Model For Substrate Binding Research Articles

Discovery of a polyurethane-degrading enzyme from the gut bacterium of plastic-eating mealworms

Although numerous polyurethane (PU)-degrading enzymes were identified from a diverse array of microorganisms in soil or compost, it is intriguing to investigate whether novel PU-degrading enzymes can be discovered in other biological environments. This study reports the discovery of an enzyme (MTL) for PU plastic degradation from the bacterial strain Mixta tenebrionis BIT-26, isolated from the gut of plastic-eating mealworms. MTL shows significant degradation activity towards three commercial PU substrates, including Impranil®DLN-SD, thermoplastic films (PEGA-HDI), and thermoset foams (PEGA-TDI), by cleaving the ester bonds in the polyester polyol moieties. The structure, molecular docking, and site-directed mutagenesis analyses elucidate the substrate binding model. A combination of structure-based comparison and mutational studies reveals the underlying architecture of the enzyme's specificity. These findings provide a fresh perspective into understanding plastic metabolism in the gut of plastic-eating insects and a prospective path for developing a biodegradation technique for plastic waste disposal.

Target-locked: A mechanism for disaggregase binding to aggregated proteins

ClpG is a novel autonomous disaggregase found in Pseudomonas aeruginosa that confers resistance to lethal heat stress. The mechanism by which ClpG specifically targets protein aggregates for disaggregation is unknown. In their recent work published in JBC, Katikaridis etal. (2023) identify an avidity-based mechanism by which four or more ClpG subunits, through specific N-terminal hydrophobic residues located on an exposed β-sheet loop, interact with multiple hydrophobic patches on an aggregated protein substrate. This study establishes a model for substrate binding to a prokaryotic disaggregase that should inform further investigations into other autonomous disaggregases.

Enhancing biocatalytical N[sbnd]N bond formation with the actinobacterial piperazate synthase KtzT

Natural compounds with nitrogen-nitrogen bonds are diverse and have applications in medicine and agriculture. l-Piperazic acid (Piz), an α-hydrazino acid, is one of few naturally occurring compounds of its kind. Yet, Piz and its derivatives are valuable building blocks for bioactive compounds. Few NNzymes, enzymes capable of forming NN bonds, have been identified thus far. The hemoenzyme KtzT from Kutzneria sp. 744 catalyzes the intramolecular NN bond formation of N5‑hydroxy-l-ornithine (OH-Orn) to form Piz, a natural building block of kutznerides. The latter has antifungal and antibiotic properties. In our study, we established an improved expression method, with significantly improved yields (ca. 35-fold) of heme-loaded enzyme, making the enzyme much more accessible for laboratory studies. In vitro biochemical characterization under conditions for NN bond formation indicated a considerable thermo- and pH-flexibility, with optimal reaction conditions at 30 °C and 10 mM Tris buffer at pH 9 together with low salinity, paving the way for more complex applications involving KtzT. We have also identified two homologous enzymes from extremophilic organisms to exhibit piperazate-forming activity. In silico structural studies, combined with phylogenetic analysis, resulted in a heme- and substrate-binding model, suggesting target enzyme residues that we propose are critical for the structural integrity and catalytic activity of KtzT. Following this approach, we investigated the potential role of a cysteine residue in a dimer-stabilizing disulfide bridge. The interplay of in vitro and in silico data therefore provides crucial functional information on this enzyme class.

Validation of a metabolite-GWAS network for Populus trichocarpa family 1 UDP-glycosyltransferases.

