The Active-Site [4Fe-4S] Cluster in the Isoprenoid Biosynthesis Enzyme IspH Adopts Unexpected Redox States during Ligand Binding and Catalysis.

(E)-4-Hydroxy-3-methylbut-2-enyl diphosphate reductase, or IspH (formerly known as LytB), catalyzes the terminal step of the bacterial methylerythritol phosphate (MEP) pathway for isoprene synthesis. This step converts (E)-4-hydroxy-3-methylbut-2-enyl diphosphate (HMBPP) into one of two possible isomeric products, either isopentenyl diphosphate (IPP) or dimethylallyl diphosphate (DMAPP). This reaction involves the removal of the C4 hydroxyl group of HMBPP and addition of two electrons. IspH contains a [4Fe-4S] cluster in its active site, and multiple cluster-based paramagnetic species of uncertain redox and ligation states can be detected after incubation with reductant, addition of a ligand, or during catalysis. To characterize the clusters in these species, 57Fe-labeled samples of IspH were prepared and studied by electron paramagnetic resonance (EPR), 57Fe electron-nuclear double resonance (ENDOR), and Mössbauer spectroscopies. Notably, this ENDOR study provides a rarely reported, complete determination of the 57Fe hyperfine tensors for all four Fe ions in a [4Fe-4S] cluster. The resting state of the enzyme (Ox) has a diamagnetic [4Fe-4S]2+ cluster. Reduction generates [4Fe-4S]+ (Red) with both S = 1/2 and S = 3/2 spin ground states. When the reduced enzyme is incubated with substrate, a transient paramagnetic reaction intermediate is detected (Int) which is thought to contain a cluster-bound substrate-derived species. The EPR properties of Int are indicative of a 3+ iron-sulfur cluster oxidation state, and the Mössbauer spectra presented here confirm this. Incubation of reduced enzyme with the product IPP induced yet another paramagnetic [4Fe-4S]+ species (Red+P) with S = 1/2. However, the g-tensor of this state is commonly associated with a 3+ oxidation state, while Mössbauer parameters show features typical for 2+ clusters. Implications of these complicated results are discussed.

Controlling One-Electron vs Two-Electron Pathways in the Multi-Electron Redox Cycle of Nickel Diethyldithiocarbamate.

The unique redox cycle of NiII(dtc)2, where dtc- is N,N-diethyldithiocarbamate, in acetonitrile displays 2e- redox chemistry upon oxidation from NiII(dtc)2 → [NiIV(dtc)3]+ but 1e- redox chemistry upon reduction from [NiIV(dtc)3]+ → NiIII(dtc)3 → NiII(dtc)2. The underlying reasons for this cycle lie in the structural changes that occur between four-coordinate NiII(dtc)2 and six-coordinate [NiIV(dtc)3]+. Cyclic voltammetry (CV) experiments show that these 1e- and 2e- pathways can be controlled by the addition of pyridine-based ligands (L) to the electrolyte solution. Specifically, the addition of these ligands resulted in a 1e- ligand-coupled electron transfer (LCET) redox wave, which produced a mixture of pyridine-bound Ni(III) complexes, [NiIII(dtc)2(L)]+, and [NiIII(dtc)2(L)2]+. Although the complexes could not be isolated, electron paramagnetic resonance (EPR) measurements using a chemical oxidant in the presence of 4-methoxypyridine confirmed the formation of trans-[NiIII(dtc)2(L)2]+. Density functional theory calculations were also used to support the formation of pyridine coordinated Ni(III) complexes through structural optimization and calculation of EPR parameters. The reversibility of the LCET process was found to be dependent on both the basicity of the pyridine ligand and the scan rate of the CV experiment. For strongly basic pyridines (e.g., 4-methoxypyridine) and/or fast scan rates, high reversibility was achieved, allowing [NiIII(dtc)2(L)x]+ to be reduced directly back to NiII(dtc)2 + xL. For weakly basic pyridines (e.g., 3-bromopyridine) and/or slow scan rates, [NiIII(dtc)2(L)x]+ decayed irreversibly to form [NiIV(dtc)3]+. Detailed kinetics studies using CV reveal that [NiIII(dtc)2(L)]+ and [NiIII(dtc)2(L)2]+ decay by parallel pathways due to a small equilibrium between the two species. The rate constants for ligand dissociation ([NiIII(dtc)2(L)2]+ → [NiIII(dtc)2(L)]+ + L) along with decomposition of [NiIII(dtc)2(L)]+ and [NiIII(dtc)2(L)2]+ species were found to increase with the electron-withdrawing character of the pyridine ligand, indicating pyridine dissociation is likely the rate-limiting step for decomposition of these complexes. These studies establish a general trend for kinetically trapping 1e- intermediates along a 2e- oxidation path.

