Synthase Active Site Research Articles

Crystal structure and biological activity studies of two different types of herbicide safeners

Two heterocyclic compounds, imidazolidine-1,3-diylbis((5-methyl-3-phenylisoxazol-4-yl)methanone) (I) and (5-methylisoxazol-3-yl)(1-oxa-4-azaspiro[4.5]decan-4-yl)methanone (II), were characterized by X-rays. Compound I was crystallized in monoclinic system, space group Cc, a= 9.81000(12) Å, b= 15.21199(16) Å, c= 14.25369(17) Å, β= 90.3862 (12)degree, Z= 4, V= 2127.02(4) Å3, F(000) = 928.0, Dc= 1.382 Mg/m3, crystal size: 0.150 x 0.130 x 0.120 mm. Compound II was crystallized in the monoclinic system, space group P21/n, a = 5.6113(5) Å, b = 11.2280(10) Å, c = 20.675(2) Å, β = 95.543(10)degree, Z = 4, V = 1296.5(2) Å3, F(000) = 536.0, Dc = 1.282 Mg/m3, crystal size: 0.130 x 0.120 X 0.110 mm. Bioactivity assays showed that both compounds have good safety activity against nicosulfuron injury to corn, comparable to the commercial safener isoxadifen-ethyl. The molecular docking model indicated that two types of herbicide safeners competed with nicosulfuron for the acetolactate synthase active site and that this is the protective mechanism of safeners.. KEYWORDS :1,3-Disubstituted imidazolidine, Aryl-substituted formyloxazolidines, Single-crystal structure, Herbicide safener activity.

Site specific redox properties in ligand differentiated di-nickel complexes inspired by the acetyl CoA synthase active site.

Bimetallic transition metal complexes with site-specific redox properties offer a versatile platform for understanding electron polarization, intramolecular electron transfer processes, and customizing electronic and magnetic properties that might impact reactivity and catalyst design. Inspired by the dissymmetric nickel sites in the Acetyl CoA Synthase (ACS) Active Site, three new bimetallic Ni(N2S2)-Ni(S2C2R2) complexes based on Ni(N2S2) metalloligand donor synthons, Nid, in mimicry of the nickel site distal to the redox-active iron sulfur cluster of ACS, and nickel dithiolene receiver units, designated as Nip, the nickel proximal to the 4Fe4S cluster, were combined to explore the influence of ligand environment on electronic structure and redox properties of each unit. The combination of synthons gave a matrix of three S-bridged dinickel complexes, characterized by X-ray crystallography, and appropriate spectroscopies. Computational modeling is connected to the electronic characteristics of the nickel donor and receiver units. This study demonstrated the intricacies of identifying sites of electrochemical redox processes, within multi-metallic systems containing non-innocent ligands.

Insilico exploration C. koseri ATP synthase inhibitors by pharmacophore-based virtual screening, molecular docking and MD simulation.

Citrobacter koseri is a gram-negative rod that causes infections in people who have significant comorbidities and are immunocompromised. Antibiotic-resistant strains are becoming more common, which complicates infection treatment and highlights the need for innovative, effective drugs to fight these resistant strains. The enzyme complex ATP synthase participates in the adenosine triphosphate (ATP) synthesis, the fundamental energy currency of cells. This study used Computer-Aided Drug Design approaches to identify potential inhibitors of C. koseri ATP synthase. SWISS-MODEL was used to predict the 3D structure of C. koseri ATP synthase. A ligand-based pharmacophore model was developed using chemical features of ampicillin. Following ligand-based virtual screening across nine databases, the 2043 screened hits were docked to the ATP synthase active site using the standard precision mode of the glide tool. Based on their binding affinities, the top ten compounds were selected for additional investigation. The binding affinities of the chosen compounds ranged from -10.021 to -8.452 kcal/mol. The top four compounds (PubChem-25230613, PubChem-74936833, CHEMBL263035, PubChem-44208924) with the best ADMET characteristics and binding modes were chosen. Thus, the feasible binding mechanisms of the selected compounds were subjected to stability analysis using the MD Simulation study, which revealed the compounds' stability as potent inhibitors within the protein binding pocket. This computational approach provides important insights into the rational design of novel therapeutics and emphasizes the importance of targeting essential metabolic pathways when combating antibiotic-resistant pathogens. Future experimental validation and optimization of the identified inhibitors is required to determine their efficacy and safety profiles for clinical use.