Metabolite genome-wide association studies (mGWASs) are increasingly used to discover the genetic basis of target phenotypes in plants such as Populus trichocarpa, a biofuel feedstock and model woody plant species. Despite their growing importance in plant genetics and metabolomics, few mGWASs are experimentally validated. Here, we present a functional genomics workflow for validating mGWAS-predicted enzyme-substrate relationships. We focus on uridine diphosphate-glycosyltransferases (UGTs), a large family of enzymes that catalyze sugar transfer to a variety of plant secondary metabolites involved in defense, signaling, and lignification. Glycosylation influences physiological roles, localization within cells and tissues, and metabolic fates of these metabolites. UGTs have substantially expanded in P. trichocarpa, presenting a challenge for large-scale characterization. Using a high-throughput assay, we produced substrate acceptance profiles for 40 previously uncharacterized candidate enzymes. Assays confirmed 10 of 13 leaf mGWAS associations, and a focused metabolite screen demonstrated varying levels of substrate specificity among UGTs. A substrate binding model case study of UGT-23 rationalized observed enzyme activities and mGWAS associations, including glycosylation of trichocarpinene to produce trichocarpin, a major higher-order salicylate in P. trichocarpa. We identified UGTs putatively involved in lignan, flavonoid, salicylate, and phytohormone metabolism, with potential implications for cell wall biosynthesis, nitrogen uptake, and biotic and abiotic stress response that determine sustainable biomass crop production. Our results provide new support for in silico analyses and evidence-based guidance for in vivo functional characterization.

Engineered P450 Atom-Transfer Radical Cyclases are Bifunctional Biocatalysts: Reaction Mechanism and Origin of Enantioselectivity.

New-to-nature radical biocatalysis has recently emerged as a powerful strategy to tame fleeting open-shell intermediates for stereoselective transformations. In 2021, we introduced a novel metalloredox biocatalysis strategy that leverages the innate redox properties of the heme cofactor of P450 enzymes, furnishing new-to-nature atom-transfer radical cyclases (ATRCases) with excellent activity and stereoselectivity. Herein, we report a combined computational and experimental study to shed light on the mechanism and origins of enantioselectivity for this system. Molecular dynamics and quantum mechanics/molecular mechanics (QM/MM) calculations revealed an unexpected role of the key beneficial mutation I263Q. The glutamine residue serves as an essential hydrogen bond donor that engages with the carbonyl moiety of the substrate to promote bromine atom abstraction and enhance the enantioselectivity of radical cyclization. Therefore, the evolved ATRCase is a bifunctional biocatalyst, wherein the heme cofactor enables atom-transfer radical biocatalysis, while the hydrogen bond donor residue further enhances the activity and enantioselectivity. Unlike many enzymatic stereocontrol rationales based on a rigid substrate binding model, our computations demonstrate a high degree of rotational flexibility of the allyl moiety in an enzyme-substrate complex and succeeding intermediates. Therefore, the enantioselectivity is controlled by the radical cyclization transition states rather than the substrate orientation in ground-state complexes in the preceding steps. During radical cyclization, anchoring effects of the Q263 residue and steric interactions with the heme cofactor concurrently control the π-facial selectivity, allowing for highly enantioselective C-C bond formation. Our computational findings are corroborated by experiments with ATRCase mutants generated from site-directed mutagenesis.

In Silico Study on Predicting Effects of H243L Mutation in<i> Bacillus subtilis</i> Levansucrase towards Sucrose Binding Affinity

Levan is a branched polysaccharide made from fructose monomers linked by β (2-6) and β (2-1) glycosidic bonds. Levan biosynthesis is catalyzed with levansucrase (EC 2.4.1.10) using sucrose as its substrate. In the present study, we are interested in investigating the elongation capability of the polymerase domain of the enzyme. The other study on Bacillus subtilis levansucrase found that the mutation of His243 into Leu has successfully prolonged the elongation of the polymer. The study, however, has not clearly accounted for the effect of the mutation. The current study aimed to employ in silico method to reveal the effect of the mutation. The initial model of substrate binding on the wild-type and H243L mutant levansucrase was prepared by molecular docking. The stability of the substrate-binding was evaluated by molecular dynamics simulation, while the binding affinity was calculated by the MM-PBSA method. The result showed that the H243L mutant was more stable in binding the substrate than the wild type. This was supported by the calculated binding affinity for H243L mutant and wild-type, which were −2.9 and +4,8 kcal/mol, respectively. Further molecular analysis suggested that mutation of His243 into Leu made the nearby Glu340 and Arg246 form additional hydrogen bonds with the substrate.

