Snapshots of the Reaction Coordinate of a Thermophilic 2'-Deoxyribonucleoside/ribonucleoside Transferase.

Nucleosides are ubiquitous to life and are required for the synthesis of DNA, RNA, and other molecules crucial for cell survival. Despite the notoriously difficult organic synthesis of nucleosides, 2'-deoxynucleoside analogues can interfere with natural DNA replication and repair and are successfully employed as anticancer, antiviral, and antimicrobial compounds. Nucleoside 2'-deoxyribosyltransferase (dNDT) enzymes catalyze transglycosylation via a covalent 2'-deoxyribosylated enzyme intermediate with retention of configuration, having applications in the biocatalytic synthesis of 2'-deoxynucleoside analogues in a single step. Here, we characterize the structure and function of a thermophilic dNDT, the protein from Chroococcidiopsis thermalis (CtNDT). We combined enzyme kinetics with structural and biophysical studies to dissect mechanistic features in the reaction coordinate, leading to product formation. Bell-shaped pH-rate profiles demonstrate activity in a broad pH range of 5.5-9.5, with two very distinct pKa values. A pronounced viscosity effect on the turnover rate indicates a diffusional step, likely product (nucleobase1) release, to be rate-limiting. Temperature studies revealed an extremely curved profile, suggesting a large negative activation heat capacity. We trapped a 2'-fluoro-2'-deoxyarabinosyl-enzyme intermediate by mass spectrometry and determined high-resolution structures of the protein in its unliganded, substrate-bound, ribosylated, 2'-difluoro-2'-deoxyribosylated, and in complex with probable transition-state analogues. We reveal key features underlying (2'-deoxy)ribonucleoside selection, as CtNDT can also use ribonucleosides as substrates, albeit with a lower efficiency. Ribonucleosides are the building blocks of RNA and other key intracellular metabolites participating in energy and metabolism, expanding the scope of use of CtNDT in biocatalysis.

Correction: Bypassing the requirement for aminoacyl-tRNA by a cyclodipeptide synthase enzyme.

[This corrects the article DOI: 10.1039/D0CB00142B.].

Bypassing the requirement for aminoacyl-tRNA by a cyclodipeptide synthase enzyme.

Cyclodipeptide synthases (CDPSs) produce a variety of cyclic dipeptide products by utilising two aminoacylated tRNA substrates. We sought to investigate the minimal requirements for substrate usage in this class of enzymes as the relationship between CDPSs and their substrates remains elusive. Here, we investigated the Bacillus thermoamylovorans enzyme, BtCDPS, which synthesises cyclo(l-Leu-l-Leu). We systematically tested where specificity arises and, in the process, uncovered small molecules (activated amino esters) that will suffice as substrates, although catalytically poor. We solved the structure of BtCDPS to 1.7 Å and combining crystallography, enzymatic assays and substrate docking experiments propose a model for how the minimal substrates interact with the enzyme. This work is the first report of a CDPS enzyme utilizing a molecule other than aa-tRNA as a substrate; providing insights into substrate requirements and setting the stage for the design of improved simpler substrates.

A lysozyme with altered substrate specificity facilitates prey cell exit by the periplasmic predator Bdellovibrio bacteriovorus.

Lysozymes are among the best-characterized enzymes, acting upon the cell wall substrate peptidoglycan. Here, examining the invasive bacterial periplasmic predator Bdellovibrio bacteriovorus, we report a diversified lysozyme, DslA, which acts, unusually, upon (GlcNAc-) deacetylated peptidoglycan. B. bacteriovorus are known to deacetylate the peptidoglycan of the prey bacterium, generating an important chemical difference between prey and self walls and implying usage of a putative deacetyl-specific "exit enzyme". DslA performs this role, and ΔDslA strains exhibit a delay in leaving from prey. The structure of DslA reveals a modified lysozyme superfamily fold, with several adaptations. Biochemical assays confirm DslA specificity for deacetylated cell wall, and usage of two glutamate residues for catalysis. Exogenous DslA, added ex vivo, is able to prematurely liberate B. bacteriovorus from prey, part-way through the predatory lifecycle. We define a mechanism for specificity that invokes steric selection, and use the resultant motif to identify wider DslA homologues.

Target highlights in CASP13: Experimental target structures through the eyes of their authors.

The functional and biological significance of selected CASP13 targets are described by the authors of the structures. The structural biologists discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP13 experiment.

Microkinetic simulations of the oxidation of CO on Pd based nanocatalysis: a model including co-dependent support interactions.

The catalysed oxidation of CO using mass-selected Pd(13) clusters supported on thin MgO films was modelled using a microkinetic simulation of the reaction. The model of the system includes reverse spill-over calculations which were intrinsically incorporated into the formulation of the kinetics. The spill-over model is based on a capture-zone approach including a co-dependence on the variables of the kinetic equations. The experimental values were determined using dual pulsed-molecular beam measurements and recorded at a range of temperatures. The experiment allowed the turn-over frequency and reaction probability to be determined as a function of mole fraction. Comparison of the kinetic model with the experimental data gives excellent agreement and strongly highlights the importance of substrate effects. In particular, the origin of the low temperature catalysis of the Pd clusters is elucidated. The model allows the mole fraction and temperature dependent values such as the sticking coefficients for these clusters to be predicted.

Micromechanical sensor for studying heats of surface reactions, adsorption, and cluster deposition processes.

We present a newly designed highly sensitive micromechanical sensor devoted to thermodynamic studies involving supported clusters. The thermally sensitive element of the sensor consists of a micromachined silicon cantilever array, onto which a thin metal film is evaporated. Due to the difference between the thermal expansion coefficients of silicon and the metal employed, thermal bending is observed when heat is exchanged with the cantilever. The sensitivity and the response time of the cantilever are studied as a function of the film material (gold or aluminum) and the thickness of the metal film. With our routinely prepared cantilevers, a minimum power of 120 nW is measurable with a submillisecond response time, corresponding to a limit of detection in the femtojoule range. The high sensitivity of the sensor is demonstrated by measuring the heat exchange which occurs during the deposition of clusters on the cantilever. Experimentally, we illustrate the 1,3-butadiene hydrogenation reaction using a cluster model catalysts created by soft-landing palladium clusters onto the cantilever surface.