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1. Investigating the reaction and substrate preference of indole-3-acetaldehyde dehydrogenase from the plant pathogen Pseudomonas syringae Pto DC3000

   https://doi.org/10.1042/BSR20202959  

   Zhang, Kaleena; Lee, Josephine S.; Liu, Regina; Chan, Zita T.; Dawson, Trenton J.; De Togni, Elisa S.; Edwards, Chris T.; Eng, Isabel K.; Gao, Ashley R.; Goicouria, Luis A.; et al (December 2020, Bioscience Reports)

   null (Ed.)

   Abstract Aldehyde dehydrogenases (ALDHs) catalyze the conversion of various aliphatic and aromatic aldehydes into corresponding carboxylic acids. Traditionally considered as housekeeping enzymes, new biochemical roles are being identified for members of ALDH family. Recent work showed that AldA from the plant pathogen Pseudomonas syringae strain PtoDC3000 (PtoDC3000) functions as an indole-3-acetaldehyde dehydrogenase for the synthesis of indole-3-acetic acid (IAA). IAA produced by AldA allows the pathogen to suppress salicylic acid-mediated defenses in the model plant Arabidopsis thaliana. Here we present a biochemical and structural analysis of the AldA indole-3-acetaldehyde dehydrogenase from PtoDC3000. Site-directed mutants targeting the catalytic residues Cys302 and Glu267 resulted in a loss of enzymatic activity. The X-ray crystal structure of the catalytically inactive AldA C302A mutant in complex with IAA and NAD+ showed the cofactor adopting a conformation that differs from the previously reported structure of AldA. These structures suggest that NAD+ undergoes a conformational change during the AldA reaction mechanism similar to that reported for human ALDH. Site-directed mutagenesis of the IAA binding site indicates that changes in the active site surface reduces AldA activity; however, substitution of Phe169 with a tryptophan altered the substrate selectivity of the mutant to prefer octanal. The present study highlights the inherent biochemical versatility of members of the ALDH enzyme superfamily in P. syringae. 

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2. Prebiotic chiral transfer from self-aminoacylating ribozymes may favor either handedness

   https://doi.org/10.1038/s41467-024-52362-x  

   Kenchel, Josh; Vázquez-Salazar, Alberto; Wells, Reno; Brunton, Krishna; Janzen, Evan; Schultz, Kyle M; Liu, Ziwei; Li, Weiwei; Parker, Eric T; Dworkin, Jason P; et al (December 2024, Nature Communications)

   Abstract Modern life is essentially homochiral, containing D-sugars in nucleic acid backbones and L-amino acids in proteins. Since coded proteins are theorized to have developed from a prebiotic RNA World, the homochirality of L-amino acids observed in all known life presumably resulted from chiral transfer from a homochiral D-RNA World. This transfer would have been mediated by aminoacyl-RNAs defining the genetic code. Previous work on aminoacyl transfer using tRNA mimics has suggested that aminoacylation using D-RNA may be inherently biased toward reactivity with L-amino acids, implying a deterministic path from a D-RNA World to L-proteins. Using a model system of self-aminoacylating D-ribozymes and epimerizable activated amino acid analogs, we test the chiral selectivity of 15 ribozymes derived from an exhaustive search of sequence space. All of the ribozymes exhibit detectable selectivity, and a substantial fraction react preferentially to produce the D-enantiomer of the product. Furthermore, chiral preference is conserved within sequence families. These results are consistent with the transfer of chiral information from RNA to proteins but do not support an intrinsic bias of D-RNA for L-amino acids. Different aminoacylation structures result in different directions of chiral selectivity, such that L-proteins need not emerge from a D-RNA World. 

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3. Functionalized vinyldiazo compounds: New players in asymmetric catalysis

   https://doi.org/10.1016/j.checat.2023.100770  

   Bao, M; De_Angeles, L; Rada, MS; Baird, M; Arman, H; Wherritt, D; Doyle, MP (October 2023, Chem Catalysis)