Significance of dimeric surfactant on kinetic study of organophosphorus compounds

AbstractDimeric surfactants have shown significant role on hydrolysis of organo‐phosphorus compounds. In this study, we have studied the kinetic hydrolysis of p‐nitrophenyl acetate (PNPA), p‐nitrophenyl benzoate (PNPB), and p‐dinitrophenyl diphenyl phosphate (PNPDPP) in presence of novel dimeric surfactants 12‐4‐12, 2Br– (butanediyl‐1,4‐bis(dimethyldodecylammonium bromide), 12–4(OH)‐12, 2Br– (2‐butanol‐1,4‐bis(dimethyldodecylammonium bromide) with conventional nucleophiles, benzohydroxamic acid (BHA), and salicylhydroxamic acid (SHA) by spectrophotometry at 27°C. Kinetic study on effect of micelles on reaction rates have been investigated and rationalization effects of micelles determination using kinetic model. The experimental kinetic data were fitted with micellar pseudophase model for determination micellar substrate binding and parameters. The second order rate constant is processed for comparing the reactivities in aqueous and micellar pseudophase.

Structural and biochemical insights into the substrate-binding mechanism of a glycoside hydrolase family 12 β-1,3-1,4-glucanase from Chaetomium sp.

β-1,3-1,4-Glucanases are a type of hydrolytic enzymes capable of catalyzing the strict cleavage of β-1,4 glycosidic bonds adjacent to β-1,3 linkages in β-D-glucans and have exhibited great potential in food and feed industrials. In this study, a novel glycoside hydrolase (GH) family 12 β-1,3-1,4-glucanase (CtGlu12A) from the thermophilic fungus Chaetomium sp. CQ31 was identified and biochemically characterized. CtGlu12A was most active at pH 7.5 and 65 °C, respectively, and exhibited a high specific activity of 999.9 U mg−1 towards lichenin. It maintained more than 80% of its initial activity in a wide pH range of 5.0–11.0, and up to 60 °C after incubation at 55 °C for 60 min. Moreover, the crystal structures of CtGlu12A with gentiobiose and tetrasccharide were resolved. CtGlu12A had a β-jellyroll fold, and performed retaining mechanism with two glutamic acids severing as the catalytic residues. In the complex structure, cellobiose molecule showed two binding modes, occupying subsites −2 to −1 and subsites + 1 to + 2, respectively. The concave cleft made mixed β-1,3-1,4-glucan substrates maintain a bent conformation to fit into the active site. Overall, this study is not only helpful for the understanding of the substrate-binding model and catalytic mechanism of GH 12 β-1,3-1,4-glucanases, but also provides a basis for further enzymatic engineering of β-1,3-1,4-glucanases.

Discovery of Novel Bacterial Chalcone Isomerases by a Sequence-Structure-Function-Evolution Strategy for Enzymatic Synthesis of (S)-Flavanones.

Chalcone isomerase (CHI) is a key enzyme in the biosynthesis of flavonoids in plants. The first bacterial CHI (CHIera) was identified from Eubacterium ramulus, but its distribution, evolutionary source, substrate scope, and stereoselectivity are still unclear. Here, we describe the identification of 66 novel bacterial CHIs from Genbank using a novel Sequence‐Structure‐Function‐Evolution (SSFE) strategy. These novel bacterial CHIs show diversity in substrate specificity towards various hydroxylated and methoxylated chalcones. The mutagenesis of CHIera according to the substrate binding models of these novel bacterial CHIs resulted in several variants with greatly improved activity towards these chalcones. Furthermore, the preparative scale conversion catalyzed by bacterial CHIs has been performed for five chalcones and revealed (S)‐selectivity with up to 96 % ee, which provides an alternative biocatalytic route for the synthesis of (S)‐flavanones in high yields.

Structural Flexibility of Peripheral Loops and Extended C-terminal Domain of Short Length Substrate Binding Protein from Rhodothermus marinus.

