(ADP-ribosyl)hydrolases: structure, function, and biology.

ADP-ribosylation is an intricate and versatile posttranslational modification involved in the regulation of a vast variety of cellular processes in all kingdoms of life. Its complexity derives from the varied range of different chemical linkages, including to several amino acid side chains as well as nucleic acids termini and bases, it can adopt. In this review, we provide an overview of the different families of (ADP-ribosyl)hydrolases. We discuss their molecular functions, physiological roles, and influence on human health and disease. Together, the accumulated data support the increasingly compelling view that (ADP-ribosyl)hydrolases are a vital element within ADP-ribosyl signaling pathways and they hold the potential for novel therapeutic approaches as well as a deeper understanding of ADP-ribosylation as a whole.

Structure and biochemical characterization of l-2-hydroxyglutarate dehydrogenase and its role in the pathogenesis of l-2-hydroxyglutaric aciduria.

l-2-hydroxyglutarate dehydrogenase (L2HGDH) is a mitochondrial membrane-associated metabolic enzyme, which catalyzes the oxidation of l-2-hydroxyglutarate (l-2-HG) to 2-oxoglutarate (2-OG). Mutations in human L2HGDH lead to abnormal accumulation of l-2-HG, which causes a neurometabolic disorder named l-2-hydroxyglutaric aciduria (l-2-HGA). Here, we report the crystal structures of Drosophila melanogaster L2HGDH (dmL2HGDH) in FAD-bound form and in complex with FAD and 2-OG and show that dmL2HGDH exhibits high activity and substrate specificity for l-2-HG. dmL2HGDH consists of an FAD-binding domain and a substrate-binding domain, and the active site is located at the interface of the two domains with 2-OG binding to the re-face of the isoalloxazine moiety of FAD. Mutagenesis and activity assay confirmed the functional roles of key residues involved in the substrate binding and catalytic reaction and showed that most of the mutations of dmL2HGDH equivalent to l-2-HGA-associated mutations of human L2HGDH led to complete loss of the activity. The structural and biochemical data together reveal the molecular basis for the substrate specificity and catalytic mechanism of L2HGDH and provide insights into the functional roles of human L2HGDH mutations in the pathogeneses of l-2-HGA.

Deciphering the stereo-specific catalytic mechanisms of cis-epoxysuccinate hydrolases producing L(+)-tartaric acid.

Microbial epoxide hydrolases, cis-epoxysuccinate hydrolases (CESHs), have been utilized for commercial production of enantiomerically pure L(+)- and D(-)-tartaric acids for decades. However, the stereo-catalytic mechanism of CESH producing L(+)-tartaric acid (CESH[L]) remains unclear. Herein, the crystal structures of two CESH[L]s in ligand-free, product-complexed, and catalytic intermediate forms were determined. These structures revealed the unique specific binding mode for the mirror-symmetric substrate, an active catalytic triad consisting of Asp-His-Glu, and an arginine providing a proton to the oxirane oxygen to facilitate the epoxide ring-opening reaction, which has been pursued for decades. These results provide the structural basis for the rational engineering of these industrial biocatalysts.

Rapid reaction studies on the chemistry of flavin oxidation in urocanate reductase.

Urocanate reductase (UrdA) is a bacterial flavin-dependent enzyme that reduces urocanate to imidazole propionate, enabling bacteria to use urocanate as an alternative respiratory electron acceptor. Elevated serum levels of imidazole propionate are associated with the development of type 2 diabetes, and, since UrdA is only present in humans in gut bacteria, this enzyme has emerged as a significant factor linking the health of the gut microbiome and insulin resistance. Here, we investigated the chemistry of flavin oxidation by urocanate in the isolated FAD domain of UrdA (UrdA') using anaerobic stopped-flow experiments. This analysis unveiled the presence of a charge-transfer complex between reduced FAD and urocanate that forms within the dead time of the stopped-flow instrument (∼1 ms), with flavin oxidation subsequently occurring with a rate constant of ∼60 s-1. The pH dependence of the reaction and analysis of an Arg411Ala mutant of UrdA' are consistent with Arg411 playing a crucial role in catalysis by serving as the active site acid that protonates urocanate during hydride transfer from reduced FAD. Mutational analysis of urocanate-binding residues suggests that the twisted conformation of urocanate imposed by the active site of UrdA' facilitates urocanate reduction. Overall, this study provides valuable insight into the mechanism of urocanate reduction by UrdA.