Design, Synthesis, and Structure-Activity Relationship of Novel Aryl-Substituted Formyl Oxazolidine Derivatives as Herbicide Safeners.

Nicosulfuron is the leading herbicide in the global sulfonylurea (SU) herbicide market; it was jointly developed by DuPont and Ishihara. Recently, the widespread use of nicosulfuron has led to increasingly prominent agricultural production hazards, such as environmental harm and influence on subsequent crops. The use of herbicide safeners can significantly alleviate herbicide injury to protect crop plants and expand the application scope of existing herbicides. A series of novel aryl-substituted formyl oxazolidine derivatives were designed using the active group combination method. Title compounds were synthesized using an efficient one-pot method and characterized by infrared (IR) spectrometry, 1H and 13C nuclear magnetic resonance (NMR), and high-resolution mass spectrometry (HRMS). The chemical structure of compound V-25 was further identified by X-ray single crystallography. The bioactivity assay and structure-activity relationship proved that nicosulfuron phytotoxicity to maize could be reduced by most title compounds. The glutathione S-transferase (GST) activity and acetolactate synthase (ALS) in vivo were determined, and compound V-12 showed inspiring activity comparable to that of the commercial safener isoxadifen-ethyl. The molecular docking model indicated that compound V-12 competed with nicosulfuron for the acetolactate synthase active site and that this is the protective mechanism of safeners. Absorption, distribution, metabolism, excretion, and toxicity (ADMET) predictions demonstrated that compound V-12 exhibited superior pharmacokinetic properties to the commercialized safener isoxadifen-ethyl. The target compound V-12 shows strong herbicide safener activity in maize; thus, it may be a potential candidate compound that can help further protect maize from herbicide damage.

New nitazoxanide derivatives: design, synthesis, biological evaluation, and molecular docking studies as antibacterial and antimycobacterial agents.

A new series inspired by combining fragments from nitazoxanide (NTZ) and 4-aminosalicylic acid (4-ASA) was synthesized and screened for in vitro antibacterial and antimycobacterial activities. The majority showed higher antibacterial potency than NTZ against all the screened strains, notably, 5f, 5j, 5n and 5o with MICs of 0.87-9.00 μM. Compounds 5c, 5n and 5o revealed higher potency than ciprofloxacin against K. pneumoniae, while 5i was equipotent. For E. faecalis, 3b, 5j, and 5k showed higher potency than ciprofloxacin. 5j was more potent against P. aeruginosa than ciprofloxacin, while 5n was more potent against S. aureus with an MIC of 0.87 μM. 5f showed equipotency to ciprofloxacin against H. pylori with an MIC of 1.74 μM. Compounds 3a and 3b (4-azidoNTZ, MIC 4.47 μM) are 2 and 5-fold more potent against Mycobacterium tuberculosis (Mtb H37Rv) than NTZ (MIC 20.23 μM) and safer. 4-Azidation and/or acetylation of NTZ improve both activities, while introducing 1,2,3-triazoles improves the antibacterial activity. Molecular docking studies within pyruvate ferredoxin oxidoreductase (PFOR), glucosamine-6-phosphate synthase (G6PS) and dihydrofolate reductase (DHFR) active sites were performed to explore the possible molecular mechanisms of actions. Acceptable drug-likeness properties were found. This study may shed light on further rational design of substituted NTZ as broad-spectrum more potent antimicrobial candidates.

Reshaping the 2‐Pyrone Synthase Active Site for Chemoselective Biosynthesis of Polyketides

AbstractEngineering enzymes with novel reactivity and applying them in metabolic pathways to produce valuable products are quite challenging due to the intrinsic complexity of metabolic networks and the need for high in vivo catalytic efficiency. Triacetic acid lactone (TAL), naturally generated by 2‐pyrone synthase (2PS), is a platform molecule that can be produced via microbial fermentation and further converted into value‐added products. However, these conversions require extra synthetic steps under harsh conditions. We herein report a biocatalytic system for direct generation of TAL derivatives under mild conditions with controlled chemoselectivity by rationally engineering the 2PS active site and then rewiring the biocatalytic pathway in the metabolic network of E. coli to produce high‐value products, such as kavalactone precursors, with yields up to 17 mg/L culture. Computer modeling indicates sterics and hydrogen‐bond interactions play key roles in tuning the selectivity, efficiency and yield.

