Protein Dynamics in the Reductive Activation of a B12-Containing Enzyme

Structural Insights into Microbial One-Carbon Metabolic Enzymes Ni-Fe-S-Dependent Carbon Monoxide Dehydrogenases and Acetyl-CoA Synthases

Ni-Fe-S-dependent carbon monoxide dehydrogenases (CODHs) are enzymes that interconvert CO and CO₂ by using their catalytic Ni-Fe-S C-cluster and their Fe-S B- and D-clusters for electron transfer. CODHs are important in the microbiota of animals such as humans, ruminants, and termites because they can facilitate the use of CO and CO₂ as carbon sources and serve to maintain redox homeostasis. The bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) is responsible for acetate production via the Wood-Ljungdahl pathway, where acetyl-CoA is assembled from two CO₂-derived one-carbon units. A Ni-Fe-S A-cluster is key to this chemistry. Whereas acetogens use the A- and C-clusters of CODH/ACS to produce acetate from CO₂, methanogens use A- and C-clusters of an acetyl-CoA decarbonylase/synthase complex (ACDS) to break down acetate en route to CO₂ and methane production. Here we review some of the recent advances in understanding the structure and mechanism of CODHs, CODH/ACSs, and ACDSs, their unusual metallocofactors, and their unique metabolic roles in the human gut and elsewhere.

Theoretical Studies of Acetyl-CoA Synthase Catalytic Mechanism

DFT calculations were performed for the A-cluster from the enzyme Acetyl-CoA synthase (ACS). The acid constants (pKa), reduction potentials, and pH-dependent reduction potential for the A-cluster with different oxidation states and ligands were calculated. Good agreement of the reduction potentials, dependent on pH in the experiment, was obtained. On the basis of the calculations, a mechanism for the methylation reaction involving two–electron reduction and protonation on the proximal nickel atom of the reduced A-cluster is proposed.

Kinetic and substrate complex characterization of RamA, a corrinoid protein reductive activase from Methanosarcina barkeri

In microbial corrinoid-dependent methyltransferase systems, adventitious Co(I)-corrinoid oxidation halts catalysis and necessitates repair by ATP-dependent reductive activases. RamA, an activase with a C-terminal ferredoxin domain with two [4Fe-4S] clusters from methanogenic archaea, has been far less studied than the bacterial activases bearing an N-terminal ferredoxin domain with one [2Fe-2S] cluster. These differences suggest RamA might prove to have other distinctive characteristics. Here, we examine RamA kinetics and the stoichiometry of the corrinoid protein:RamA complex. Like bacterial activases, K+ stimulates RamA. Potassium stimulation had been questioned due to differences in the primary structure of bacterial and methanogen activases. Unlike one bacterial activase, ATP is not inhibitory allowing the first determination of apparent kinetic parameters for any corrinoid activase. Unlike bacterial activases, a single RamA monomer complexes a single corrinoid protein monomer. Alanine replacement of a RamA serine residue corresponding to the serine of one bacterial activase which ligates the corrinoid cobalt during complex formation led to only moderate changes in the kinetics of RamA. These results reveal new differences in the two types of corrinoid activases, and provide direct evidence for the proposal that corrinoid activases act as catalytic monomers, unlike other enzymes that couple ATP hydrolysis to difficult reductions.

Revealing the initial steps in homogeneous photocatalysis by time-resolved spectroscopy

Photocatalysis attracts currently intense research since it can provide efficient routes for generating solar fuels and allows to apply sunlight for an environmentally friendly synthesis of valuable chemical compounds. Accordingly, in future photocatalysis may contribute significantly to a sustainable economy. However, up to now photocatalysis has made it only into some niche applications. The reasons are manifold including too low yields, insufficient stability, and scarce availability of the precious metals and rare earths used in most cases. The design of better systems is the goal of many research activities. They call for a detailed knowledge of the individual steps and the microscopic mechanisms. Time-resolved spectroscopy is a powerful tool to improve our understanding of the individual steps of a photocatalytic process and of the efficiencies and losses associated with them. This allows to address specific weaknesses of the components of a photocatalytic system and to pursue a rational design of the corresponding compounds. In this review an overview is given about what insights can be gained by time-resolved spectroscopy referring mostly to our own results while it has to be stressed that many other groups are also highly successfully working in this area. We restrict ourselves to homogeneous systems which are often easier to analyze and focus on the primary steps occurring after optical excitation. This includes intramolecular relaxation and intersystem crossing in the photosensitizer as well as the first electron transfer step resulting from the interaction of the sensitizer with other components of the system. Ultrafast pump-probe spectroscopy turns out to be particularly helpful in analyzing new photosensitizers based on abundant metals, i.e. copper and iron. These sensitizers can suffer from short lifetimes of the metal-to-ligand charge transfer states which are typically involved in the intermolecular charge transfer processes. The latter are investigated on the pico- to microsecond timescale by quenching experiments making use of a streak camera and by pump-probe spectroscopy applying a YAG-laser system for excitation. The experiments with the streak camera allow to discriminate between oxidative and reductive pathways and to determine the corresponding bimolecular quenching rates which are compared to their diffusion limit to obtain a measure for the quenching efficiency. By applying transient absorption spectroscopy, it is furthermore possible to observe appearing charge transfer products and to determine their concentrations. In this way the efficiency of the electron transfer itself can be deduced and the relevance of lossy quenching events can be estimated.

Flavodoxin hydroquinone provides electrons for the ATP-dependent reactivation of protein-bound corrinoid cofactors

Corrinoid-dependent enzyme systems rely on the super-reduced state of the protein-bound corrinoid cofactor to be functional, for example, in methyl transfer reactions. Due to the low redox potential of the [Co^II ]/[Co^I ] couple, autoxidation of the corrinoid cofactor occurs and leads to the formation of the inactive [Co^II ]-state. For the reactivation, which is an energy-demanding process, electrons have to be transferred from a physiological donor to the corrinoid cofactor by the help of a reductive activator protein. In this study, we identified reduced flavodoxin as electron donor for the ATP-dependent reduction of protein-bound corrinoid cofactors of bacterial O-demethylase enzyme systems. Reduced flavodoxin was generated enzymatically using pyruvate:ferredoxin/flavodoxin oxidoreductase rather than hydrogenase. Two of the four flavodoxins identified in Acetobacterium dehalogenans and Desulfitobacterium hafniense DCB-2 were functional in supplying electrons for corrinoid reduction. They exhibited a midpoint potential of about -400 mV (E_SHE , pH 7.5) for the semiquinone/hydroquinone transition. Reduced flavodoxin could be replaced by reduced clostridial ferredoxin. It was shown that the low-potential electrons of reduced flavodoxin are first transferred to the iron-sulfur cluster of the reductive activator and finally to the protein-bound corrinoid cofactor. This study further highlights the importance of reduced flavodoxin, which allows maintaining a variety of enzymatic reaction cycles by delivering low-potential electrons.