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Gupta N, Bhattacharya S, Urbanová K, Dutta A, Hazra AK, Fernández-Cusimamani E, Leuner O. Systematic analysis of antimicrobial activity, phytochemistry, and in silico molecular interaction of selected essential oils and their formulations from different Indian spices against foodborne bacteria. Heliyon 2023; 9:e22480. [PMID: 38107328 PMCID: PMC10724571 DOI: 10.1016/j.heliyon.2023.e22480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 12/19/2023] Open
Abstract
Essential oils (EOs) from Indian spices like Elettaria cardamomum (L.) Maton (small green cardamom), Syzygium aromaticum (L.) Merr. & L.M. Perry (clove), Cinnamomum zeylanicum Blume (cinnamon quills), and Cinnamomum tamala (Buch.-Ham.) T. Nees & C. H. Eberm (Indian bay leaves) exhibit a broad spectrum range of biological activity including antibacterial and antifungal activity. Yet, there is a lack of data regarding the antimicrobial activity of their formulations. Also, the link between the antimicrobial effect of individual EO with their chemical composition and molecular interaction with bacterial pathogens has not been systematically explored. Therefore, the objectives of the current study were to evaluate the antimicrobial activity and phytochemical characterization of EOs and to bridge the gap between them through in-silico molecular interactions. The antibacterial activity of EOs of four different spices and their formulations against foodborne pathogens such as Bacillus subtilis, Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa was evaluated using the disc volatilization method. The chemical profile of the individual EO was determined through GC-MS analysis and molecular interactions of identified major components with bacterial proteins were carried out through molecular docking studies. All EOs and their formulations exhibited antibacterial activity ranging from 5.92 to 24.55 mm and 11-23.52 mm, respectively. Among all EOs, cinnamon and formulation C (cardamom: cinnamon- 2:1) exhibited the highest antibacterial activity. The composition of the EOs included sesquiterpenes, monoterpenoids, monoterpenes, and, phenylpropanoids such as (E)-cinnamaldehyde, δ-cadinene, α-copaene, eugenol, caryophyllene, eugenol acetate, methyl eugenol, menthadiene, eucalyptol, α-terpinyl acetate, and sabinene. Furthermore, docking study revealed that the abundant compounds from cinnamon EO mainly α-copaene and δ-cadinene had a high binding affinity towards the bacterial essential proteins which increases the bacterial susceptibility towards cinnamon EO. The selected EOs and their formulations were systematically analysed and they were effective against foodborne pathogens. The current findings suggest the application of these EOs against food pathogens with further research.
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Affiliation(s)
- Neha Gupta
- Department of Crop Sciences and Agroforestry, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, Suchdol, 165 00 Prague 6, Czech Republic
| | - Soham Bhattacharya
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, Prague 6 – Suchdol, 165 00, Czech Republic
| | - Klára Urbanová
- Department of Sustainable Technologies, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Adrish Dutta
- Department of Crop Sciences and Agroforestry, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, Suchdol, 165 00 Prague 6, Czech Republic
| | | | - Eloy Fernández-Cusimamani
- Department of Crop Sciences and Agroforestry, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, Suchdol, 165 00 Prague 6, Czech Republic
| | - Olga Leuner
- Department of Crop Sciences and Agroforestry, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, Suchdol, 165 00 Prague 6, Czech Republic
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Kim S, Park BG, Jin H, Lee D, Teoh JY, Kim YJ, Lee S, Kim SJ, Moh SH, Yoo D, Choi W, Hahn JS. Efficient production of natural sunscreens shinorine, porphyra-334, and mycosporine-2-glycine in Saccharomyces cerevisiae. Metab Eng 2023; 78:137-147. [PMID: 37257683 DOI: 10.1016/j.ymben.2023.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/10/2023] [Accepted: 05/28/2023] [Indexed: 06/02/2023]
Abstract
Mycosporine-like amino acids (MAAs) are promising natural sunscreens mainly produced in marine organisms. Until now, metabolic engineering efforts to produce MAAs in heterologous hosts have mainly focused on shinorine production, and the low production levels are still not suitable for industrial applications. In this study, we successfully developed Saccharomyces cerevisiae strains that can efficiently produce various disubstituted MAAs, including shinorine, porphyra-334, and mycosporine-2-glycine (M2G), which are formed by conjugating serine, threonine, and glycine to mycosporine-glycine (MG), respectively. We first generated an MG-producing strain by multiple integration of the biosynthetic genes from cyanobacteria and applying metabolic engineering strategies to increase sedoheptulose-7-phosphate pool, a substrate for MG production. Next, five mysD genes from cyanobacteria, which encode D-Ala-D-Ala ligase homologues that conjugate an amino acid to MG, were introduced into the MG-producing strain to determine the substrate preference of each MysD enzyme. MysDs from Lyngbya sp., Nostoclinckia, and Euhalothece sp. showed high specificity toward serine, threonine, and glycine, resulting in efficient production of shinorine, porphyra-334, and M2G, respectively. This is the first report on the production of porphyra-334 and M2G in S. cerevisiae. Furthermore, we identified that the substrate specificity of MysD was determined by the omega loop region of 43-45 amino acids predicted based on its structural homology to a D-Ala-D-Ala ligase from Thermus thermophilus involved in peptidoglycan biosynthesis. The substrate specificities of two MysD enzymes were interchangeable by swapping the omega loop region. Using the engineered strain expressing mysD from Lyngbya sp. or N. linckia, up to 1.53 g/L shinorine or 1.21 g/L porphyra-334 was produced by fed-batch fermentation in a 5-L bioreactor, the highest titer reported so far. These results suggest that S. cerevisiae is a promising host for industrial production of different types of MAAs, providing a sustainable and eco-friendly alternative for the development of natural sunscreens.