Substrate binding proteins (SBPs) bind to specific ligands in the periplasmic regions of cells and then bind to membrane proteins to participate in transport or signal transduction. Typically, SBPs consist of two α/β domains and recognize the substrate by a flexible hinge region between the two domains. Conversely, the short-length SBPs are often observed in protein databases, which are located around methyl-accepting chemotaxis protein genes. We previously determined the crystal structure of Rhodothermus marinus SBP (named as RmSBP), consisting of a single α/β domain; however, the substrate recognition mechanism is still unclear. To better understand the functions of short length RmSBP, we performed a comprehensive study, involving comparative structure analysis, computational substrate docking, and X-ray crystallographic data. RmSBP shares a high level of similarity in the α/β domain region with other SBPs, but it has a distinct topology in the C-terminal domain. The substrate binding model suggested that conformational changes in the peripheral region of RmSBP was required to recognize the substrate. We determined the crystal structures of RmSBP at pH 5.5, 6.0, and 7.5. RmSBP showed structural flexibility in the β1–α2 loop, β5–β6 loop, and extended C-terminal domains, based on the electron density map and temperature B-factor analysis. These results provide information that will further our understanding on the functions of the short length SBP.Supplementary InformationThe online version contains supplementary material available at 10.1007/s10930-021-09970-z.

A substrate binding model for the KEOPS tRNA modifying complex

The KEOPS complex, which is conserved across archaea and eukaryotes, is composed of four core subunits; Pcc1, Kae1, Bud32 and Cgi121. KEOPS is crucial for the fitness of all organisms examined. In humans, pathogenic mutations in KEOPS genes lead to Galloway–Mowat syndrome, an autosomal-recessive disease causing childhood lethality. Kae1 catalyzes the universal and essential tRNA modification N6-threonylcarbamoyl adenosine, but the precise roles of all other KEOPS subunits remain an enigma. Here we show using structure-guided studies that Cgi121 recruits tRNA to KEOPS by binding to its 3’ CCA tail. A composite model of KEOPS bound to tRNA reveals that all KEOPS subunits form an extended tRNA-binding surface that we have validated in vitro and in vivo to mediate the interaction with the tRNA substrate and its modification. These findings provide a framework for understanding the inner workings of KEOPS and delineate why all KEOPS subunits are essential.

Mathematical Modeling of In Vitro‐In Vivo Atypical Kinetics of Diazepam

Cytochrome P450 (CYP) and uridine 5'‐diphospho‐glucuronosyltransferase (UGT) enzymes are responsible for metabolism of most marketed drugs. Due to the large binding sites of certain CYPs and UGTs, CYP and UGT substrates tend to show non ‐ Michaelis‐Menten kinetics (atypical kinetics). Although several in vitro data provide evidence for the existence of atypical kinetics, this characteristic is seldom observed with in vivo data. The purpose of this project is to characterize the atypical kinetics of diazepam and its sequential metabolism in in vitro and in vivo systems. Numerical methods will be used to obtain kinetic parameters, which will be used for in vitro‐in vivo correlations (IVIVC).Diazepam, which exhibits atypical kinetics in vitro, and its primary metabolites (temazepam, nordiazepam), and secondary metabolite (oxazepam) were characterized with in vitro studies with pooled male Sprague Dawley rat liver microsome (MRLM), pooled female Sprague Dawley (FRLM), and purified rat cyp isoforms (cyp3a1, cyp3a2, and cyp2c11) separately. Rat microsomal partition and rat plasma protein binding assays were conducted via equilibrium dialysis to determine the free fraction of the drug. Two substrate binding (ESS) models provided better fits than one substrate (ES) models, as determined from the resulting AICc values. Preliminary in vitro data from MRLM and cyp3a1 showed obvious sigmoidal saturation curves for temazepam formation. Only cyp3a1 show significant sigmoidal curves for nordiazepam formation. For cyp3a1, Km and Vmax values for temazepam and nordiazepam calculated with the EES model are significantly different from those with the ES model. The intrinsic clearance (CLint) values calculated from the MRLM and cyp3a1 ESS models is not constant within the observed range of diazepam plasma levels of rats. No obvious sigmoidicity of diazepam saturation curves was observed for cyp3a2 (male‐specific) and cyp2c11 (male‐specific) isoforms, which are other cyp isoforms responsible for diazepam metabolism in male rats. In order to characterize in vitro‐in vivo correlations for diazepam, in vivo PK studies with female and male rats are currently underway.Support or Funding InformationThis research was supported by NIGMS grants: R01GM114369 and R01GM104178.

β-glucosidase from Hevea brasiliensis seeds: Purification, homology modeling, and insights into the substrate-binding model.

