Essential and Ubiquitous: The Emergence of Lanthanide Metallobiochemistry

Daumann, Lena J.

doi:10.1002/anie.201904090

Cited by 110 publications

(103 citation statements)

References 64 publications

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“…Biochemical assays are powerful analytical techniques used to identify or quantify proteins, to study the binding of substrates and inhibitors, and to measure the activity of enzymes. The family of methanol dehydrogenase enzymes (MDH) has recently taken the spotlight again after it was discovered that many bacteria utilize lanthanide-dependent MDH of the XoxF family [1][2][3][4][5][6][7]. This finding has fueled an entirely new area of research-lanthanide-dependent bacterial metabolism and biochemistry.…”

Section: Introductionmentioning

confidence: 99%

Understanding the chemistry of the artificial electron acceptors PES, PMS, DCPIP and Wurster’s Blue in methanol dehydrogenase assays

Jahn

Jonasson

et al. 2020

J Biol Inorg Chem

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Methanol dehydrogenases (MDH) have recently taken the spotlight with the discovery that a large portion of these enzymes in nature utilize lanthanides in their active sites. The kinetic parameters of these enzymes are determined with a spectrophotometric assay first described by Anthony and Zatman 55 years ago. This artificial assay uses alkylated phenazines, such as phenazine ethosulfate (PES) or phenazine methosulfate (PMS), as primary electron acceptors (EAs) and the electron transfer is further coupled to a dye. However, many groups have reported problems concerning the bleaching of the assay mixture in the absence of MDH and the reproducibility of those assays. Hence, the comparison of kinetic data among MDH enzymes of different species is often cumbersome. Using mass spectrometry, UV-Vis and electron paramagnetic resonance (EPR) spectroscopy, we show that the side reactions of the assay mixture are mainly due to the degradation of assay components. Light-induced demethylation (yielding formaldehyde and phenazine in the case of PMS) or oxidation of PES or PMS as well as a reaction with assay components (ammonia, cyanide) can occur. We suggest here a protocol to avoid these side reactions. Further, we describe a modified synthesis protocol for obtaining the alternative electron acceptor, Wurster's blue (WB), which serves both as EA and dye. The investigation of two lanthanide-dependent methanol dehydrogenases from Methylorubrum extorquens AM1 and Methylacidiphilum fumariolicum SolV with WB, along with handling recommendations, is presented.

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Section: Introductionmentioning

confidence: 99%

Understanding the chemistry of the artificial electron acceptors PES, PMS, DCPIP and Wurster’s Blue in methanol dehydrogenase assays

Jahn

Jonasson

et al. 2020

J Biol Inorg Chem

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“…Finally, we refer the interested reader to a recent overview on the roles of lanthanides in biochemistry by Daumann. [189] Other cations. There are, of course, many other cations that could be mentioned here, but a full list would be beyond the scope of this review.…”

Section: Local Picture Of Cation Binding Sites Of Proteinsmentioning

confidence: 99%

Multivalent ions and biomolecules: Attempting a comprehensive perspective

2020

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Ions are ubiquitous in nature. They play a key role for many biological processes on the molecular scale, from molecular interactions, to mechanical properties, to folding, to self‐organisation and assembly, to reaction equilibria, to signalling, to energy and material transport, to recognition etc. Going beyond monovalent ions to multivalent ions, the effects of the ions are frequently not only stronger (due to the obviously higher charge), but qualitatively different. A typical example is the process of binding of multivalent ions, such as Ca2+, to a macromolecule and the consequences of this ion binding such as compaction, collapse, potential charge inversion and precipitation of the macromolecule. Here we review these effects and phenomena induced by multivalent ions for biological (macro)molecules, from the “atomistic/molecular” local picture of (potentially specific) interactions to the more global picture of phase behaviour including, e. g., crystallisation, phase separation, oligomerisation etc. Rather than attempting an encyclopedic list of systems, we rather aim for an embracing discussion using typical case studies. We try to cover predominantly three main classes: proteins, nucleic acids, and amphiphilic molecules including interface effects. We do not cover in detail, but make some comparisons to, ion channels, colloidal systems, and synthetic polymers. While there are obvious differences in the behaviour of, and the relevance of multivalent ions for, the three main classes of systems, we also point out analogies. Our attempt of a comprehensive discussion is guided by the idea that there are not only important differences and specific phenomena with regard to the effects of multivalent ions on the main systems, but also important similarities. We hope to bridge physico‐chemical mechanisms, concepts of soft matter, and biological observations and connect the different communities further.

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“…Furthermore, ar elaxedo ptimization procedure (except for Ca atoms of the amino acids of the outer shell of the metal ion) adopted in the present study represents another difference. Based on these results and encouraged by the increasing interesto ft he scientific communityi nM DH, [1][2][3][4][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23] we have undertaken as tudy of the reactionm echanism for Eu and Yb lanthanides with the aim of rationalizingt heir different "catalytic" behavior with respect to the more active cerium-containing MDH and to the availablee xperimental observations. [16] The methanol oxidation to formaldehyde mediated by MDH can proceed through two different three-step catalytic pathways:t he so-called additionelimination-protonation reactiona nd the addition-retroeneprotonation mechanism.…”

Section: Es-pqqc Omplexesmentioning

confidence: 99%

How Lanthanide Ions Affect the Addition–Elimination Step of Methanol Dehydrogenases

Prejanò

Russo

Marino

2020

Chemistry A European J

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The recently discovered methanol dehydrogenase, XoxF, is a widespread enzyme used by methylotrophic bacteria to oxidize methanol for carbon and energy, and requires lanthanide ions for its activity. This enzyme represents an essential component of methanol utilization by both methanol‐ and methane‐utilizing bacteria. The present investigation looks on the electronic, energetic and geometrical behavior of the methanol dehydrogenase from Methylacidiphilum fumariolicum SolV, which is strictly dependent on early lanthanide metals with +3 oxidation states, by examining enzyme‐substrate complexes of all the lanthanides. We focus on the catalytic reaction mechanism of two methanol dehydrogenases having as cofactor europium and ytterbium belonging to the mid‐ and later‐ series of lanthanides, in comparison with the methanol dehydrogenase containing the cerium, one early lanthanide. Our results provide evidence for the influence of the lanthanide contraction effect in all the elementary steps of the catalytic reaction mechanism. This indication may prove useful for developing new catalytic machineries of enzymes that adopt new‐to‐nature transformations.

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Essential and Ubiquitous: The Emergence of Lanthanide Metallobiochemistry

Cited by 110 publications

References 64 publications

Understanding the chemistry of the artificial electron acceptors PES, PMS, DCPIP and Wurster’s Blue in methanol dehydrogenase assays

Understanding the chemistry of the artificial electron acceptors PES, PMS, DCPIP and Wurster’s Blue in methanol dehydrogenase assays

Multivalent ions and biomolecules: Attempting a comprehensive perspective

How Lanthanide Ions Affect the Addition–Elimination Step of Methanol Dehydrogenases

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