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Affiliation(s)
- Sojeong Kim
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Beom Gi Park
- CutisBio Co., Ltd., 842 Nonhyeon-ro, Gangnam-gu, Seoul, 06025, Republic of Korea
| | - Hyunbin Jin
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Daeyeol Lee
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jie Ying Teoh
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Yung Jae Kim
- CutisBio Co., Ltd., 842 Nonhyeon-ro, Gangnam-gu, Seoul, 06025, Republic of Korea
| | - Sak Lee
- BioFD&C Co., Ltd., 30 Songdomirae-ro, Yeonsu-gu, Incheon, 21990, Republic of Korea
| | - Soo-Jung Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Sang Hyun Moh
- BioFD&C Co., Ltd., 30 Songdomirae-ro, Yeonsu-gu, Incheon, 21990, Republic of Korea
| | - Dongwon Yoo
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Wonwoo Choi
- CutisBio Co., Ltd., 842 Nonhyeon-ro, Gangnam-gu, Seoul, 06025, Republic of Korea
| | - Ji-Sook Hahn
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
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Paymal SB, Barale SS, Supanekar SV, Sonawane KD. Structure based virtual screening, molecular dynamic simulation to identify the oxadiazole derivatives as inhibitors of Enterococcus D-Ala-D-Ser ligase for combating vancomycin resistance. Comput Biol Med 2023; 159:106965. [PMID: 37119552 DOI: 10.1016/j.compbiomed.2023.106965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 04/03/2023] [Accepted: 04/19/2023] [Indexed: 05/01/2023]
Abstract
Vancomycin resistance in enterococci mainly arises due to alteration in terminal peptidoglycan dipeptide. A comprehensive structural analysis for substrate specificity of dipeptide modifying d-Alanine: d-Serine ligase (Ddls) is essential to screen its inhibitors for combating vancomycin resistance. In this study modeled 3D structure of EgDdls from E. gallinarum was used for structure based virtual screening (SBVS) of oxadiazole derivatives. Initially, fifteen oxadiazole derivatives were identified as inhibitors at the active site of EgDdls from PubChem database. Further, four EgDdls inhibitors were evaluated using pharmacokinetic profile and molecular docking. The results of molecular docking showed that oxadiazole inhibitors could bind preferentially at ATP binding pocket with the lowest binding energy. Further, molecular dynamics simulation results showed stable behavior of EgDdls in complex with screened inhibitors. The residues Phe172, Lys174, Glu217, Phe292, and Asn302 of EgDdls were mainly involved in interactions with screened inhibitors. Furthermore, MM-PBSA calculation showed electrostatic and van der Waals interactions mainly contribute to overall binding energy. The PCA analysis showed motion of central domain and omega loop of EgDdls. This is involved in the formation of native dipeptide and stabilized after binding of 2-(1-(Ethylsulfonyl) piperidin-4-yl)-5-(furan-2-yl)-1,3,4-oxadiazole, which could be reason for the inhibition of EgDdls. Hence, in this study we have screened inhibitors of EgDdls which could be useful to alleviate the vancomycin resistance problem in enterococci, involved in hospital-acquired infections, especially urinary tract infections (UTI).
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Affiliation(s)
- Sneha B Paymal
- Department of Microbiology, Shivaji University, Vidyanagar, Kolhapur, 416004, Maharashtra, India; Rayat Institute of Research and Development (RIRD), Satara, 415001, Maharashtra, India
| | - Sagar S Barale
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Vidyanagar, Kolhapur, 416004, Maharashtra, India
| | | | - Kailas D Sonawane
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Vidyanagar, Kolhapur, 416004, Maharashtra, India; Department of Microbiology, Shivaji University, Vidyanagar, Kolhapur, 416004, Maharashtra, India; Department of Chemistry, Shivaji University, Vidyanagar, Kolhapur, 416004, Maharashtra, India.