The isolation of β-glucosidase from Hevea brasiliensis (Hbglu) seeds was investigated and a homology model was built on the MODELLER software to understand the structure feature. The quality of the model was evaluated on PROCHEK. The refined model was used for molecular docking on AutoDock 4.2 to determine the substrate- binding sites and potential substrates based on their calculated binding affinities. The substrate specificity of Hbglu was verified through the kinetic measurement of hydrolytic activities. Molecular dynamic simulations of cyanogenic β-glucosidase and ligand-bound complex showed that the free energy (ΔG) for the binding of p-nitrophenyl-β-D-glucopyranoside and daidzein-7-O-β-D-glucoside were -8.6 and -7.92kcal/mol, respectively. Thus, daidzein-7-O-β-D-glucoside is a potential substrate. Future studies on the physicochemical properties and catalytic mechanisms will provide information on the molecular biological properties of Hbglu. PRACTICAL APPLICATIONS: This study reported the 3D structural simulation of β-glucosidase from Hbglu. The docking condition between Hbglu and various different substrates were assessed on Autodock. The results can be used as reference in designing enzymes, and improving the utilization of β-glucosidases for the hydrolysis of flavor precursors from fruits, teas, and wines and for the production of flavonoid compounds and cyanogenic glycoside degradation.

Mobility of Lewis acids within the secondary coordination sphere: toward a model for cooperative substrate binding.

Distance dependence of appended Lewis acids in N2H4 binding and deprotonation was evaluated within a series of zinc complexes. Variation of spacer-length to a tethered trialkylborane Lewis acid revealed distinct preferences for binding and stabilization of the resulting deprotonated N2H3- unit.

Mechanism of 6-Hydroxynicotinate 3-Monooxygenase, a Flavin-Dependent Decarboxylative Hydroxylase Involved in Bacterial Nicotinic Acid Degradation.

6-Hydroxynicotinate 3-monooxygenase (NicC) is a Group A FAD-dependent monooxygenase that catalyzes the decarboxylative hydroxylation of 6-hydroxynicotinic acid (6-HNA) to 2,5-dihydroxypyridine (2,5-DHP) with concomitant oxidation of NADH in nicotinic acid degradation by aerobic bacteria. Two mechanisms for the decarboxylative hydroxylation half-reaction have been proposed [Hicks, K., et al. (2016) Biochemistry 55, 3432-3446]. Results with Bordetella bronchiseptica RB50 NicC here show that a homocyclic analogue of 6-HNA, 4-hydroxybenzoic acid (4-HBA), is decarboxylated and hydroxylated by NicC with a 420-fold lower catalytic efficiency than is 6-HNA. The 13( V/ K), measured with wild-type NicC by isotope ratio mass spectrometry following the natural abundance of 13C in the CO2 product, is inverse for both 6-HNA (0.9989 ± 0.0002) and 4-HBA (0.9942 ± 0.0004) and becomes negligible (0.9999 ± 0.0004) for 5-chloro-6-HNA, an analogue that is 10-fold more catalytically efficient than 6-HNA. Covalently bound 6-HNA complexes of NicC are not observed by mass spectrometry. Comparative steady-state kinetic and Kd6HNA analyses of active site NicC variants (C202A, H211A, H302A, H47E, Y215F, and Y225F) identify Tyr215 and His47 as critical determinants both of 6-HNA binding ( KdY215F/ KdWT > 240; KdH47E/ KdWT > 350) and in coupling rates of 2,5-DHP and NAD+ product formation ([2,5-DHP]/[NAD+] = 1.00 (WT), 0.005 (Y215F), and 0.07 (H47E)]. Results of these functional analyses are in accord with an electrophilic aromatic substitution reaction mechanism in which His47-Tyr215 may serve as the general base to catalyze substrate hydroxylation and refine the structural model for substrate binding by NicC.

A multi-axial RNA joint with a large range of motion promotes sampling of an active ribozyme conformation.

