Pseudomonas aeruginosa 4-amino-4-deoxychorismate lyase: spatial conservation of an active site tyrosine and classification of two types of enzyme

Decoding transaminase motifs: Tracing the unknown patterns for enhancing the accuracy of computational screening methodologies

Transaminases, enzymes known for their amino group transfer capabilities, encompass four distinct subfamilies: D-alanine transaminase (DATA), L-selective Branched chain aminotransferase (BCAT), and 4-amino-4-deoxychorismate lyase (ADCL) and R-selective aminotransferase (RATA). RATA enzymes are particularly valuable in biocatalysis for synthesizing chiral amines and resolving racemic mixtures, yet their identification in sequence databases is challenging due to the lack of robust motif-based screening methods. Constructing a sequence dataset of transaminases, and categorizing them to various subfamilies, the conserved motifs are screened over the experimentally known ones, and the novel motifs are explored. Phylogenetic clustering of these subfamilies and structural localization of the identified motifs on the Alphafold-predicted protein models of the representative sequences validate their functional importance. For the ADCL, BCAT, DATA, and RATA datasets, we identified 5, 7, 10, and 2 novel motifs, with 3, 5, 7, and 2 motifs localized on secondary structures, confirming their structural importance. Furthermore, the analysis revealed 1, 3, 2, and 1 unique residue patterns of 293-KxxxR-297; 336-KxxxxY-341, 379-ExxxxNxF-386, and 453-ExFxxGT-459; 187-HxxRL-191, and 284-DxRWxxCDIK-293; and 191-HxxRL-195, integrating of which in the known computational tools would improve their accuracy. The conserved residue pattern or motif-based computational approach for robustly screening the transaminases holds promise for unveiling the novel RATA enzymes, facilitating their exploitation in biocatalytic applications.

Catalytic Mechanism of Pyridoxal 5'-Phosphate-Dependent Aminodeoxychorismate Lyase: A Computational QM/MM Study

Aminodeoxychorismate lyase (ADCL) is a kind of pyridoxal-5'-phosphate (PLP)-dependent enzyme that catalyzes the conversion of 4-amino-4-deoxychorismate (ADC) to p-aminobenzoate (PABA), which is a key step for the biosynthesis of folate. To illuminate the reaction details at the atomistic level, an enzyme-substrate reactant model has been constructed, and QM/MM calculations have been performed. Our calculation results reveal that the overall catalytic cycle contains 11 elementary steps, which can be described by three stages, including the transamination reaction of PLP, the release of pyruvate and aromatization of ADC, and the recovery to the initial aldimine. During the reaction, a series of intramolecular proton transfer are involved, which are the key for the C-N bond formation and cleavage as well as the aromatization of the ADC ring. In addition to forming the Schiff base with the pocket residue Lys251 and substrate in the internal aldimine and the external aldimine, respectively, the coenzyme PLP also plays a critical role in the intramolecular proton transfer by employing its hydroxyl oxygen anion and phosphate group. These findings may provide useful information for further understanding the catalytic mechanism of other PLP-dependent enzymes.

Metabolic bifunctionality of Rv0812 couples folate and peptidoglycan biosynthesis in Mycobacterium tuberculosis

Comparative sequence analysis has enabled the annotation of millions of genes from organisms across the evolutionary tree. However, this approach has inherently biased the annotation of phylogenetically ubiquitous, rather than species-specific, functions. The ecologically unusual pathogen Mycobacterium tuberculosis (Mtb) has evolved in humans as its sole reservoir and emerged as the leading bacterial cause of death worldwide. However, the physiological factors that define Mtb’s pathogenicity are poorly understood. Here, we report the structure and function of a protein that is required for optimal in vitro fitness and bears homology to two distinct enzymes, Rv0812. Despite diversification of related orthologues into biochemically distinct enzyme families, rv0812 encodes a single active site with aminodeoxychorismate lyase and D–amino acid transaminase activities. The mutual exclusivity of substrate occupancy in this active site mediates coupling between nucleic acid and cell wall biosynthesis, prioritizing PABA over D-Ala/D-Glu biosynthesis. This bifunctionality reveals a novel, enzymatically encoded fail-safe mechanism that may help Mtb and other bacteria couple replication and division.

Strategic Moves of "Superbugs" Against Available Chemical Scaffolds: Signaling, Regulation, and Challenges

Superbugs' resistivity against available natural products has become an alarming global threat, causing a rapid deterioration in public health and claiming tens of thousands of lives yearly. Although the rapid discovery of small molecules from plant and microbial origin with enhanced bioactivity has provided us with some hope, a rapid hike in the resistivity of superbugs has proven to be the biggest therapeutic hurdle of all times. Moreover, several distinct mechanisms endowed by these notorious superbugs make them immune to these antibiotics subsequently causing our antibiotic wardrobe to be obsolete. In this unfortunate situation, though the time frame for discovering novel "hit molecules" down the line remains largely unknown, our small hope and untiring efforts injected in hunting novel chemical scaffolds with unique molecular targets using high-throughput technologies may safeguard us against these life-threatening challenges to some extent. Amid this crisis, the current comprehensive review highlights the present status of knowledge, our search for bacteria Achilles' heel, distinct molecular signaling that an opportunistic pathogen bestows to trespass the toxicity of antibiotics, and facile strategies and appealing therapeutic targets of novel drugs. Herein, we also discuss multidimensional strategies to combat antimicrobial resistance.