Structural basis of chorismate isomerization by Arabidopsis ISOCHORISMATE SYNTHASE1.

Salicylic acid (SA) plays a crucial role in plant defense against biotrophic and semi-biotrophic pathogens. In Arabidopsis (Arabidopsis thaliana), isochorismate synthase 1 (AtICS1) is a key enzyme for the pathogen-induced biosynthesis of SA via catalytic conversion of chorismate into isochorismate, an essential precursor for SA synthesis. Despite the extensive knowledge of ICS1-related menaquinone, siderophore, tryptophan (MST) enzymes in bacteria, the structural mechanisms for substrate binding and catalysis in plant isochorismate synthase (ICS) enzymes are unknown. This study reveals that plant ICS enzymes catalyze the isomerization of chorismate through a magnesium-dependent mechanism, with AtICS1 exhibiting the most substantial catalytic activity. Additionally, we present high-resolution crystal structures of apo AtICS1 and its complex with chorismate, offering detailed insights into the mechanisms of substrate recognition and catalysis. Importantly, our investigation indicates the existence of a potential substrate entrance channel and a gating mechanism regulating substrate into the catalytic site. Structural comparisons of AtICS1 with MST enzymes suggest a shared structural framework with conserved gating and catalytic mechanisms. This work provides valuable insights into the structural and regulatory mechanisms governing substrate delivery and catalysis in AtICS1, as well as other plant ICS enzymes.

Structures and Electron Transport Paths in the Four Families of Flavin-Based Electron Bifurcation Enzymes.

Oxidoreductases facilitating electron transfer between molecules are pivotal in metabolic pathways. Flavin-based electron bifurcation (FBEB), a recently discovered energy coupling mechanism in oxidoreductases, enables the reversible division of electron pairs into two acceptors, bridging exergonic and otherwise unfeasible endergonic reactions. This chapter explores the four distinct FBEB complex families and highlights a decade of structural insights into FBEB complexes. In this chapter, we discuss the architecture, electron transfer routes, and conformational changes across all FBEB families, revealing the structural foundation that facilitate these remarkable functions.

Diverse triterpene skeletons are derived from the expansion and divergent evolution of 2,3-oxidosqualene cyclases in plants.

Triterpenoids are one of the largest groups of secondary metabolites and exhibit diverse structures, which are derived from C30 skeletons that are biosynthesized via the isoprenoid pathway by cyclization of 2,3-oxidosqualene. Triterpenoids have a wide range of biological activities, and are used in functional foods, drugs, and as industrial materials. Due to the low content levels in their native plants and limited feasibility and efficiency of chemical synthesis, heterologous biosynthesis of triterpenoids is the most promising strategy. Herein, we classified 121 triterpene alcohols/ketones according to their conformation and ring numbers, among which 51 skeletons have been experimentally characterized as the products of oxidosqualene cyclases (OSCs). Interestingly, 24 skeletons that have not been reported from nature source were generated by OSCs in heterologous expression. Comprehensive evolutionary analysis of the identified 152 OSCs from 75 species in 25 plant orders show that several pentacyclic triterpene synthases repeatedly originated in multiple plant lineages. Comparative analysis of OSC catalytic reaction revealed that stabilization of intermediate cations, steric hindrance, and conformation of active center amino acid residues are primary factors affecting triterpene formation. Optimization of OSC could be achieved by changing of side-chain orientations of key residues. Recently, methods, such as rationally design of pathways, regulation of metabolic flow, compartmentalization engineering, etc., were introduced in improving chassis for the biosynthesis of triterpenoids. We expect that extensive study of natural variation of large number of OSCs and catalytical mechanism will provide basis for production of high level of triterpenoids by application of synthetic biology strategies.

Structures of the NDP-pyranose mutase belonging to glycosyltransferase family 75 reveal residues important for Mn2+ coordination and substrate binding.