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Aouf A, Bouaouina S, Abdelgawad MA, Abourehab MAS, Farouk A. In Silico Study for Algerian Essential Oils as Antimicrobial Agents against Multidrug-Resistant Bacteria Isolated from Pus Samples. Antibiotics (Basel) 2022; 11:1317. [PMID: 36289975 PMCID: PMC9598771 DOI: 10.3390/antibiotics11101317] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/23/2022] [Accepted: 09/24/2022] [Indexed: 11/26/2022] Open
Abstract
In the context of the globally growing problem of resistance to most used antibacterial agents, essential oils offer promising solutions against multidrug-resistant (MDR) bacterial pathogens. The present study aimed to evaluate the prevalence, etiology, and antibiotic-resistance profiles of bacteria responsible for pyogenic infections in Regional Military University Hospital of Constantine. Disc diffusion and broth microdilution (MIC) methods were used to evaluate the antimicrobial activity of essential oils from five Algerian aromatic plants growing wild in the north of Algeria-Salvia officinalis (Sage), Thymus vulgaris (Thyme), Mentha pulegium L. (Mentha), Rosmarinus officinalis (Rosemary), and Pelargonium roseum (Geranium)-against reference and MDR strains. During three months of the prospective study, 112 isolates out of 431 pus samples were identified. Staphylococcus aureus was the most predominant species (25%), followed by Klebsiella pneumoniae (21.42%), Pseudomonas aeruginosa (21%), and Escherichia coli (17.95%). Among pus isolates, 65 were MDR (58.03%). The radial streak-line assay showed that R. officinalis and M. pulegium L. had weak activity against the tested strains, whereas P. roseum showed no activity at all. Meanwhile, T. vulgaris was the most potent, with an inhibition zone of 12-26 mm and an MIC value ranging between 0.25 and 1.25%, followed by S. officinalis with an inhibition zone of 8-12 mm and an MIC value ranging between 0.62 and 2.5%. Generally, A. baumannii and S. aureus ATCC6538P were the most sensitive strains, whereas P. aeruginosa ATCC27853 was the most resistant strain to the oils. Gas chromatography-mass spectrometry analysis of chemical composition revealed the presence of borneol (76.42%) and thymol (17.69%) as predominant in thyme, whereas camphor (36.92%) and α- thujone (34.91%) were the major volatiles in sage. The in-silico study revealed that sesquiterpenes and thymol had the highest binding free energies against the vital enzymes involved in biosynthesis and repair of cell walls, proteins, and nucleic acids compared to monoterpenes. The results demonstrated that T. vulgaris and S. officinalis are ideal candidates for developing future potentially active remedies against MDR strains.
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Affiliation(s)
- Abdelhakim Aouf
- Laboratory of Applied Microbiology, Faculty of Life Sciences and Nature, University of Ferhat Abbas, Setif 19000, Algeria
| | - Sarah Bouaouina
- Laboratory of Applied Microbiology, Faculty of Life Sciences and Nature, University of Ferhat Abbas, Setif 19000, Algeria
| | - Mohamed A. Abdelgawad
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka 72341, Saudi Arabia
| | - Mohammed A. S. Abourehab
- Department of Pharmaceutics, College of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Minia University, Minia 61519, Egypt
| | - Amr Farouk
- Flavour and Aroma Chemistry Department, National Research Center, Cairo 12622, Egypt
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Mogany T, Kumari S, Swalaha FM, Bux F. In silico analysis of enzymes involved in mycosporine-like amino acids biosynthesis in Euhalothece sp.: Structural and functional characterization. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Sharon I, Grogg M, Hilvert D, Schmeing TM. Structure and Function of the β-Asp-Arg Polymerase Cyanophycin Synthetase 2. ACS Chem Biol 2022; 17:670-679. [PMID: 35179888 DOI: 10.1021/acschembio.1c01007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyanophycin is a biopolymer composed of long chains of β-Asp-Arg. It is widespread in nature, being synthesized by many clades of bacteria, which use it as a cellular reservoir of nitrogen, carbon, and energy. Two enzymes are known to produce cyanophycin: cyanophycin synthetase 1 (CphA1), which builds cyanophycin from the amino acids Asp and Arg by alternating between two separate reactions for backbone extension and side chain modification, and cyanophycin synthetase 2 (CphA2), which polymerizes β-Asp-Arg dipeptides. CphA2 is evolutionarily related to CphA1, but questions about CphA2's altered structure and function remain unresolved. Cyanophycin and related molecules have drawn interest as green biopolymers. Because it only has a single active site, CphA2 could be more useful than CphA1 for biotechnological applications seeking to produce modified cyanophycin. In this study, we report biochemical assays on nine cyanobacterial CphA2 enzymes and report the crystal structure of CphA2 from Gloeothece citriformis at 3.0 Å resolution. The structure reveals a homodimeric, three-domain architecture. One domain harbors the polymerization active site and the two other domains have structural roles. The structure and biochemical assays explain how CphA2 binds and polymerizes β-Asp-Arg and highlights differences in in vitro oligomerization and activity between CphA2 enzymes. Using the structure and distinct activity profile as a guide, we introduced a single point mutation that converted Gloeothece citriformis CphA2 from a primer-dependent enzyme into a primer-independent enzyme.
