Methyl-coenzyme M reductase (MCR) is the key enzyme of methanogenesis and anaerobic methane oxidation. The activity of MCR is dependent on the unique nickel-containing tetrapyrrole known as coenzyme F430. We used comparative genomics to identify the coenzyme F430 biosynthesis (cfb) genes and characterized the encoded enzymes from Methanosarcina acetivorans C2A. The pathway involves nickelochelation by a nickel-specific chelatase, followed by amidation to form Ni-sirohydrochlorin a,c-diamide. Next, a primitive homolog of nitrogenase mediates a six-electron reduction and γ-lactamization reaction before a Mur ligase homolog forms the six-membered carbocyclic ring in the final step of the pathway. These data show that coenzyme F430 can be synthesized from sirohydrochlorin using Cfb enzymes produced heterologously in a nonmethanogen host and identify several targets for inhibitors of biological methane formation.

Peptide boronic acids and peptidyl trifluoromethyl ketones (TFKs) inhibit serine proteases by forming monoanionic, tetrahedral adducts to serine in the active sites. Investigators regard these adducts as analogs of monoanionic, tetrahedral intermediates. Density functional theory (DFT) calculations and fractional charge analysis show that tetrahedral adducts of model peptidyl TFKs are structurally and electrostatically very similar to corresponding tetrahedral intermediates. In contrast, the DFT calculations show the structures and electrostatic properties of analogous peptide boronate adducts to be significantly different. The peptide boronates display highly electrostatically positive boron, with correspondingly negative ligands in the tetrahedra. In addition, the computed boron-oxygen and boron-carbon bond lengths in peptide boronates (which are identical or very similar to the corresponding bonds in a peptide boronate adduct of α-lytic protease determined by X-ray crystallography at subangstrom resolution) are significantly longer than the corresponding bond lengths in model tetrahedral intermediates. Since protease-peptidyl TFKs incorporate low-barrier hydrogen bonds (LBHBs) between an active site histidine and aspartate, while the protease-peptide boronates do not, these data complement the spectroscopic and chemical evidence for the participation of LBHBs in catalysis by serine proteases. Moreover, while the potency of these classes of inhibitors can be correlated to the structures of the peptide moieties, the present results indicate that the strength of their bonds to serine contribute significantly to their inhibitory properties.

Ubiquitous in the world's oceans, dinoflagellates are capable of fantastic displays of bright‐blue bioluminescence. This luminosity is a consequence of the oxidation of an open‐chain tetrapyrrole, dinoflagellate luciferin (LH2), by the enzyme dinoflagellate luciferase (LCF). While many other bioluminescence systems are well understood, the reaction mechanism of LCF remains enigmatic. A comprehensive density functional theory investigation was used to evaluate several competing mechanisms of LCF catalysis employing distinct excited‐state luminophores. The results provide strong evidence in favor of a mechanism of dinoflagellate bioluminescence involving an excited‐state gem‐diol(ate) intermediate. Analysis of the molecular orbitals relevant to the emission process indicates that catalysis from the E isomer of LH2 is likely to proceed via a chemically initiated electron‐exchange luminescence reaction, whereas that from the Z isomer may involve the formation of a biologically unprecedented twisted intramolecular charge transfer state.

The bioluminescence reaction in dinoflagellates involves the oxidation of an open-chain tetrapyrrole by the enzyme dinoflagellate luciferase (LCF). The activity of LCF is tightly regulated by pH, where the enzyme is essentially inactive at pH ∼8 and optimally active at pH ∼6. Little is known about the mechanism of LCF or the structure of the active form of the enzyme, although it has been proposed that several intramolecularly conserved histidine residues in the N-terminal region are important for the pH regulation mechanism. Here, constant pH accelerated molecular dynamics was employed to gain insight into the conformational activation of LCF induced by acidification.

Methyl‐coenzyme M reductase (MCR) is the key enzyme of methanogenesis and the anaerobic oxidation of methane (AOM). MCR catalyzes the reversible conversion of methyl‐coenzyme M (MeS‐CoM) and coenzyme B (CoB‐SH) to the mixed heterodisulfide, CoB‐S‐S‐CoM, and methane. The methane forming and oxidizing activities of MCR are dependent on the unique, nickel‐containing tetrapyrrole, coenzyme F430. In addition to housing F430, the active site regions of MCR from both methanogens and anaerobic methanotrophic archaea (ANME) contain several unusual posttranslational modifications (PTMs). Given the unique ability of MCR to catalyze the AOM, there is much interest in the mechanism and formation of holo MCR for potential applications in gas‐to‐liquid (GTL) conversion strategies (see Methane‐to‐Methanol Conversion ). This chapter details current progress in the understanding of coenzyme F430 biosynthesis, the maturation of MCR, and differences in structural features of methanogenic and methanotrophic MCR that may be important for the AOM.