Reshaping the 2-Pyrone Synthase Active Site for Chemoselective Biosynthesis of Polyketides.

Engineering enzymes with novel reactivity and applying them in metabolic pathways to produce valuable products are quite challenging due to the intrinsic complexity of metabolic networks and the need for high in vivo catalytic efficiency. Triacetic acid lactone (TAL), naturally generated by 2-pyrone synthase (2PS), is a platform molecule that can be produced via microbial fermentation and further converted into value-added products. However, these conversions require extra synthetic steps under harsh conditions. We herein report a biocatalytic system for direct generation of TAL derivatives under mild conditions with controlled chemoselectivity by rationally engineering the 2PS active site and then rewiring the biocatalytic pathway in the metabolic network of E. coli to produce high-value products, such as kavalactone precursors, with yields up to 17 mg/L culture. Computer modeling indicates sterics and hydrogen-bond interactions play key roles in tuning the selectivity, efficiency and yield.

Antioxidant, Antimicrobial, and Molecular Docking Studies of Novel Chalcones and Schiff Bases Bearing 1, 4-naphthoquinone Moiety

Background: The 1,4-naphthoquinone ring has attracted prominent interest in the field of medicinal chemistry due to its potent pharmacological activities such as antioxidant, antibacterial, antifungal, and anticancer. Objective: Herein, a series of new Schiff bases (4-6) and chalcones (8a-c & 9a-d) bearing 1,4- naphthoquinone moiety were synthesized in good yields and were subjected to in-vitro antimicrobial, antioxidant, and molecular docking testing. Methods: A facile protocol has been described in this study for the synthesis of new derivatives (4-7, 8ac, and 9a-d) bearing 1,4-naphthoquinone moiety. The chemical structures of all the synthesized compounds were identified by 1H-NMR, 13C-NMR, MS, and elemental analyses. Moreover, these derivatives were assessed for their in-vitro antimicrobial activity against gram-positive, gram-negative bacteria, and fungal strains. Further studies were conducted to test their antioxidant activity using DPPH (2,2-diphenyl- 1-picrylhydrazyl) scavenging assay. Molecular docking studies were realized to identify the most likely interactions of the novel compounds within the protein receptor. Results: The antimicrobial results showed that most of the compounds displayed good efficacy against both bacterial and fungal strains. The antioxidant study revealed that compounds 9d, 9a, 9b, 8c, and 6 exhibited the highest radical scavenging activity. Docking studies of the most active antimicrobial compounds within GLN- 6-P, recorded good scores with several binding interactions with the active sites. Conclusion: Based on the obtained results, it was found that compounds 8b, 9b, and 9c displayed the highest activity against both bacterial and fungal strains. The obtained findings from the DPPH radical scavenging method revealed that compounds 9d and 9a exhibited the strongest scavenging potential. The molecular docking studies proved that the most active antimicrobial compounds 8b, 9b and 9c displayed the highest energy binding scores within the glucosamine-6-phosphate synthase (GlcN-6-P) active site.

Profile of Myracrodruon urundeuva Volatile Compounds Ease of Extraction and Biodegradability and In Silico Evaluation of Their Interactions with COX-1 and iNOS.