The ω-transaminase engineering database (oTAED): A navigation tool in protein sequence and structure space

The ω-Transaminase Engineering Database (oTAED) was established as a publicly accessible resource on sequences and structures of the biotechnologically relevant ω-transaminases (ω-TAs) from Fold types I and IV. The oTAED integrates sequence and structure data, provides a classification based on fold type and sequence similarity, and applies a standard numbering scheme to identify equivalent positions in homologous proteins. The oTAED includes 67 210 proteins (114 655 sequences) which are divided into 169 homologous families based on global sequence similarity. The 44 and 39 highly conserved positions which were identified in Fold type I and IV, respectively, include the known catalytic residues and a large fraction of glycines and prolines in loop regions, which might have a role in protein folding and stability. However, for most of the conserved positions the function is still unknown. Literature information on positions that mediate substrate specificity and stereoselectivity was systematically examined. The standard numbering schemes revealed that many positions which have been described in different enzymes are structurally equivalent. For some positions, multiple functional roles have been suggested based on experimental data in different enzymes. The proposed standard numbering schemes for Fold type I and IV ω-TAs assist with analysis of literature data, facilitate annotation of ω-TAs, support prediction of promising mutation sites, and enable navigation in ω-TA sequence space. Thus, it is a useful tool for enzyme engineering and the selection of novel ω-TA candidates with desired biochemical properties.

Discovery and structural characterisation of new fold type IV-transaminases exemplify the diversity of this enzyme fold

Transaminases are useful biocatalysts for the production of amino acids and chiral amines as intermediates for a broad range of drugs and fine chemicals. Here, we describe the discovery and characterisation of new transaminases from microorganisms which were enriched in selective media containing (R)-amines as sole nitrogen source. While most of the candidate proteins were clearly assigned to known subgroups of the fold IV family of PLP-dependent enzymes by sequence analysis and characterisation of their substrate specificity, some of them did not fit to any of these groups. The structure of one of these enzymes from Curtobacterium pusillum, which can convert d-amino acids and various (R)-amines with high enantioselectivity, was solved at a resolution of 2.4 Å. It shows significant differences especially in the active site compared to other transaminases of the fold IV family and thus indicates the existence of a new subgroup within this family. Although the discovered transaminases were not able to convert ketones in a reasonable time frame, overall, the enrichment-based approach was successful, as we identified two amine transaminases, which convert (R)-amines with high enantioselectivity, and can be used for a kinetic resolution of 1-phenylethylamine and analogues to obtain the (S)-amines with e.e.s >99%.

Completing the folate biosynthesis pathway in Plasmodium falciparum: p-aminobenzoate is produced by a highly divergent promiscuous aminodeoxychorismate lyase

We identified the aminodeoxychorismate lyase from Plasmodium falciparum. This enzyme participates in the biosynthesis of folate and could be a new target for antimalarial therapy. The enzyme has little similarity to its bacterial counterparts and shows a minor D-amino acid transaminase activity.

Structure and catalytic mechanism of yeast 4-amino-4-deoxychorismate lyase

Saccharomyces cerevisiae Abz2 is a pyridoxal 5'-phosphate (PLP)-dependent lyase that converts 4-amino-4-deoxychorismate (ADC) to para-aminobenzoate and pyruvate. To investigate the catalytic mechanism, we determined the 1.9 Å resolution crystal structure of Abz2 complexed with PLP, representing the first eukaryotic ADC lyase structure. Unlike Escherichia coli ADC lyase, whose dimerization is critical to the formation of the active site, the overall structure of Abz2 displays as a monomer of two domains. At the interdomain cleft, a molecule of cofactor PLP forms a Schiff base with residue Lys-251. Computational simulations defined a basic clamp to orientate the substrate ADC in a proper pose, which was validated by site-directed mutageneses combined with enzymatic activity assays. Altogether, we propose a putative catalytic mechanism of a unique class of monomeric ADC lyases led by yeast Abz2.

The AEROPATH project targeting Pseudomonas aeruginosa: crystallographic studies for assessment of potential targets in early-stage drug discovery

Bacterial infections are increasingly difficult to treat owing to the spread of antibiotic resistance. A major concern is Gram-negative bacteria, for which the discovery of new antimicrobial drugs has been particularly scarce. In an effort to accelerate early steps in drug discovery, the EU-funded AEROPATH project aims to identify novel targets in the opportunistic pathogen Pseudomonas aeruginosa by applying a multidisciplinary approach encompassing target validation, structural characterization, assay development and hit identification from small-molecule libraries. Here, the strategies used for target selection are described and progress in protein production and structure analysis is reported. Of the 102 selected targets, 84 could be produced in soluble form and the de novo structures of 39 proteins have been determined. The crystal structures of eight of these targets, ranging from hypothetical unknown proteins to metabolic enzymes from different functional classes (PA1645, PA1648, PA2169, PA3770, PA4098, PA4485, PA4992 and PA5259), are reported here. The structural information is expected to provide a firm basis for the improvement of hit compounds identified from fragment-based and high-throughput screening campaigns.