Members of glycosyltransferase family 75 (GT75) not only reversibly catalyze the autoglycosylation of a conserved arginine residue with specific NDP-sugars but also exhibit NDP-pyranose mutase activity that reversibly converts specific NDP-pyranose to NDP-furanose. The latter activity provides valuable NDP-furanosyl donors for glycosyltransferases and requires a divalent cation as a cofactor instead of FAD used by UDP-D-galactopyranose mutase. However, details of the mechanism for NDP-pyranose mutase activity are not clear. Here we report the first crystal structures of GT75 family NDP-pyranose mutases. The novel structures of GT75 member MtdL in complex with Mn2+ and GDP, GDP-D-glucopyranose, GDP-L-fucopyranose, GDP-L-fucofuranose, respectively, combined with site-directed mutagenesis studies, reveal key residues involved in Mn2+ coordination, substrate binding, and catalytic reactions. We also provide a possible catalytic mechanism for this unique type of NDP-pyranose mutase. Taken together, our results highlight key elements of an enzyme family important for furanose biosynthesis.

Repair of topoisomerase 1-induced DNA damage by tyrosyl-DNA phosphodiesterase 2 (TDP2) is dependent on its magnesium binding.

Topoisomerases are enzymes that relax DNA supercoiling during replication and transcription. Camptothecin, a topoisomerase 1 (TOP1) inhibitor, and its analogs trap TOP1 at the 3'-end of DNA as a DNA-bound intermediate, resulting in DNA damage that can kill cells. Drugs with this mechanism of action are widely used to treat cancers. It has previously been shown that tyrosyl-DNA phosphodiesterase 1 (TDP1) repairs TOP1-induced DNA damage generated by camptothecin. In addition, tyrosyl-DNA phosphodiesterase 2 (TDP2) plays critical roles in repairing topoisomerase 2 (TOP2)-induced DNA damage at the 5'-end of DNA and in promoting the repair of TOP1-induced DNA damage in the absence of TDP1. However, the catalytic mechanism by which TDP2 processes TOP1-induced DNA damage has not been elucidated. In this study, we found that a similar catalytic mechanism underlies the repair of TOP1- and TOP2-induced DNA damage by TDP2, with Mg2+-TDP2 binding playing a role in both repair mechanisms. We show chain-terminating nucleoside analogs are incorporated into DNA at the 3'-end and abort DNA replication to kill cells. Furthermore, we found that Mg2+-TDP2 binding also contributes to the repair of incorporated chain-terminating nucleoside analogs. Overall, these findings reveal the role played by Mg2+-TDP2 binding in the repair of both 3'- and 5'-blocking DNA damage.

The Pseudomonas aeruginosa PAO1 metallo flavoprotein d-2-hydroxyglutarate dehydrogenase requires Zn2+ for substrate orientation and activation.

Pseudomonas aeruginosa PAO1 d-2-hydroxyglutarate (D2HG) dehydrogenase (PaD2HGDH) oxidizes D2HG to 2-ketoglutarate during the vital l-serine biosynthesis and is a potential therapeutic target against P. aeruginosa. PaD2HGDH, which oxidizes d-malate as an alternative substrate, has been demonstrated to be a metallo flavoprotein that requires Zn2+ for activity. However, the role of Zn2+ in the enzyme has not been elucidated, making it difficult to rationalize why nature employs both a redox center and a metal ion for catalysis in PaD2HGDH and other metallo flavoenzymes. In this study, recombinant His-tagged PaD2HGDH was purified to high levels in the presence of Zn2+ or Co2+ to investigate the metal's role in catalysis. We found that the flavin reduction step was reversible and partially rate limiting for the enzyme's turnover at pH 7.4 with either D2HG or d-malate with similar rate constants for both substrates, irrespective of whether Zn2+ or Co2+ was bound to the enzyme. The steady-state pL profiles of the kcat and kcat/Km values with d-malate demonstrate that Zn2+ mediates the activation of water coordinated to the metal. Our data are consistent with a dual role for the metal, which orients the hydroxy acid substrate in the enzyme's active site and rapidly deprotonates the substrate to yield an alkoxide species for hydride transfer to the flavin. Thus, we propose a catalytic mechanism for PaD2HGDH oxidation that establishes Zn2+ as a cofactor required for substrate orientation and activation during enzymatic turnover.

Modulation of Potential-Limiting Steps in Lithium-Sulfur Batteries by Catalyst Synergy.