Myracrodruon urundeuva Fr. Allem. (Anacardiaceae) is a tree popularly known as the “aroeira-do-sertão”, native to the caatinga and cerrado biomes, with a natural dispersion ranging from the Northeast, Midwest, to Southeast Brazil. Its wood is highly valued and overexploited, due to its characteristics such as durability and resistance to decaying. The diversity of chemical constituents in aroeira seed has shown biological properties against microorganisms and helminths. As such, this work aimed to identify the profile of volatile compounds present in aroeira seeds. Headspace solid phase microextraction was employed (HS-SPME) using semi-polar polydimethylsiloxane-divinylbenzene fiber (PDMS/DVB) for the extraction of VOCs. 22 volatile organic compounds were identified: nine monoterpenes and eight sesquiterpenes, in addition to six compounds belonging to different chemical classes such as fatty acids, terpenoids, salicylates and others. Those that stood out were p-mentha-1,4, 4(8)-diene, 3-carene (found in all samples), caryophyllene and cis-geranylacetone. A virtual docking analysis suggested that around 65% of the VOCs molar content from the aroeiras seeds present moderate a strong ability to bind to cyclooxygenase I (COX-I) active site, oxide nitric synthase (iNOS) active site (iNOSas) or to iNOS cofactor site (iNOScs), corroborating an anti-inflamatory potential. A pharmacophoric descriptor analysis allowed to infer the more determinant characteristics of these compounds’ conferring affinity to each site. Taken together, our results illustrate the high applicability for the integrated use of SPME, in silico virtual screening and chemoinformatics tools at the profiling of the biotechnological and pharmaceutical potential of natural sources.

Design, Synthesis, and In Silico Molecular Docking Study of Some Novel Thiochromene Derivatives with Antimicrobial Potential

In continuation of our research work to discover novel selective antimicrobial agents, new derivatives of thiochromene derivatives 4, 7–18a,b were constructed. These novel candidates were evaluated in vitro for their antimicrobial potential toward B. subtilis and S. aureus as examples of Gram-positive bacteria, E. coli and P. aeruginosa as examples of Gram-negative bacteria, A. flavus and C. albicans as examples of fungi. The results displayed that all the screened compounds 4 and 7–18a,b recorded moderate to excellent antimicrobial activity especially compound 17 was the most active toward all the tested microbes (zone of inhibition = 23–27 mm). Concerning antifungal activity, compounds 14 and 17 displayed higher antifungal activity against C. albicans potency (zone of inhibition = 23, 20 mm, respectively) than amphotericin B (zone of inhibition = 19 mm). Molecular docking simulation study of the novel thiochromene derivatives 4, 7–18a,b within dihydropteroate synthase active site displayed good scoring with various binding interactions within the active site.

Molecular Dynamics of Electrostatic Channeling on the Surface of Malate Dehydrogenase-Citrate Synthase

Multi-enzyme catalytic cascade reactions exist in many metabolic pathways in nature; the benefits of these reactions include high efficiency and reduced time and labor costs [1].The design and application of efficient cascade reactions in biofuel cells, sensors, and chemical conversion requires an understanding of intermediate channeling between adjacent cascade active sites. Electrostatic channeling, for example, utilizes electrostatic force to control the direct transfer of charged intermediates [2]. Here, we study the electrostatic channeling of an oxaloacetate (OAA) intermediate between malate dehydrogenase (MDH) and citrate synthase (CS) active sites within the tricarboxylic acid (TCA) cycle.The MDH-CS supramolecular assembly includes a positively charged surface between neighboring active sites that guides the movement of the negatively charged oxaloacetate, thus improving the transfer efficiency [3].To study the interaction between OAA and the charged enzyme surface and identify OAA’s transfer pathways, we simulated this system using molecular dynamics (MD). Specifically, since both MDH and CS have two identical subunits and thus two active sites, we ran 50 MD simulations for 10 ns near each of the four active sites, resulting in 200 parallel runs of simulations. Then we analyzed the resulting MD dataset with a Markov State Model (MSM) [4].We identified multiple energy basins in MSM, including four active site basins, a desorption basin, and an intermediate basin. MSM successfully predicted the the transition rates between those energy basins and identified the dominant transport pathways of OAA from MDH to CS. The visualization demonstrates that the dominant transport pathway crosses Arg65, providing further support for the experimental observation that Arg65 plays an critical role in the electrostatic transport process of OAA [3].This study improves the field’s understanding of natural substrate channeling mechanisms and can help with the design of artificial cascade reactions. References K. C. Nicolaou, D. J. Edmonds, and P. G. Bulger, Angew. Chemie - Int. Ed., 45, 7134–7186 (2006). doi:10.1002/anie.200601872. I. Wheeldon, S. D. Minteer, S. Banta, S. Calabrese Barton, P. Atanassov, and M. Sigman, Nat. Chem (2016). doi:10.1038/NCHEM.2459 B. Bulutoglu, K. E. Garcia, F. Wu, S. D. Minteer, and S. Banta, ACS Chem. Biol., 11, 2847–2853 (2016). doi:10.1021/acschembio.6b00523F. Noé, C. Schütte, E. Vanden-Eijnden, L. Reich, and T. R. Weikl, Proc. Natl. Acad. Sci. U. S. A., 106, 19011–19016 (2009). doi:10.1073/pnas.0905466106 Figure 1

GC-MS analysis and molecular docking of bioactive compounds of Camellia sinensis and Camellia assamica.