Investigating the dynamics of structural elements in functional RNAs is important to better understand their mechanism and for engineering RNAs with novel functions. Previously, we performed rational engineering studies with the Varkud satellite (VS) ribozyme and switched its specificity toward non-natural hairpin substrates through modification of a critical kissing-loop interaction (KLI). We identified functional VS ribozyme variants with surrogate KLIs (ribosomal RNA L88/L22 and human immunodeficiency virus-1 TAR/TAR*), but they displayed ∼100-fold lower cleavage activity. Here, we characterized the dynamics of KLIs to correlate dynamic properties with function and improve the activity of designer ribozymes. Using temperature replica exchange molecular dynamics, we determined that the natural KLI in the VS ribozyme supports conformational sampling of its closed and active state, whereas the surrogate KLIs display more restricted motions. Based on in vitro selection, the cleavage activity of a VS ribozyme variant with the TAR/TAR* KLI could be markedly improved by partly destabilizing the KLI but increasing conformation sampling. We formulated a mechanistic model for substrate binding in which the KLI dynamics contribute to formation of the active site. Our model supports the modular nature of RNA in which subdomain structure and dynamics contribute to define the thermodynamics and kinetics relevant to RNA function.

Is Inhibitor Binding the Sole Requirement in Determining Inhibition of ABCG2 Mediated Transport?

We recently demonstrated the feasibility of ABCG2 inhibition, when coupled with a cytotoxin, as a strategy to improve acute myeloid leukemia therapy using a murine Abcg2 knockout model (1). A high throughput phenotypic screen (based upon inhibition of ABCG2 transport) with a goal of re‐purposing known therapeutic compounds, was used to identify new ABCG2 inhibitors. Among them was a kinase inhibitor (KI) that had not been previously reported to interact with ABCG2. KIs have been reported as ABCG2 inhibitors, possibly by interacting with the transporter, but also by affecting its phosphorylation state and/or subcellular localization. We systematically interrogated this new ABCG2 inhibitor and compared to known ABCG2 kinase inhibitors.Despite numerous reports of inhibition of ABCG2 by KI, it is unknown if a relationship exists between binding to ABCG2 and transport inhibition. Furthermore, it is not known if ABCG2 inhibition is strictly related to a compound's physiochemical properties (e.g., LogP) or a specific pharmacophore or the binding pocket on ABCG2. To determine if a relationship exists between KI binding to ABCG2 and transport inhibition, we employed the membrane protein cellular thermal shift assay (CETSA). CETSA is based on the principle that ligand binding induces target protein thermal stability, leading to increased temperature required for protein unfolding. This method enables the determination of in cellulo ligand binding to the native protein. The ABCG2 melting temperature (Tm) was first established from the sigmoidal thermal denaturation curve. We then used Ko143, a well known ABCG2 inhibitor, and determined that Ko143 dramatically elevated the Tm of ABCG2. We then screened over a dozen known KIs (including our newly identified KI) for their ability to inhibit the transport by ABCG2 of the specific substrate, the fluorescent dye pheophorbide a. In parallel, the EC50 of KI binding to ABCG2 was determined by CETSA. Among many of the KI, a strong relationship was observed between the EC50s for KI binding to ABCG2 and the IC50s for their transport inhibition. Future studies will determine if the binding to ABCG2 depends upon either ATPase activity or ATP‐binding. Furthermore, from these findings, and the recently published ABCG2 structure, a substrate binding model was developed. Inexplicably some KI inhibited ABCG2, but displayed either a weak or no thermal shift, indicating little or no binding to ABCG2. Because some kinases reportedly affect ABCG2 subcellular localization, we are determining if these KIs affect the plasma membrane localization of ABCG2 by using a combination of confocal microscopy and surface biotinylation.In conclusion, the CETSA assay was used, for the first time, to determine the relationship between binding and inhibition of ABCG2 transport for many ABCG2 inhibitors (represented by KIs here). This advance allows the classification of inhibitors into those that bind vs those that inhibit by a mechanism that is independent of binding to ABCG2.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Mycolyltransferase from Mycobacterium tuberculosis in covalent complex with tetrahydrolipstatin provides insights into antigen 85 catalysis