Electrocatalysis is considered to be an effective method to solve the sluggish kinetics of lithium-sulfur batteries. However, a single catalyst cannot simultaneously catalyze multi-step sulfur reductions. And once the catalyst surface is covered by the initially deposited solid products, the subsequent catalytic activity will significantly deteriorate. Here, microporous ZIF-67 and its derivative nano-metallic Co0 are used as dual-catalyst aiming to address these drawbacks. The dual catalytic center effectively cooperates the adsorption and electron transfer for multi-steps of sulfur reductions, transforming the potential-limited step (Li2S4→Li2S2/Li2S) into a thermodynamic spontaneous reaction. ZIF-67 first adsorbs soluble Li2S4 to form a coordination structure of ZIF-Li2S4. Then nano-metallic Co0 attracts uncoordinated S atoms in ZIF-Li2S4 and facilitates the breaking of S-S bonds to form transient reductive ZIF-Li2S2 and Co-S2 via. spontaneous electron transfer. These intermediates facilitate continuous conversion to Li2S with reduced formation energy, which is beneficial to the regeneration of the catalyst. As a result, the cathode with ZIF@CNTs/Co@CNFs synergetic catalyst achieves initial areal capacity of 4.7 mAh cm-2 and maintains 3.5 mAh cm-2 at low electrolyte/sulfur ratio (E/S) of 5 µL mg-1. This study provides valuable guidance for improving the electrochemical performance of lithium-sulfur batteries through catalyst synergistic strategies for multi-step reactions.

Revealing a Double-Volcano-Like Structure-Activity Relationship for Substitution-Functionalized Metal-Phthalocyanine Catalysts toward Electrochemical CO2 Reduction.

Electron-donating/-withdrawing groups (EDGs/EWGs) substitution is widely used to regulate the catalytic performance of transition-metal phthalocyanine (MPc) toward electrochemical CO2 reduction, but the corresponding structure-activity relationships and regulation mechanisms are still ambiguous. Herein, by investigating a series of substitution-functionalized MPc (MPc-X), this work reveals a double-volcano-like relationship between the electron-donating/-withdrawing abilities of the substituents and the catalytic activities of MPc-X. The weak-EDG/-EWG substitution enhances whereas the strong-EDG/-EWG substitution mostly lowers the CO selectivity of MPc. Experimental and calculation results demonstrate that the electronic properties of the substituents influence the symmetry and energy of the highest occupied molecular orbitals of MPc-X, which in turn determine the CO2 adsorption/activation and lead to diverse CO2 reduction pathways on the EWG or EDG substituted MPc via different CO2 adsorption modes. This work provides mechanism insights that could be guidance for the design and regulation of molecular catalysts.

Precise Design and Modification Engineering of Single-Atom Catalytic Materials for Oxygen Reduction.

Due to their unique electronic and structural properties, single-atom catalytic materials (SACMs) hold great promise for the oxygen reduction reaction (ORR). Coordinating environmental and engineering strategies is the key to improving the ORR performance of SACMs. This review summarizes the latest research progress and breakthroughs of SACMs in the field of ORR catalysis. First, the research progress on the catalytic mechanism of SACMs acting on ORR is reviewed, including the latest research results on the origin of SACMs activity and the analysis of pre-adsorption mechanism. The study of the pre-adsorption mechanism is an important breakthrough direction to explore the origin of the high activity of SACMs and the practical and theoretical understanding of the catalytic process. Precise coordination environment modification, including in-plane, axial, and adjacent site modifications, can enhance the intrinsic catalytic activity of SACMs and promote the ORR process. Additionally, several engineering strategies are discussed, including multiple SACMs, high loading, and atomic site confinement. Multiple SACMs synergistically enhance catalytic activity and selectivity, while high loading can provide more active sites for catalytic reactions. Overall, this review provides important insights into the design of advanced catalysts for ORR.

Hierarchical MOFs with Good Catalytic Properties and Structural Stability in Oxygen-Rich and High-Temperature Environments.

