Determining the oxidation state of elements by X ray crystallography

Protein-mediated redox reactions play a critical role in many biological processes and often occur at centres that contain metal ions as cofactors. In order to understand the exact mechanisms behind these reactions it is important to not only characterize the three-dimensional structures of these proteins and their cofactors, but also to identify the oxidation states of the cofactors involved and to correlate this knowledge with structural information. The only suitable approach for this based on crystallographic measurements is spatially resolved anomalous dispersion (SpReAD) refinement, a method that has been used previously to determine the redox states of metals in iron–sulfur cluster-containing proteins. In this article, the feasibility of this approach for small, non-iron–sulfur redox centres is demonstrated by employing SpReAD analysis to characterize Sulfolobus tokodaii sulerythrin, a ruberythrin-like protein that contains a binuclear metal centre. Differences in oxidation states between the individual iron ions of the binuclear metal centre are revealed in sulerythrin crystals treated with H(2)O(2). Furthermore, data collection at high X-ray doses leads to photoreduction of this metal centre, showing that careful control of the total absorbed dose is a prerequisite for successfully determining the oxidation state through SpReAD analysis

Bio-inspired CO₂ conversion by iron sulfide catalysts under sustainable conditions

The mineral greigite presents similar surface structures to the active sites found in many modern-day enzymes. We show that particles of greigite can reduce CO2 under ambient conditions into chemicals such as methanol, formic, acetic and pyruvic acid. Our results also lend support to the Origin of Life theory on alkaline hydrothermal vents

Frontiers, Opportunities, and Challenges in Biochemical and Chemical Catalysis of CO_2 Fixation

Two major energy-related problems confront the world in the next 50 years. First, increased worldwide competition for gradually depleting fossil fuel reserves (derived from past photosynthesis) will lead to higher costs, both monetarily and politically. Second, atmospheric CO_2 levels are at their highest recorded level since records began. Further increases are predicted to produce large and uncontrollable impacts on the world climate. These projected impacts extend beyond climate to ocean acidification, because the ocean is a major sink for atmospheric CO2.1 Providing a future energy supply that is secure and CO_2-neutral will require switching to nonfossil energy sources such as wind, solar, nuclear, and geothermal energy and developing methods for transforming the energy produced by these new sources into forms that can be stored, transported, and used upon demand

Discovery of the Lanthipeptide Curvocidin and Structural Insights into its Trifunctional Synthetase CuvL

Lanthipeptides are ribosomally-synthesized natural products from bacteria featuring stable thioether-crosslinks and various bioactivities. Herein, we report on a new clade of tricyclic class-IV lanthipeptides with curvocidin from Thermomonospora curvata as its first representative. We obtained crystal structures of the corresponding lanthipeptide synthetase CuvL that showed a circular arrangement of its kinase, lyase and cyclase domains, forming a central reaction chamber for the iterative substrate processing involving nine catalytic steps. The combination of experimental data and artificial intelligence-based structural models identified the N-terminal subdomain of the kinase domain as the primary site of substrate recruitment. The ribosomal precursor peptide of curvocidin employs an amphipathic α-helix in its leader region as an anchor to CuvL, while its substrate core shuttles within the central reaction chamber. Our study thus reveals general principles of domain organization and substrate recruitment of class-IV and class-III lanthipeptide synthetases.Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659Research Training Group RTG 2473 "Bioactive Peptides"RTG 2473 "Bioactive Peptides"Peer Reviewe

Anaerobic Carbon Monoxide Dehydrogenase Diversity in the Homoacetogenic Hindgut Microbial Communities of Lower Termites and the Wood Roach

Anaerobic carbon monoxide dehydrogenase (CODH) is a key enzyme in the Wood-Ljungdahl (acetyl-CoA) pathway for acetogenesis performed by homoacetogenic bacteria. Acetate generated by gut bacteria via the acetyl-CoA pathway provides considerable nutrition to wood-feeding dictyopteran insects making CODH important to the obligate mutualism occurring between termites and their hindgut microbiota. To investigate CODH diversity in insect gut communities, we developed the first degenerate primers designed to amplify cooS genes, which encode the catalytic (β) subunit of anaerobic CODH enzyme complexes. These primers target over 68 million combinations of potential forward and reverse cooS primer-binding sequences. We used the primers to identify cooS genes in bacterial isolates from the hindgut of a phylogenetically lower termite and to sample cooS diversity present in a variety of insect hindgut microbial communities including those of three phylogenetically-lower termites, Zootermopsis nevadensis, Reticulitermes hesperus, and Incisitermes minor, a wood-feeding cockroach, Cryptocercus punctulatus, and an omnivorous cockroach, Periplaneta americana. In total, we sequenced and analyzed 151 different cooS genes. These genes encode proteins that group within one of three highly divergent CODH phylogenetic clades. Each insect gut community contained CODH variants from all three of these clades. The patterns of CODH diversity in these communities likely reflect differences in enzyme or physiological function, and suggest that a diversity of microbial species participate in homoacetogenesis in these communities

Cation distribution and mixing thermodynamics in Fe/Ni thiospinels

The structural analogy between Ni-doped greigite minerals (Fe3S4) and the (Fe, Ni)S clusters present in biological enzymes has led to suggestions that these minerals could have acted as catalysts for the origin of life. However, little is known about the distribution and stability of Ni dopants in the greigite structure. We present here a theoretical investigation of mixed thiospinels (Fe1−xNix)3S4, using a combination of density functional theory (DFT) calculations and Monte Carlo simulations. We find that the equilibrium distribution of the cations deviates significantly from a random distribution: at low Ni concentrations, Ni dopants are preferably located in octahedral sites, while at higher Ni concentrations the tetrahedral sites become much more favourable. The thermodynamic mixing behaviour between greigite and polydymite (Ni3S4) is dominated by the stability field of violarite (FeNi2S4), for which the mixing enthalpy exhibits a deep negative minimum. The analysis of the free energy of mixing shows that Ni doping of greigite is very unstable with respect to the formation of a separate violarite phase. The calculated variation of the cubic cell parameter with composition is found to be non-linear, exhibiting significant deviation from Vegard’s law, but in agreement with experiment

ATP dependent substrate reduction at an [Fe8S9] double cubane cluster

Significance Our ability to reduce stable small molecules, such as dinitrogen or carbon dioxide, is as vital as it is demanding and requires energetic electrons and a catalyst. In nature, these requirements are met by two-component enzymes: an electron-donating metallo-ATPase and the principal catalyst, a metalloprotein with a low-potential cofactor. Here, we present a two-component enzyme in which the catalyst houses a double-cubane type [Fe 8 S 9 ]-cluster. Iron–sulfur clusters with so high nuclearity were so far only known from nitrogenase, an enzyme notorious for its capacity to reduce various small molecules. The enzyme not only shares structural features with nitrogenase, but is also able to reduce acetylene, indicating its potential employment for reductive reactions of our choice. </jats:p