Mycobacterium tuberculosis antigen 85 (Ag85) enzymes catalyze the transfer of mycolic acid (MA) from trehalose monomycolate to produce the mycolyl arabinogalactan (mAG) or trehalose dimycolate (TDM). These lipids define the protective mycomembrane of mycobacteria. The current model of substrate binding within the active sites of Ag85s for the production of TDM is not sterically and geometrically feasible; additionally, this model does not account for the production of mAG. Furthermore, this model does not address how Ag85s limit the hydrolysis of the acyl-enzyme intermediate while catalyzing acyl transfer. To inform an updated model, we obtained an Ag85 acyl-enzyme intermediate structure that resembles the mycolated form. Here, we present a 1.45-Å X-ray crystal structure of M. tuberculosis Ag85C covalently modified by tetrahydrolipstatin (THL), an esterase inhibitor that suppresses M. tuberculosis growth and mimics structural attributes of MAs. The mode of covalent inhibition differs from that observed in the reversible inhibition of the human fatty-acid synthase by THL. Similarities between the Ag85-THL structure and previously determined Ag85C structures suggest that the enzyme undergoes structural changes upon acylation, and positioning of the peptidyl arm of THL limits hydrolysis of the acyl-enzyme adduct. Molecular dynamics simulations of the modeled mycolated-enzyme form corroborate the structural analysis. From these findings, we propose an alternative arrangement of substrates that rectifies issues with the previous model and suggest a direct role for the β-hydroxy of MA in the second half-reaction of Ag85 catalysis. This information affords the visualization of a complete mycolyltransferase catalytic cycle.

A complete structural characterization of the desferrioxamine E biosynthetic pathway from the fire blight pathogen Erwinia amylovora.

The Gram-negative bacterium Erwinia amylovora is the etiological agent of fire blight, a devastating disease which affects Rosaceae such as apple, pear and quince. The siderophore desferrioxamine E plays an important role in bacterial pathogenesis by scavenging iron from the host. DfoJ, DfoA and DfoC are the enzymes responsible for desferrioxamine production starting from lysine. We have determined the crystal structures of each enzyme in the desferrioxamine E pathway and demonstrate that the biosynthesis involves the concerted action of DfoJ, followed by DfoA and lastly DfoC. These data provide the first crystal structures of a Group II pyridoxal-dependent lysine decarboxylase, a cadaverine monooxygenase and a desferrioxamine synthetase. DfoJ is a homodimer made up of three domains. Each monomer contributes to the completion of the active site, which is positioned at the dimer interface. DfoA is the first structure of a cadaverine monooxygenase. It forms homotetramers whose subunits are built by two domains: one for FAD and one for NADP+ binding, the latter of which is formed by two subdomains. We propose a model for substrate binding and the role of residues 43-47 as gate keepers for FAD binding and the role of Arg97 in cofactors turnover. DfoC is the first structure of a desferrioxamine synthetase and the first of a multi-enzyme siderophore synthetase coupling an acyltransferase domain with a Non-Ribosomal Peptide Synthetase (NRPS)-Independent Siderophore domain (NIS).

Identification of two antiviral inhibitors targeting 3C-like serine/3C-like protease of porcine reproductive and respiratory syndrome virus and porcine epidemic diarrhea virus

Porcine reproductive and respiratory syndrome virus (PRRSV) and porcine epidemic diarrhea virus (PEDV) are highly virulent and contagious porcine pathogens that cause tremendous economic losses to the swine industry worldwide. Currently, there is no effective treatment for PRRSV and PEDV, and commercial vaccines do not induce sterilizing immunity. In this study, we screened a library of 1000 compounds and identified two specific inhibitors, designated compounds 2 and 3, which target the PRRSV 3C-like serine protease (3CLSP). First, we evaluated the inhibitory effects of compounds 2 and 3 on PRRSV 3CLSP activity. Next, we determined the anti-PRRSV capacity of compounds 2 and 3 in MARC-145 cells and obtained EC50 and CC50 values of 57μM (CC50=479.9μM) and 56.8μM (CC50=482.8μM), respectively. Importantly, compounds 2 and 3 also targeted the PEDV 3C-like protease (3CL protease) and inhibited PEDV replication, showing EC50 and CC50 values of 100μM (CC50=533.8μM) and 57.9μM (CC50=522.3μM), respectively. Finally, our results indicated that the active sites (His39 in 3CLSP and His41 in 3CL protease) were conservative, and contacted compounds 2 and 3 via hydrogen bonds and hydrophobic forces in the putative substrate-binding models. In summary, compounds 2 and 3 exhibit broad-spectrum antiviral activity and may facilitate the development of antiviral drugs against PRRSV and PEDV.