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Affiliation(s)
- Itai Sharon
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montréal H3G 0B1, Quebec, Canada
| | - Marcel Grogg
- Laboratory of Organic Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
| | - T. Martin Schmeing
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montréal H3G 0B1, Quebec, Canada
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Synthesis, in vitro antimicrobial evaluation, and molecular docking studies of new isatin-1,2,3-triazole hybrids. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131855] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Antimicrobial activity of methanolic extracts of Vernonia cinerea against Xanthomonas oryzae and identification of their compounds using in silico techniques. PLoS One 2021; 16:e0252759. [PMID: 34125862 PMCID: PMC8202908 DOI: 10.1371/journal.pone.0252759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/22/2021] [Indexed: 12/25/2022] Open
Abstract
Bacterial Leaf Blight (BLB) disease is an extremely ruinous disease in rice, caused by Xanthomonas oryzae pv. oryzae (Xoo). Although various chemicals are available to manage BLB, they are toxic to the environment as well as humans. Hence there is a need to develop new pesticides as alternatives to hazardous chemicals. Therefore, a study was carried out to discover new potent natural pesticides against Xoo from different solvent extracts of Vernonia cinerea. Among all the fractions, the methanolic extract showed the highest inhibition zone. Further, to gain mechanistic insight of inhibitory action, 40 molecules of methanolic extracts were subjected for in silico study against two enzymes D-alanine—D-alanine ligase (Ddl) and Peptide deformylase (PDF). In silico study showed Rutin and Methanone, [1,4-dimethyl-7-(1- methylethyl)-2- azulenyl]phenyl have a good binding affinity with Ddl while Phenol, 2,4-bis(1-phenylethyl)- and 1,2-Benzenedicarboxylic acid, diisooctyl ester showed an excellent binding affinity to PDF. Finally, the system biology approach was applied to understand the agrochemical’s effect in the cell system of bacteria against both the enzymes. Conclusively, these four-hit compounds may have strong potential against Xoo and can be used as biopesticides in the future.
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Jianu C, Stoin D, Cocan I, David I, Pop G, Lukinich-Gruia AT, Mioc M, Mioc A, Șoica C, Muntean D, Rusu LC, Goleț I, Horhat DI. In Silico and In Vitro Evaluation of the Antimicrobial and Antioxidant Potential of Mentha × smithiana R. GRAHAM Essential Oil from Western Romania. Foods 2021; 10:815. [PMID: 33918674 PMCID: PMC8069324 DOI: 10.3390/foods10040815] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 01/17/2023] Open
Abstract
This study was conducted to identify the volatile compounds of Mentha × smithiana essential oil (MSEO) and evaluate its antioxidant and antibacterial potential. The essential oil (EO) content was assessed by gas chromatography-mass spectrometry (GC-MS). Carvone (55.71%), limonene (18.83%), trans-carveol (3.54%), cis-carveol (2.72%), beta-bourbonene (1.94%), and caryophyllene oxide (1.59%) were the main identified compounds. The MSEO displayed broad-spectrum antibacterial effects and was also found to be the most effective antifungal agent against Candida albicans and Candida parapsilosis. The antioxidant activity of MSEO was tested against cold-pressed sunflower oil by peroxide, thiobarbituric acid, 1,1-diphenyl-2-picrylhydrazyl radical (DPPH), and β-carotene/linoleic acid bleaching methods. The EO showed strong antioxidant effects as reflected by IC50 values of 0.83 ± 0.01 mg/mL and relative antioxidative activity of 87.32 ± 0.03% in DPPH and β-carotene/linoleic acid bleaching assays, respectively. Moreover, in the first 8 days of the incubation period, the inhibition of primary and secondary oxidation compounds induced by the MSEO (0.3 mg/mL) was significantly stronger (p < 0.05) than that of butylated hydroxyanisole. In silico molecular docking studies were conducted to highlight the underlying antimicrobial mechanism as well as the in vitro antioxidant potential. Recorded data showed that the antimicrobial activity of MSEO compounds could be exerted through the D-Alanine-d-alanine ligase (DDl) inhibition and may be attributed to a cumulative effect. The most active compounds are minor components of the MSEO. Docking results also revealed that several mint EO components could exert their in vitro antioxidant activity by employing xanthine oxidase inhibition. Consequently, MSEO could be a new natural source of antioxidants and antiseptics, with potential applications in the food and pharmaceutical industries as an alternative to the utilization of synthetic additives.
