Hiding in Plain Sight: The Bimetallic Magnesium Covalent Bond in Enzyme Active Sites

Abstract

The transfer of phosphate groups is an essential function of many intracellular biological enzymes. The transfer is, in many cases, facilitated by a protein scaffold involving two closely spaced magnesium “ions”. It has long been a mystery as to how these “ions” can retain their closely spaced positions throughout enzymatic phosphate transfer: Coulomb’s law would dictate large repulsive forces between these ions at observed distances. Here we show, however, that the electron density can be borrowed from nearby electron rich oxygens to populate a bonding molecular orbital, largely localized between the magnesium “ions”. The result is that the Mg-Mg core of these phosphate transfer enzymes is surprisingly similar to metastable [Mg2]2+ ion in the gas phase, an ion which has been identified experimentally and studied with high level quantum mechanical calculations. This similarity is confirmed with comparative computations of the electron density for [Mg2]2+ in the gas phase and for the Mg-Mg core in the structures derived from QM/MM studies on high resolution x-ray crystal structures. That there is a level of covalent bonding between the two Mg “ions” at the core of these enzymes is a novel concept which enables an improved vision of how these enzymes function at the molecular level. The concept is broader than magnesium—other biologically relevant metals (e.g., Mn and Zn) can also form similar stabilizing covalent Me-Me bonds in both organometallic and inorganic crystals.

Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide

“…3 ). The product metal, therefore, inhibits the reverse reaction, promoting the forward (synthesis) reaction, consistent with stable product complexes (DNA/PP i ) of pols μ or β that do not form dNTP and DNA −1 , and computational studies 17 , 18 , 47 . Notably, a PP i analog (PNP) that decreases the chemical and overall equilibrium, permits crystallographic characterization of the reverse reaction 48 .…”

Taming the Antiferromagnetic Beast: Computational Design of Ultrashort Mn−Mn Bonds Stabilized by N‐Heterocyclic Carbenes

“…The positive ΔH ex values of ligands without benzene moieties (I-III) show that the η 6 coordination is more important for the stabilization than the carbene moieties. The MnÀ Mn bond lengths of these complexes (1-3), which are in the range of 1.73-1.75 Å, are shorter than those of the carbene complexes featuring η 6 coordination (1.87-2.08 Å), but still [c] 150 + 11.0 (À 2.9) À 94.1 + 179.7 12' [d] DACBz 2.02 1.36 1.58 2.041 [c] 159 (4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18) are significantly larger than that of Mn 2 Bz 2 , highlighting once more the thermodynamic stability of these systems.…”

“…As a consequence, compounds featuring metal‐metal bonds are now widely used in organometallic catalysis, [9] small molecule activation, [10] photochemistry, [11] and in the development of metal‐organic frameworks [12] and extended metal atom chains [13] . Metal‐metal bonds also play a crucial role in biological processes, not only stabilizing low‐valence states and initiating oxidative addition reactions in metalloenzymes, [14] but also allowing the transfer of phosphate groups in for example DNA polymerases [15] …”

“…[13] Metal-metal bonds also play a crucial role in biological processes, not only stabilizing low-valence states and initiating oxidative addition reactions in metalloenzymes, [14] but also allowing the transfer of phosphate groups in for example DNA polymerases. [15] In striking difference with other homonuclear diatomic molecules featuring first-row transition metals, the naked Mn 2 species is a weakly bonded van der Waals dimer featuring antiferromagnetic coupling and a very long metal-metal distance of 3.7-3.9 Å. [16] Up to now, only a few systems featuring MnÀ Mn bonds in the range of 2.2-2.7 Å are known.…”

Mapping Functional Substrate–Enzyme Interactions in the pol β Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs

“…The interactions among these components are interdependent such that chemistry depends upon hydrogen bonding between the template base and incoming nucleotide base, as well as interactions between the enzyme and the triphosphate group of the incoming nucleotide, among others. A key component in this network of interactions is the integrity of a charge neutralization system between two closely positioned divalent metal ions, water molecules, enzyme side chains, and the triphosphate group of the incoming nucleotide 8 .…”