lately, MDH enzymes containing lanthanide ions in the active site have been isolated in drastic conditions from
Methylacidiphilum fumariolicum bacterium. The present theoretical study performed
in the framework of the density functional theory employing the quantum mechanical
cluster approach mainly focused on the catalytic mechanism of cerium containing
MDH enzyme. In order to rationalize the effect of the metal ion substitution on the
catalytic activity, geometrical and electronic properties of the “Michaelis–Menten”
enzyme–methanol complexes of Ce-MDH and Eu-MDH are also discussed as well as
the substrate’s activation mediated by the metal ion. With the aim to better describe
the Lewis acidity of metal ions in the methanol oxidation, the comparison of the
catalytic performance between Ce-MDH and Ca-MDH was also made.
1 Introduction
Metal ions are ubiquitous and widely distributed in nature and account extremely
important roles in chemistry, geochemistry, biochemistry, material sciences, and
medicine. Approximately one-third of the structures in the Protein Data Bank (PDB)
contains metal ions.
Metals such as copper (Cu), iron (Fe), lanthanides (Ln), cobalt (Co), zinc (Zn),
molybdenum (Mo), and tungsten (W) are particularly important for methanotrophy
[1].
In particular, rare earth elements (REE) including lanthanum and lanthanoid (17
elements) as well as scandium and yttrium are found in bacteria, archaebacteria,
fungi, vegetables, and animals [2]. They are known to act as calcium analogs in the
T. Marino (B) · M. Prejanò · N. Russo
Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, 87036 Rende, Italy
e-mail: tiziana.marino65@unical.it
© Springer Nature Switzerland AG 2019
E. Broclawik et al. (eds.), Transition Metals in Coordination Environments,
Challenges and Advances in Computational Chemistry and Physics 29,
https://doi.org/10.1007/978-3-030-11714-6_16
487
and Eu-Containing Methanol
Dehydrogenase Enzymes Can Influence
the Catalysis: A Theoretical Point of View
Tiziana Marino, Mario Prejanò and Nino Russo
Abstract Methanol dehydrogenase (MDH) enzymes are quinoproteins that require
calcium or magnesium ion as well as pyrroloquinoline quinone as a cofactor for
activity in the oxidation of methanol to formaldehyde. Lately, MDH enzymes containing lanthanide ions in the active site have been isolated in drastic conditions from
Methylacidiphilum fumariolicum bacterium. The present theoretical study performed
in the framework of the density functional theory employing the quantum mechanical
cluster approach mainly focused on the catalytic mechanism of cerium containing
MDH enzyme. In order to rationalize the effect of the metal ion substitution on the
catalytic activity, geometrical and electronic properties of the “Michaelis–Menten”
enzyme–methanol complexes of Ce-MDH and Eu-MDH are also discussed as well as
the substrate’s activation mediated by the metal ion. With the aim to better describe
the Lewis acidity of metal ions in the methanol oxidation, the comparison of the
catalytic performance between Ce-MDH and Ca-MDH was also made.
1 Introduction
Metal ions are ubiquitous and widely distributed in nature and account extremely
important roles in chemistry, geochemistry, biochemistry, material sciences, and
medicine. Approximately one-third of the structures in the Protein Data Bank (PDB)
contains metal ions.
Metals such as copper (Cu), iron (Fe), lanthanides (Ln), cobalt (Co), zinc (Zn),
molybdenum (Mo), and tungsten (W) are particularly important for methanotrophy
[1].
In particular, rare earth elements (REE) including lanthanum and lanthanoid (17
elements) as well as scandium and yttrium are found in bacteria, archaebacteria,
fungi, vegetables, and animals [2]. They are known to act as calcium analogs in the
T. Marino (B) · M. Prejanò · N. Russo
Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, 87036 Rende, Italy
e-mail: tiziana.marino65@unical.it
© Springer Nature Switzerland AG 2019
E. Broclawik et al. (eds.), Transition Metals in Coordination Environments,
Challenges and Advances in Computational Chemistry and Physics 29,
https://doi.org/10.1007/978-3-030-11714-6_16
487