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Affiliation(s)
- Călin Jianu
- Faculty of Food Engineering, Banat’s University of Agricultural Sciences and Veterinary Medicine “King Michael I of Romania” from Timisoara, Calea Aradului 119, RO-300645 Timișoara, Romania; (C.J.); (D.S.); (I.C.)
| | - Daniela Stoin
- Faculty of Food Engineering, Banat’s University of Agricultural Sciences and Veterinary Medicine “King Michael I of Romania” from Timisoara, Calea Aradului 119, RO-300645 Timișoara, Romania; (C.J.); (D.S.); (I.C.)
| | - Ileana Cocan
- Faculty of Food Engineering, Banat’s University of Agricultural Sciences and Veterinary Medicine “King Michael I of Romania” from Timisoara, Calea Aradului 119, RO-300645 Timișoara, Romania; (C.J.); (D.S.); (I.C.)
| | - Ioan David
- Faculty of Food Engineering, Banat’s University of Agricultural Sciences and Veterinary Medicine “King Michael I of Romania” from Timisoara, Calea Aradului 119, RO-300645 Timișoara, Romania; (C.J.); (D.S.); (I.C.)
| | - Georgeta Pop
- Faculty of Agriculture, Banat’s University of Agricultural Sciences and Veterinary Medicine “King Michael I of Romania” from Timisoara, Calea Aradului 119, RO-300645 Timișoara, Romania;
| | | | - Marius Mioc
- Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy, 2nd Eftimie Murgu Square, RO-300041 Timisoara, Romania; (M.M.); (A.M.); (C.Ș.)
| | - Alexandra Mioc
- Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy, 2nd Eftimie Murgu Square, RO-300041 Timisoara, Romania; (M.M.); (A.M.); (C.Ș.)
| | - Codruța Șoica
- Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy, 2nd Eftimie Murgu Square, RO-300041 Timisoara, Romania; (M.M.); (A.M.); (C.Ș.)
| | - Delia Muntean
- Faculty of Medicine, “Victor Babes” University of Medicine and Pharmacy, 2nd Eftimie Murgu Square, RO-300041 Timisoara, Romania; (D.M.); (D.I.H.)
- Multidisciplinary Research Center on Antimicrobial Resistance, “Victor Babes” University of Medicine and Pharmacy, 2nd Eftimie Murgu Square, RO-300041 Timisoara, Romania
| | - Laura-Cristina Rusu
- Faculty of Dental Medicine, “Victor Babes” University of Medicine and Pharmacy, 2nd Eftimie Murgu Square, RO-300041 Timisoara, Romania;
- Multidisciplinary Center for Research, Evaluation, Diagnosis and Therapies in Oral Medicine, “Victor Babes” University of Medicine and Pharmacy, Spl. Tudor Vladimirescu 14A, RO-300173 Timisoara, Romania
| | - Ionuț Goleț
- Faculty of Economics and Business Administration, West University of Timișoara, 300233 Timisoara, Romania;
| | - Delia Ioana Horhat
- Faculty of Medicine, “Victor Babes” University of Medicine and Pharmacy, 2nd Eftimie Murgu Square, RO-300041 Timisoara, Romania; (D.M.); (D.I.H.)
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Zhang Y, Gong S, Wang X, Muhammad M, Li Y, Meng S, Li Q, Liu D, Zhang H. Insights into the Inhibition of Aeromonas hydrophila d-Alanine-d-Alanine Ligase by Integration of Kinetics and Structural Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:7509-7519. [PMID: 32609505 DOI: 10.1021/acs.jafc.0c00682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Aeromonas hydrophila, a pathogenic bacterium, is harmful to humans, domestic animals, and fishes and, moreover, of public health concern due to the emergence of multiple drug-resistant strains. The cell wall has been discovered as a novel and efficient drug target against bacteria, and d-alanine-d-alanine ligase (Ddl) is considered as an essential enzyme in bacterial cell wall biosynthesis. Herein, we studied the A. hydrophila HBNUAh01 Ddl (AhDdl) enzyme activity and kinetics and determined the crystal structure of AhDdl/d-Ala complex at 2.7 Å resolution. An enzymatic assay showed that AhDdl exhibited higher affinity to ATP (Km: 54.1 ± 9.1 μM) compared to d-alanine (Km: 1.01 ± 0.19 mM). The kinetic studies indicated a competitive inhibition of AhDdl by d-cycloserine (DCS), with an inhibition constant (Ki) of 120 μM and the 50% inhibitory concentrations (IC50) value of 0.5 mM. Meanwhile, structural analysis indicated that the AhDdl/d-Ala complex structure adopted a semi-closed conformation form, and the active site was extremely conserved. Noteworthy is that the substrate d-Ala occupied the second d-Ala position, not the first d-Ala position. These results provided more insights for understanding the details of the catalytic mechanism and resources for the development of novel drugs against the diseases caused by A. hydrophila.