Archaeal pseudomurein and bacterial murein cell wall biosynthesis share a common evolutionary ancestry.

Bacteria near-universally contain a cell wall sacculus of murein (peptidoglycan), the synthesis of which has been intensively studied for over 50 years. In striking contrast, archaeal species possess a variety of other cell wall types, none of them closely resembling murein. Interestingly though, one type of archaeal cell wall termed pseudomurein found in the methanogen orders Methanobacteriales and Methanopyrales is a structural analogue of murein in that it contains a glycan backbone that is cross-linked by a L-amino acid peptide. Here, we present taxonomic distribution, gene cluster and phylogenetic analyses that confirm orthologues of 13 bacterial murein biosynthesis enzymes in pseudomurein-containing methanogens, most of which are distantly related to their bacterial counterparts. We also present the first structure of an archaeal pseudomurein peptide ligase from Methanothermus fervidus DSM1088 (Mfer336) to a resolution of 2.5 Å and show that it possesses a similar overall tertiary three domain structure to bacterial MurC and MurD type murein peptide ligases. Taken together the data strongly indicate that murein and pseudomurein biosynthetic pathways share a common evolutionary history.

Synthesis, characterization, and electrocatalytic activity of bis(pyridylimino)isoindoline Cu(II) and Ni(II) complexes.

Two NNN pincer complexes of Cu(ii) and Ni(ii) with BPIMe- [BPIMe- = 1,3-bis((6-methylpyridin-2-yl)imino)isoindolin-2-ide] have been prepared and characterized structurally, spectroscopically, and electrochemically. The single crystal structures of the two complexes confirmed their distorted trigonal bipyramidal geometry attained by three equatorial N-atoms from the ligand and two axially positioned water molecules to give [Cu(BPIMe)(H2O)2]ClO4 and [Ni(BPIMe)(H2O)2]ClO4. Electrochemical studies of Cu(ii) and Ni(ii) complexes have been performed in acetonitrile to identify metal-based and ligand-based redox activity. When subjected to a saturated CO2 atmosphere, both complexes displayed catalytic activity for the reduction of CO2 with the Cu(ii) complex displaying higher activity than the Ni(ii) analogue. However, both complexes were shown to decompose into catalytically active heterogeneous materials on the electrode surface over extended reductive electrolysis periods. Surface analysis of these materials using energy dispersive spectroscopy as well as their physical appearance suggests the reductive deposition of copper and nickel metal on the electrode surface. Electrocatalysis and decomposition are proposed to be triggered by ligand reduction, where complex stability is believed to be tied to fluxional ligand coordination in the reduced state.

Mode of action uncovered for the specific reduction of methane emissions from ruminants by the small molecule 3-nitrooxypropanol.

Ruminants, such as cows, sheep, and goats, predominantly ferment in their rumen plant material to acetate, propionate, butyrate, CO2, and methane. Whereas the short fatty acids are absorbed and metabolized by the animals, the greenhouse gas methane escapes via eructation and breathing of the animals into the atmosphere. Along with the methane, up to 12% of the gross energy content of the feedstock is lost. Therefore, our recent report has raised interest in 3-nitrooxypropanol (3-NOP), which when added to the feed of ruminants in milligram amounts persistently reduces enteric methane emissions from livestock without apparent negative side effects [Hristov AN, et al. (2015) Proc Natl Acad Sci USA 112(34):10663-10668]. We now show with the aid of in silico, in vitro, and in vivo experiments that 3-NOP specifically targets methyl-coenzyme M reductase (MCR). The nickel enzyme, which is only active when its Ni ion is in the +1 oxidation state, catalyzes the methane-forming step in the rumen fermentation. Molecular docking suggested that 3-NOP preferably binds into the active site of MCR in a pose that places its reducible nitrate group in electron transfer distance to Ni(I). With purified MCR, we found that 3-NOP indeed inactivates MCR at micromolar concentrations by oxidation of its active site Ni(I). Concomitantly, the nitrate ester is reduced to nitrite, which also inactivates MCR at micromolar concentrations by oxidation of Ni(I). Using pure cultures, 3-NOP is demonstrated to inhibit growth of methanogenic archaea at concentrations that do not affect the growth of nonmethanogenic bacteria in the rumen.