The methanol extract of Camellia sinensis (MES) and acetone extract of Camellia assamica (AEA) were subjected to the thin layer chromatography to separate the bioactive compounds. The antimicrobial activity of all the fractions was carried out against pathogenic microorganisms by the agar-well diffusion method. The most effective bioactive fraction of each plant species was analysed by GC-MS. Fraction L of methanol extract of C. sinensis (MES) and fraction 5 of acetone extract of C. assamica (AEA) were found very effective against selected pathogenic strains. GC-MS analysis of this fraction showed the presence of n-heptadecanol-1 (68.63%) in MES and 2',6'dihydroxyacetophenone, bis(trimethylsilyl) (17.58%) in AEA with the highest area. The compounds n-heptadecanol-1 and 2',6'dihydroxyacetophenone, bis(trimethylsilyl) ether were used for docking to analyse its therapeutic potential. The ligand compound n-heptadecanol-1 (HEP) from MES of C. sinensis and 2',6'dihydroxyacetophenone, bis(trimethylsilyl) ether from AEA of C. assamica were docked with the target protein dihydropteoate synthase (DHPS) active sites of Escherichia coli and Staphylococcus aureus active sites via Auto Dock Vina, thereby forecasting the finest binding position of ligands. AutoDock Vina docked results revealed the involvement of binding energy for the establishment of the protein-ligand structure complex, besides generating an interpretation of all apparent molecular interactions accountable for its activity. Further, the protein-ligand complex of MES, EcDHPS + HEP and SaDHPS + HEP exhibiting the best binding affinity were - 4.8kcal/mol and - 3.6kcal/mol. The protein-ligand complex of AEA, i.e., EcDHPS + DHA and SaDHPS + DHA exhibited the best binding affinity of - 4.8kcal/mol and - 4.8kcal/mol.

Adaptation of bacteria to glyphosate: a microevolutionary perspective of the enzyme 5-enolpyruvylshikimate-3-phosphate synthase.

Glyphosate is the leading herbicide worldwide, but it also affects prokaryotes because it targets the central enzyme (5-enolpyruvylshikimate-3-phosphate, EPSP) of the shikimate pathway in the synthesis of the three essential aromatic amino acids in bacteria, fungi and plants. Our results reveal that bacteria may easily become resistant to glyphosate through changes in the 5-enolpyruvylshikimate-3-phosphate synthase active site. This indicates the importance of examining how glyphosate affects microbe-mediated ecosystem functions and human microbiomes.

Design, Synthesis, and SAR of Novel 1,3-Disubstituted Imidazolidine or Hexahydropyrimidine Derivatives as Herbicide Safeners.

Herbicide safeners enhance herbicide detoxification in crops without reducing their herbicidal efficacy against target weeds. To alleviate maize injury caused by the sulfonylurea herbicide nicosulfuron, a series of 1,3-disubstituted imidazolidine or hexahydropyrimidine derivatives were rationally designed via bioisosterism and active subunit combinations. Thirty novel compounds were synthesized using an efficient one-pot method and low-cost raw materials and characterized by IR, 1H NMR, 13C NMR, and high-resolution mass spectrometer (HRMS). Bioactivity and structure-activity relationship (SAR) were evaluated for herbicide safeners tested against nicosulfuron injury. Most of the compounds effectively protected sensitive maize against nicosulfuron damage. The parent skeletons and substituents of the target compounds both substantially influenced their safener activity. Compound I-3 exhibited superior bioactivity compared to the safener isoxadifen-ethyl. Molecular docking simulations disclosed that compound I-3 competed with nicosulfuron for the acetolactate synthase active site and demonstrated that this is the protective mechanism of safeners. The target compound I-3 presented with strong herbicide safener activity in maize and is, therefore, a potential candidate for the development of a novel herbicide safener.