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Affiliation(s)
- Yingli Zhang
- College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P. R. China
| | - Siyu Gong
- College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P. R. China
| | - Xuan Wang
- College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P. R. China
| | - Murtala Muhammad
- Department of Biochemistry, Kano University of Science and Technology, Wudil 713281, Nigeria
| | - Yangyang Li
- College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P. R. China
| | - Shuaishuai Meng
- Engineering Research Center of Industrial Microbiology, Ministry of Education; Collaborative Innovation Center of Haixi Green Bio-Manufacturing Technology, Ministry of Education; College of Life Sciences, Fujian Normal University, Fuzhou 350117, P. R. China
| | - Qin Li
- Engineering Research Center of Industrial Microbiology, Ministry of Education; Collaborative Innovation Center of Haixi Green Bio-Manufacturing Technology, Ministry of Education; College of Life Sciences, Fujian Normal University, Fuzhou 350117, P. R. China
| | - Dong Liu
- College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P. R. China
| | - Huaidong Zhang
- Engineering Research Center of Industrial Microbiology, Ministry of Education; Collaborative Innovation Center of Haixi Green Bio-Manufacturing Technology, Ministry of Education; College of Life Sciences, Fujian Normal University, Fuzhou 350117, P. R. China
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Pederick JL, Thompson AP, Bell SG, Bruning JB. d-Alanine-d-alanine ligase as a model for the activation of ATP-grasp enzymes by monovalent cations. J Biol Chem 2020; 295:7894-7904. [PMID: 32335509 DOI: 10.1074/jbc.ra120.012936] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/23/2020] [Indexed: 12/18/2022] Open
Abstract
The ATP-grasp superfamily of enzymes shares an atypical nucleotide-binding site known as the ATP-grasp fold. These enzymes are involved in many biological pathways in all domains of life. One ATP-grasp enzyme, d-alanine-d-alanine ligase (Ddl), catalyzes ATP-dependent formation of the d-alanyl-d-alanine dipeptide essential for bacterial cell wall biosynthesis and is therefore an important antibiotic drug target. Ddl is activated by the monovalent cation (MVC) K+, but despite its clinical relevance and decades of research, how this activation occurs has not been elucidated. We demonstrate here that activating MVCs bind adjacent to the active site of Ddl from Thermus thermophilus and used a combined biochemical and structural approach to characterize MVC activation. We found that TtDdl is a type II MVC-activated enzyme, retaining activity in the absence of MVCs. However, the efficiency of TtDdl increased ∼20-fold in the presence of activating MVCs, and it was maximally activated by K+ and Rb+ ions. A strict dependence on ionic radius of the MVC was observed, with Li+ and Na+ providing little to no TtDdl activation. To understand the mechanism of MVC activation, we solved crystal structures of TtDdl representing distinct catalytic stages in complex with K+, Rb+, or Cs+ Comparison of these structures with apo TtDdl revealed no evident conformational change on MVC binding. Of note, the identified MVC binding site is structurally conserved within the ATP-grasp superfamily. We propose that MVCs activate Ddl by altering the charge distribution of its active site. These findings provide insight into the catalytic mechanism of ATP-grasp enzymes.
