Insights Into the Known 13C Depletion of Methane—Contribution of the Kinetic Isotope Effects on the Serine Hydroxymethyltransferase Reaction

We determined the kinetic isotope effect on the serine hydroxymethyltransferase reaction (SHMT), which provides important C1 metabolites that are essential for the biosynthesis of DNA bases, O-methyl groups of lignin and methane. An isotope effect on the SHMT reaction was suggested being responsible for the well-known isotopic depletion of methane. Using the cytosolic SHMT from pig liver, we measured the natural carbon isotope ratios of both atoms involved in the bond splitting by chemical degradation of the remaining serine before and after partial turnover. The kinetic isotope effect 13(VMax/Km) was 0.994 0.006 and 0.995 0.007 on position C-3 and C-2, respectively. The results indicated that the SHMT reaction does not contribute to the 13C depletion observed for methyl groups in natural products and methane. However, from the isotopic pattern of caffeine, isotope effects on the methionine synthetase reaction and on reactions forming Grignard compounds, the involved formation and fission of metal organic bonds are likely responsible for the observed general depletion of “activated” methyl groups. As metal organic bond formations in methyl transferases are also rate limiting in the formation of methane, they may likely be the origin of the known 13C depletion in methane.

Nitrogen Kinetic Isotope Effects of Nitrification by the Complete Ammonia Oxidizer Nitrospira inopinata

Nitrification is an important nitrogen cycle process in terrestrial and aquatic environments. The discovery of comammox has changed the view that canonical AOA, AOB, and NOB are the only chemolithoautotrophic organisms catalyzing nitrification.

Validating Experiment for the Reaction H2 + NH2- by Dynamical Computations on an Accurate Full-Dimensional Potential Energy Surface

Ion-neutral molecular reactions play key roles in the field of ion related chemistry. As a prototypical multi-channel ion-molecular reaction, the reaction H2 + NH2- → NH3 + H- has been studied for decades. In this work, we develop a globally accurate potential energy surface (PES) for the title system H2 + NH2- based on nearly hundreds of thousands points over a wide dynamically relevant region. The permutational invariants polynomials neural network (PIP-NN) method is used for fitting and the total root mean squared error (RMSE) is extremely small, only 0.026 kcal mol-1. Extensive dynamical and rate coefficient calculations are carried out on this new PIP-NN PES by the quasi-classical trajectory (QCT) method. The calculated rate coefficients for H2 / D2 + NH2- agree well with the experimental results that show a inverse temperature dependence from 50 to 300 K, consistent with the capture nature of this barrierless reaction. A significant kinetic isotope effect has been well reproduced by the QCT computations. In addition, we report a unique phenomenon of significant reactivity suppression by exciting the rotational mode of H2, particular at low collision energies. Further analysis shows that the excitation of rotational mode of H2 would prevent the formation of the reactant complex and thus suppress reactivity.

A Substrate-triggered µ-Peroxodiiron(III) Intermediate in the 4-Choro-L-Lysine-Fragmenting Heme-Oxygenase-like Diiron Oxidase (HDO) BesC: Substrate Dissociation from, and C4 Targeting by, the Intermediate

ABSTRACTThe enzyme BesC from the β-ethynyl-L-serine biosynthetic pathway in Streptomyces cattleya fragments 4-chloro-L-lysine (produced from L-Lysine by BesD) to ammonia, formaldehyde, and 4-chloro-L-allylglycine and can analogously fragment L-Lys itself. BesC belongs to the emerging family of O2-activating non-heme-diiron enzymes with the "heme-oxygenase-like" protein fold (HDOs). Here we show that binding of L-Lys or an analog triggers capture of O2 by the protein’s diiron(II) cofactor to form a blue µ-peroxodiiron(III) intermediate analogous to those previously characterized in two other HDOs, the olefin-installing fatty acid decarboxylase, UndA, and the guanidino-N-oxygenase domain of SznF. The ∼ 5- and ∼ 30-fold faster decay of the intermediate in reactions with 4-thia-L-Lys and (4RS)-chloro-DL-lysine than in the reaction with L-Lys itself, and the primary deuterium kinetic isotope effects (D-KIEs) on decay of the intermediate and production of L-allylglycine in the reaction with 4,4,5,5-[2H]-L-Lys, imply that the peroxide intermediate or a successor complex with which it reversibly interconverts initiates the oxidative fragmentation by abstracting hydrogen from C4. Surprisingly, the sluggish substrate L-Lys can dissociate after triggering the intermediate to form, thereby allowing one of the better substrates to bind and react. Observed linkage between Fe(II) and substrate binding suggests that the triggering event involves a previously documented (in SznF) ordering of the dynamic HDO architecture that contributes one of the iron sites, a hypothesis consistent with the observation that the diiron(III) product cluster produced upon decay of the intermediate spontaneously degrades, as it has been shown to do in all other HDOs studied to date.

Penultimate deglaciation Asian monsoon response to North Atlantic circulation collapse

During glacial terminations, massive iceberg discharges and meltwater pulses in the North Atlantic triggered a shutdown of the Atlantic Meridional Overturning Circulation (AMOC). Speleothem calcium carbonate oxygen isotope records (δ18OCc) indicate that the collapse of the AMOC caused dramatic changes in the distribution and variability of the East Asian and Indian monsoon rainfall. However, the mechanisms linking changes in the intensity of the AMOC and Asian monsoon δ18OCc are not fully understood. Part of the challenge arises from the fact that speleothem δ18OCc depends on not only the δ18O of precipitation but also temperature and kinetic isotope effects. Here we quantitatively deconvolve these parameters affecting δ18OCc by applying three geochemical techniques in speleothems covering the penultimate glacial termination. Our data suggest that the weakening of the AMOC during meltwater pulse 2A caused substantial cooling in East Asia and a shortening of the summer monsoon season, whereas the collapse of the AMOC during meltwater pulse 2B (133,000 years ago) also caused a dramatic decrease in the intensity of the Indian summer monsoon. These results reveal that the different modes of the AMOC produced distinct impacts on the monsoon system.