Nonheme iron-thiolate complexes as structural models of sulfoxide synthase active sites.

Two mononuclear iron(ii)-thiolate complexes have been prepared that represent structural models of the nonheme iron enzymes EgtB and OvoA, which catalyze the O2-dependent formation of carbon-sulfur bonds in the biosynthesis of thiohistidine compounds. The series of Fe(ii) complexes reported here feature tripodal N4 chelates (LA and LB) that contain both pyridyl and imidazolyl donors (LA = (1H-imidazol-4-yl)-N,N-bis((pyridin-2-yl)methyl)methanamine; LB = N,N-bis((1-methylimidazol-2-yl)methyl)-2-pyridylmethylamine). Further coordination with monodentate aromatic or aliphatic thiolate ligands yielded the five-coordinate, high-spin Fe(ii) complexes [FeII(LA)(SMes)]BPh4 (1) and [FeII(LB)(SCy)]BPh4 (2), where SMes = 2,4,6-trimethylthiophenolate and SCy = cyclohexanethiolate. X-ray crystal structures revealed that 1 and 2 possess trigonal bipyramidal geometries formed by the N4S ligand set. In each case, the thiolate ligand is positioned cis to an imidazole donor, replicating the arrangement of Cys- and His-based substrates in the active site of EgtB. The geometric and electronic structures of 1 and 2 were analyzed with UV-vis absorption and Mössbauer spectroscopies in tandem with density functional theory (DFT) calculations. Exposure of 1 and 2 to nitric oxide (NO) yielded six-coordinate FeNO adducts that were characterized with infrared and electron paramagnetic resonance (EPR) spectroscopies, confirming that these complexes are capable of binding diatomic molecules. Reaction of 1 and 2 with O2 causes oxidation of the thiolate ligands to disulfide products. The implications of these results for the development of functional models of EgtB and OvoA are discussed.

Design, synthesis, anticancer evaluation and docking studies of new pyrimidine derivatives as potent thymidylate synthase inhibitors

Cancer is a perplexing and challenging problem for researchers. In this study, a series of 6-aryl-5-cyano-pyrimidine derivatives were designed, synthesized and evaluated for their anticancer activity against HePG-2, MCF-7 and HCT-116 cell lines. Compounds 2, 3d, 4a-c, 5, 8 and 12 displayed high anticancer activity, comparable to that of 5-fluorouracil. Additionally, those compounds with effective anticancer activity were further assessed for their ability to inhibit thymidylate synthase (TS) enzyme. All the tested compounds demonstrated a marked TS inhibitory activity (33.66–74.98%), with IC50 ranging from 3.89 to 15.74 nM. Moreover, apoptosis studies were conducted on the most potent compound 8, to evaluate its proapoptotic potential. Interestingly, compound 8 induced the level of active caspase 3, and elevated the Bax/Bcl2 ratio 44 folds in comparison to the control. Finally, a molecular docking study was conducted to detect the probable interaction between the active compounds and the thymidylate synthase active site.

Predicting Productive Binding Modes for Substrates and Carbocation Intermediates in Terpene Synthases-Bornyl Diphosphate Synthase as a Representative Case.

Terpene synthases comprise a family of enzymes that convert acyclic oligo-isoprenyl diphosphates to terpene natural products with complex, polycyclic carbon backbones via the generation and protection of carbocation intermediates. To accommodate this chemistry, terpene synthase active sites generally are lined with alkyl and aromatic, i.e., nonpolar, sidechains. Predicting the correct, mechanistically relevant binding modes for entire terpene synthase reaction pathways remains an unsolved challenge. Here we describe a method for identifying such modes: TerDockin, a series of protocols to predict the orientation of carbon skeletons of substrates and derived carbocations relative to the bound diphosphate group in terpene synthase active sites. Using this recipe for bornyl diphosphate synthase, we have predicted binding modes that are consistent with all current experimental observations, including the results of isotope labeling experiments and known stereoselectivity. In addition, the predicted binding modes recapitulate key findings of a seminal study involving more computationally demanding QM/MM molecular dynamics methods on part of this pathway. This work illustrates the value of the TerDockin approach as a starting point for more involved calculations and sets the stage for the rational engineering of this family of enzymes.