Metal-organic framework materials are ideal materials characterized by open frameworks, adjustable components, and high catalytic activity. They are extensively utilized for catalysis. Due to decomposition and structural collapse under high temperatures and an oxygen-rich environment, the potential of thermal catalysis is greatly limited. In this research, Co-rich hollow spheres (Co-HSs) with a gradient composition are designed and synthesized to investigate their thermal catalytic properties in the ammonium perchlorate（AP）system. The results demonstrate that Co-HSs@AP exhibits good thermal catalytic activity and a high-temperature decomposition of 292.5 °C, which is 121.6 °C lower than pure AP. The hierarchical structure confers structural stability during the thermal decomposition process. Thermogravimetry-infrared indicates that the inclusion of Co-HSs successfully boosts the level of reactive oxygen species and achieves thorough oxidation of NH3. Based on the above phenomenon, macro dynamics calculations are carried out. The results show that Co-HSs can promote the circulation of lattice oxygen and reactive oxygen species and the multidimensional diffusion of NH3 in an oxygen-rich environment. This material has significant potential for application in the fields of thermal catalysis and ammonia oxidation.

Single-Crystal Ferroelectric-Based (K,Na)NbO3 Microcuboid/CuO Nanodot Heterostructures with Enhanced Photo-Piezocatalytic Activity.

Developing single-crystal-based heterostructured ferroelectrics with high-performance photo-piezocatalytic activity is highly desirable to utilize large piezopotentials and more reactive charges that can trigger the desired redox reactions. To that end, a single-crystal-based (K,Na)NbO3 (KNN) microcuboid/CuO nanodot heterostructure with enhanced photo-piezocataytic activity, prepared using a facile strategy that leveraged the synergy between heterojunction formation and an intense single-crystal-based piezoelectric effect, is reported herein. The catalytic rhodamine B degrading activity of KNN/CuO is investigated under light irradiation, ultrasonication, or co-excitation with both stimulations. Compared to polycrystalline KNN powders and bare KNN single-crystals, single-crystal-based KNN/CuO exhibits a higher piezocurrent density and an optimal energy band structure, resulting in 5.23 and 2.37 times higher piezocatalytic degradation activities, respectively. Furthermore, the maximum photo-piezocatalytic rate constant (≈0.093 min-1 ) of KNN/CuO under 25 min ultrasonication and light irradiation is superior to that of other KNN-based catalysts, and 1.6 and 48.6 times higher than individual piezocatalytic and photocatalytic reaction rate constants, respectively. The excellent photo-piezocatalytic activity is attributed to the enhanced charge-carrier separation and proper alignment of band structure to the required redox levels by the appropriate p-n heterojunction and high piezoelectric potential. This report provides useful insight into the relationships between heterojunctions, piezoelectric responses, and catalytic mechanisms for single-crystal-based heterostructured catalysts.

A Bioinspired Single-Atom Fe Nanozyme with Excellent Laccase-Like Activity for Efficient Aflatoxin B1 Removal.

The applications of natural laccases are greatly restricted because of their drawbacks like poor biostability, high costs, and low recovery efficiency. M/NC single atom nanozymes (M/NC SAzymes) are presenting as great substitutes due to their superior enzyme-like activity, excellent selectivity and high stability. In this work, inspired by the catalytic active center of natural enzyme, a biomimetic Fe/NC SAzyme (Fe-SAzyme) with O2-Fe-N4 coordination is successfully developed, exhibiting excellent laccase-like activity. Compared with their natural counterpart, Fe-SAzyme has shown superior catalytic efficiency and excellent stability under a wide range of pH (3.0-9.0), temperature (4-80 °C) and NaCl strength (0-300 mm). Interestingly, density functional theory (DFT) calculations reveal that the high catalytic performance is attributed to the activation of O2 by O2-Fe-N4 sites, which weakened the O─O bonds in the oxygen-to-water oxidation pathway. Furthermore, Fe-SAzyme is successfully applied for efficient aflatoxin B1 removal based on its robust laccase-like catalytic activity. This work provides a strategy for the rational design of laccase-like SAzymes, and the proposed catalytic mechanism will help to understand the coordination environment effect of SAzymes on laccase-like catalytic processes.

Revealing the Effect of Electronic Configuration in Cux Species on CO2 Photoreduction Characteristic Products.