   The catalytic uses of metal carbenes for addition, insertion, and cycloaddition reactions are dependent on their carbene precursor. The limited methods available for the preparation of diazo esters, which are the most common carbene precursors, restricts their ability to impart structural diversity in metal carbene reactions. Here we report a new methodology for the preparation of diverse vinyldiazoacetate esters and their effective uses in highly enantiocontrolled cyclopropanation, N-H bond insertion, O-H bond insertion, and [3+2] cycloaddition reactions. 1,2,3-Triazine 1-oxides with a sp3-C-H bond at the 5-position undergo base catalyzed Dimroth-type rearrangement to form multiply substituted oximidovinyldiazoacetates in high yields at or below room temperature, and these diverse vinyldiazo compounds undergo catalytic metal carbene transformations to produce oximidovinylcyclopropanes, α-oximidovinyl-α-amino acids and α-hydroxy acids, as well as tricyclic indole derivatives in high yields and enantioselectivities. The new access to vinyldiazo compounds has applicability to a vast array of metal carbene transformations. 

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4. A single diiron enzyme catalyses the oxidative rearrangement of tryptophan to indole nitrile

   https://doi.org/10.1038/s41557-024-01603-z  

   Adak, Sanjoy; Ye, Naike; Calderone, Logan A; Duan, Meng; Lubeck, Wilson; Schäfer, Rebecca_J B; Lukowski, April L; Houk, K N; Pandelia, Maria-Eirini; Drennan, Catherine L; et al (December 2024, Nature Chemistry)

   Abstract Nitriles are uncommon in nature and are typically constructed from oximes through the oxidative decarboxylation of amino acid substrates or from the derivatization of carboxylic acids. Here we report a third nitrile biosynthesis strategy featuring the cyanobacterial nitrile synthase AetD. During the biosynthesis of the eagle-killing neurotoxin, aetokthonotoxin, AetD transforms the 2-aminopropionate portion of 5,7-dibromo-l-tryptophan to a nitrile. Employing a combination of structural, biochemical and biophysical techniques, we characterized AetD as a non-haem diiron enzyme that belongs to the emerging haem-oxygenase-like dimetal oxidase superfamily. High-resolution crystal structures of AetD together with the identification of catalytically relevant products provide mechanistic insights into how AetD affords this unique transformation, which we propose proceeds via an aziridine intermediate. Our work presents a unique template for nitrile biogenesis and portrays a substrate binding and metallocofactor assembly mechanism that may be shared among other haem-oxygenase-like dimetal oxidase enzymes. 

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5. Imaging active site chemistry and protonation states: NMR crystallography of the tryptophan synthase α-aminoacrylate intermediate

   https://doi.org/10.1073/pnas.2109235119  

   Holmes, Jacob B.; Liu, Viktoriia; Caulkins, Bethany G.; Hilario, Eduardo; Ghosh, Rittik K.; Drago, Victoria N.; Young, Robert P.; Romero, Jennifer A.; Gill, Adam D.; Bogie, Paul M.; et al (January 2022, Proceedings of the National Academy of Sciences)

   NMR-assisted crystallography—the integrated application of solid-state NMR, X-ray crystallography, and first-principles computational chemistry—holds significant promise for mechanistic enzymology: by providing atomic-resolution characterization of stable intermediates in enzyme active sites, including hydrogen atom locations and tautomeric equilibria, NMR crystallography offers insight into both structure and chemical dynamics. Here, this integrated approach is used to characterize the tryptophan synthase α-aminoacrylate intermediate, a defining species for pyridoxal-5′-phosphate–dependent enzymes that catalyze β-elimination and replacement reactions. For this intermediate, NMR-assisted crystallography is able to identify the protonation states of the ionizable sites on the cofactor, substrate, and catalytic side chains as well as the location and orientation of crystallographic waters within the active site. Most notable is the water molecule immediately adjacent to the substrate β-carbon, which serves as a hydrogen bond donor to the ε-amino group of the acid–base catalytic residue βLys87. From this analysis, a detailed three-dimensional picture of structure and reactivity emerges, highlighting the fate of the L-serine hydroxyl leaving group and the reaction pathway back to the preceding transition state. Reaction of the α-aminoacrylate intermediate with benzimidazole, an isostere of the natural substrate indole, shows benzimidazole bound in the active site and poised for, but unable to initiate, the subsequent bond formation step. When modeled into the benzimidazole position, indole is positioned with C3 in contact with the α-aminoacrylate C β and aligned for nucleophilic attack. Here, the chemically detailed, three-dimensional structure from NMR-assisted crystallography is key to understanding why benzimidazole does not react, while indole does. 

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