Cross-species complementation of bacterial- and eukaryotic-type cardiolipin synthases.

The glycerophospholipid cardiolipin is a unique constituent of bacterial and mitochondrial membranes. It is involved in forming and stabilizing high molecular mass membrane protein complexes and in maintaining membrane architecture. Absence of cardiolipin leads to reduced efficiency of the electron transport chain, decreased membrane potential, and, ultimately, impaired respiratory metabolism. For the protozoan parasite Trypanosoma brucei cardiolipin synthesis is essential for survival, indicating that the enzymes involved in cardiolipin production represent potential drug targets. T. brucei cardiolipin synthase (TbCLS) is unique as it belongs to the family of phospholipases D (PLD), harboring a prokaryotic-type cardiolipin synthase (CLS) active site domain. In contrast, most other eukaryotic CLS, including the yeast ortholog ScCrd1, are members of the CDP-alcohol phosphatidyltransferase family. To study if these mechanistically distinct CLS enzymes are able to catalyze cardiolipin production in a cell that normally expresses a different type of CLS, we expressed TbCLS and ScCrd1 in CLS-deficient yeast and trypanosome strains, respectively. Our results show that TbCLS complemented cardiolipin production in CRD1 knockout yeast and partly restored wild-type colony forming capability under stress conditions. Remarkably, CL remodeling appeared to be impaired in the transgenic construct, suggesting that CL production and remodeling are tightly coupled processes that may require a clustering of the involved proteins into specific CL-synthesizing domains. In contrast, no complementation was observed by heterologous expression of ScCrd1 in conditional TbCLS knockout trypanosomes, despite proper mitochondrial targeting of the protein.

Ligand binding at the A-cluster in full-length or truncated acetyl-CoA synthase studied by X-ray absorption spectroscopy.

Bacteria integrate CO2 reduction and acetyl coenzyme-A (CoA) synthesis in the Wood-Ljungdal pathway. The acetyl-CoA synthase (ACS) active site is a [4Fe4S]-[NiNi] complex (A-cluster). The dinickel site structure (with proximal, p, and distal, d, ions) was studied by X-ray absorption spectroscopy in ACS variants comprising all three protein domains or only the C-terminal domain with the A-cluster. Both variants showed two square-planar Ni(II) sites and an OH- bound at Ni(II)p in oxidized enzyme and a H2O at Ni(I)p in reduced enzyme; a Ni(I)p-CO species was induced by CO incubation and a Ni(II)-CH3- species with an additional water ligand by a methyl group donor. These findings render a direct effect of the N-terminal and middle domains on the A-cluster structure unlikely.

Crystal Structures Capture Three States in the Catalytic Cycle of a Pyridoxal Phosphate (PLP) Synthase

PLP synthase (PLPS) is a remarkable single-enzyme biosynthetic pathway that produces pyridoxal 5'-phosphate (PLP) from glutamine, ribose 5-phosphate, and glyceraldehyde 3-phosphate. The intact enzyme includes 12 synthase and 12 glutaminase subunits. PLP synthesis occurs in the synthase active site by a complicated mechanism involving at least two covalent intermediates at a catalytic lysine. The first intermediate forms with ribose 5-phosphate. The glutaminase subunit is a glutamine amidotransferase that hydrolyzes glutamine and channels ammonia to the synthase active site. Ammonia attack on the first covalent intermediate forms the second intermediate. Glyceraldehyde 3-phosphate reacts with the second intermediate to form PLP. To investigate the mechanism of the synthase subunit, crystal structures were obtained for three intermediate states of the Geobacillus stearothermophilus intact PLPS or its synthase subunit. The structures capture the synthase active site at three distinct steps in its complicated catalytic cycle, provide insights into the elusive mechanism, and illustrate the coordinated motions within the synthase subunit that separate the catalytic states. In the intact PLPS with a Michaelis-like intermediate in the glutaminase active site, the first covalent intermediate of the synthase is fully sequestered within the enzyme by the ordering of a generally disordered 20-residue C-terminal tail. Following addition of ammonia, the synthase active site opens and admits the Lys-149 side chain, which participates in formation of the second intermediate and PLP. Roles are identified for conserved Asp-24 in the formation of the first intermediate and for conserved Arg-147 in the conversion of the first to the second intermediate.