As of the present time, the in-depth study of the structure-activity relationship between electronic configuration and CO2 photoreduction performance is often overlooked. Herein, a series of Cux species modified CeO2 nanodots are constructed in situ by flame spray pyrolysis (FSP) to achieve an efficient photocatalytic CO2-to-C2 conversion with an electron utilization of up to 142.5 µmol g-1. Through an in-depth study of the electronic behavior and catalytic pathways, it is found that the Cu0/Cu+ species in the coexistence state of Cu0/Cu+/Cu2+ can optimize the energy band structure, photocurrent stability, and provide a kinetic basis for the active surface catalytic reaction process that requires the conversion of multiple electrons into C2 products, which ultimately enhances the CO2-to-C2H6 photoreduction by 3.8-fold and that for CO2-to-C2H4 photoreduction by 5.2-fold. Besides, the Cu2+ species in the coexistence state of Cu0/Cu+/Cu2+ are able to regulate the electronic behavior and the choice of the catalytic pathway, enabling the transitions between CO2-to-C2H6 and CO2-to-C2H4. This work indicates that electronic configuration optimization is an effective strategy to significantly enhance the CO2 photoreduction performance and provides new ideas for the design and synthesis of high-performance heterostructure photocatalysts.

Formation of Bridged Disulfide in Epidithiodioxopiperazines.

Epidithiodioxopiperazine (ETP) alkaloids, featuring a 2,5-diketopiperazine core and transannular disulfide bridge, exhibit a broad spectrum of biological activities. However, the structural complexity has prevented efficient chemical synthesis and further clinical research. In the past few decades, many achievements have been made in the biosynthesis of ETPs. Here, we discuss the biosynthetic progress and summarize them as two comprehensible metabolic principles for better understanding the complex pathways of α, α'- and α, ß'-disulfide bridged ETPs. Specifically, we systematically outline the catalytic machineries to install α, α'- and α, ß'-disulfide by flavin-containing oxygenases. This concept would contribute to the medical and industrial applications of ETPs.

Synthesis of C-N bonds by nicotinamide-dependent oxidoreductase: an overview.

Compounds containing chiral C-N bonds play a vital role in the composition of biologically active natural products and small pharmaceutical molecules. Therefore, the development of efficient and convenient methods for synthesizing compounds containing chiral C-N bonds is a crucial area of research. Nicotinamide-dependent oxidoreductases (NDOs) emerge as promising biocatalysts for asymmetric synthesis of chiral C-N bonds due to their mild reaction conditions, exceptional stereoselectivity, high atom economy, and environmentally friendly nature. This review aims to present the structural characteristics and catalytic mechanisms of various NDOs, including imine reductases/ketimine reductases, reductive aminases, EneIRED, and amino acid dehydrogenases. Additionally, the review highlights protein engineering strategies employed to modify the stereoselectivity, substrate specificity, and cofactor preference of NDOs. Furthermore, the applications of NDOs in synthesizing essential medicinal chemicals, such as noncanonical amino acids and chiral amine compounds, are extensively examined. Finally, the review outlines future perspectives by addressing challenges and discussing the potential of utilizing NDOs to establish efficient biosynthesis platforms for C-N bond synthesis. In conclusion, NDOs provide an economical, efficient, and environmentally friendly toolbox for asymmetric synthesis of C-N bonds, thus contributing significantly to the field of pharmaceutical chemical development.

Recent research progresses of Sn/Bi/In-based electrocatalysts for electroreduction CO2 to formate.

Carbon dioxide electroreduction reaction (CO2RR) can take full advantage of sustainable power to reduce the continuously increasing carbon emissions. Recycling CO2 to produce formic acid or formate is a technologically and economically viable route to accomplish CO2 cyclic utilization. Developing efficient and cost-effective electrocatalysts with high selectivity towards formate is prioritized for the industrialized applications of CO2RR electrolysis. From the previous explored CO2RR catalysts, Sn, Bi and In based materials have drawn increasing attentions due to the high selectivity towards formate. However, there are still confronted with several challenges for the practical applications of these materials. Therefore, a rational design of the catalysts for formate is urgently needed for the target of industrialized applications. Herein, we comprehensively summarized the recent development in the advanced electrocatalysts for the CO2RR to formate. Firstly, the reaction mechanism of CO2RR is introduced. Then the preparation and design strategies of the highly active electrocatalysts are presented. Especially the innovative design mechanism in engineering materials for promoting catalytic performance, and the efforts on mechanistic exploration using in situ (ex situ) characterization techniques are reviewed. Subsequently, some perspectives and expectations are proposed about current challenges and future potentials in CO2RR research.