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Affiliation(s)
- Jordan L Pederick
- Institute for Photonics and Advanced Sensing, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia.,Department of Molecular and Cellular Biology, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Andrew P Thompson
- Department of Molecular and Cellular Biology, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Stephen G Bell
- Department of Chemistry, The University of Adelaide, Adelaide, South Australia, Australia
| | - John B Bruning
- Institute for Photonics and Advanced Sensing, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia .,Department of Molecular and Cellular Biology, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
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12
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The Biological Properties and Potential Interacting Proteins of d-Alanyl-d-alanine Ligase A from Mycobacterium tuberculosis. Molecules 2018; 23:molecules23020324. [PMID: 29401644 PMCID: PMC6017538 DOI: 10.3390/molecules23020324] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 01/23/2018] [Accepted: 02/01/2018] [Indexed: 12/12/2022] Open
Abstract
(1) Background: d-alanine-d-alanine ligase (DdlA), an effective target for drug development to combat against Mycobacterium tuberculosis (Mtb), which threatens human health globally, supplies a substrate of d-alanyl-d-alanine for peptidoglycan crosslinking by catalyzing the dimerization of two d-alanines. To obtain a better understanding of DdlA profiles and develop a colorimetric assay for high-throughput inhibitor screening, we focused on explicating and characterizing Tb-DdlA. (2) Methods and Results: Rv2981c (ddlA) was expressed in Escherichia coli, and the purified Tb-DdlA was identified using (anti)-polyhistidine antibody followed by DdlA activity confirmation by measuring the released orthophosphate via colorimetric assay and the yielded d-alanyl-d-alanine through high performance thin layer chromatography (HP-TLC). The kinetic assays on Tb-DdlA indicated that Tb-DdlA exhibited a higher affinity to ATP (KmATP: 50.327 ± 4.652 μmol/L) than alanine (KmAla: 1.011 ± 0.094 mmol/L). A colorimetric assay for Tb-DdlA activity was developed for high-throughput screening of DdlA inhibitors in this study. In addition, we presented an analysis on Tb-DdlA interaction partners by pull-down assay and MS/MS. Eight putative interaction partners of Tb-DdlA were identified. (3) Conclusions: Our dataset provided a valuable resource for exploring Tb-DdlA biology, and developed an easy colorimetric assay for screening of Tb-DdlA inhibitors.
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13
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Duclert-Savatier N, Bouvier G, Nilges M, Malliavin TE. Building Graphs To Describe Dynamics, Kinetics, and Energetics in the d-ALa:d-Lac Ligase VanA. J Chem Inf Model 2016; 56:1762-75. [PMID: 27579990 PMCID: PMC5039762 DOI: 10.1021/acs.jcim.6b00211] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
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The d-Ala:d-Lac ligase, VanA, plays a critical
role in the resistance of vancomycin. Indeed, it is involved in the
synthesis of a peptidoglycan precursor, to which vancomycin cannot
bind. The reaction catalyzed by VanA requires the opening of the so-called
“ω-loop”, so that the substrates can enter the
active site. Here, the conformational landscape of VanA is explored
by an enhanced sampling approach: the temperature-accelerated molecular
dynamics (TAMD). Analysis of the molecular dynamics (MD) and TAMD
trajectories recorded on VanA permits a graphical description of the
structural and kinetics aspects of the conformational space of VanA,
where the internal mobility and various opening modes of the ω-loop
play a major role. The other important feature is the correlation
of the ω-loop motion with the movements of the opposite domain,
defined as containing the residues A149–Q208. Conformational
and kinetic clusters have been determined and a path describing the
ω-loop opening was extracted from these clusters. The determination
of this opening path, as well as the relative importance of hydrogen
bonds along the path, permit one to propose some key residue interactions
for the kinetics of the ω-loop opening.
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Affiliation(s)
- Nathalie Duclert-Savatier
- Département de Biologie Structurale et Chimie, Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528 , 25, rue du Dr Roux, 75015 Paris, France
| | - Guillaume Bouvier
- Département de Biologie Structurale et Chimie, Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528 , 25, rue du Dr Roux, 75015 Paris, France
| | - Michael Nilges
- Département de Biologie Structurale et Chimie, Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528 , 25, rue du Dr Roux, 75015 Paris, France
| | - Thérèse E Malliavin
- Département de Biologie Structurale et Chimie, Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528 , 25, rue du Dr Roux, 75015 Paris, France
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14
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Miki Y, Okazaki S, Asano Y. Engineering an ATP-dependent D-Ala:D-Ala ligase for synthesizing amino acid amides from amino acids. J Ind Microbiol Biotechnol 2016; 44:667-675. [PMID: 27585794 DOI: 10.1007/s10295-016-1833-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/21/2016] [Indexed: 12/01/2022]
Abstract
We successfully engineered a new enzyme that catalyzes the formation of D-Ala amide (D-AlaNH2) from D-Ala by modifying ATP-dependent D-Ala:D-Ala ligase (EC 6.3.2.4) from Thermus thermophilus, which catalyzes the formation of D-Ala-D-Ala from two molecules of D-Ala. The new enzyme was created by the replacement of the Ser293 residue with acidic amino acids, as it was speculated to bind to the second D-Ala of D-Ala-D-Ala. In addition, a replacement of the position with Glu performed better than that with Asp with regards to specificity for D-AlaNH2 production. The S293E variant, which was selected as the best enzyme for D-AlaNH2 production, exhibited an optimal activity at pH 9.0 and 40 °C for D-AlaNH2 production. The apparent K m values of this variant for D-Ala and NH3 were 7.35 mM and 1.58 M, respectively. The S293E variant could catalyze the synthesis of 9.3 and 35.7 mM of D-AlaNH2 from 10 and 50 mM D-Ala and 3 M NH4Cl with conversion yields of 93 and 71.4 %, respectively. This is the first report showing the enzymatic formation of amino acid amides from amino acids.
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Affiliation(s)
- Yuta Miki
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan.,Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan.,MicroBiopharm Japan Co.Ltd., 1-3-1 Kyobashi, Chuo-ku, Tokyo, 104-0031, Japan
| | - Seiji Okazaki
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan.,Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan. .,Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan.
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15
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Fakhar Z, Naiker S, Alves CN, Govender T, Maguire GEM, Lameira J, Lamichhane G, Kruger HG, Honarparvar B. A comparative modeling and molecular docking study on Mycobacterium tuberculosis targets involved in peptidoglycan biosynthesis. J Biomol Struct Dyn 2016; 34:2399-417. [PMID: 26612108 DOI: 10.1080/07391102.2015.1117397] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
An alarming rise of multidrug-resistant Mycobacterium tuberculosis strains and the continuous high global morbidity of tuberculosis have reinvigorated the need to identify novel targets to combat the disease. The enzymes that catalyze the biosynthesis of peptidoglycan in M. tuberculosis are essential and noteworthy therapeutic targets. In this study, the biochemical function and homology modeling of MurI, MurG, MraY, DapE, DapA, Alr, and Ddl enzymes of the CDC1551 M. tuberculosis strain involved in the biosynthesis of peptidoglycan cell wall are reported. Generation of the 3D structures was achieved with Modeller 9.13. To assess the structural quality of the obtained homology modeled targets, the models were validated using PROCHECK, PDBsum, QMEAN, and ERRAT scores. Molecular dynamics simulations were performed to calculate root mean square deviation (RMSD) and radius of gyration (Rg) of MurI and MurG target proteins and their corresponding templates. For further model validation, RMSD and Rg for selected targets/templates were investigated to compare the close proximity of their dynamic behavior in terms of protein stability and average distances. To identify the potential binding mode required for molecular docking, binding site information of all modeled targets was obtained using two prediction algorithms. A docking study was performed for MurI to determine the potential mode of interaction between the inhibitor and the active site residues. This study presents the first accounts of the 3D structural information for the selected M. tuberculosis targets involved in peptidoglycan biosynthesis.
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Affiliation(s)
- Zeynab Fakhar
- a Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa
| | - Suhashni Naiker
- a Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa
| | - Claudio N Alves
- b Laboratório de Planejamento de Fármacos, Instituto de Ciências Exatas e Naturais , Instituto de Ciências Biológicas, Universidade Federal do Pará , CEP 66075-110, Belém , Pará , Brazil
| | - Thavendran Govender
- a Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa
| | - Glenn E M Maguire
- a Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa.,c School of Chemistry and Physics , University of KwaZulu-Natal , 4001 Durban , South Africa
| | - Jeronimo Lameira
- b Laboratório de Planejamento de Fármacos, Instituto de Ciências Exatas e Naturais , Instituto de Ciências Biológicas, Universidade Federal do Pará , CEP 66075-110, Belém , Pará , Brazil
| | - Gyanu Lamichhane
- d Division of Infectious Diseases, Center for Tuberculosis Research , Johns Hopkins University School of Medicine , Baltimore , MD 21205 , USA
| | - Hendrik G Kruger
- a Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa
| | - Bahareh Honarparvar
- a Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa
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16
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Tran HT, Hong MK, Ngo HPT, Huynh KH, Ahn YJ, Wang Z, Kang LW. Structure of D-alanine-D-alanine ligase from Yersinia pestis: nucleotide phosphate recognition by the serine loop. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:12-21. [PMID: 26894530 DOI: 10.1107/s2059798315021671] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 11/15/2015] [Indexed: 01/14/2023]
Abstract
D-Alanyl-D-alanine is an essential precursor of bacterial peptidoglycan and is synthesized by D-alanine-D-alanine ligase (DDL) with hydrolysis of ATP; this reaction makes DDL an important drug target for the development of antibacterial agents. Five crystal structures of DDL from Yersinia pestis (YpDDL) were determined at 1.7-2.5 Å resolution: apo, AMP-bound, ADP-bound, adenosine 5'-(β,γ-imido)triphosphate-bound, and D-alanyl-D-alanine- and ADP-bound structures. YpDDL consists of three domains, in which four loops, loop 1, loop 2 (the serine loop), loop 3 (the ω-loop) and loop 4, constitute the binding sites for two D-alanine molecules and one ATP molecule. Some of them, especially the serine loop and the ω-loop, show flexible conformations, and the serine loop is mainly responsible for the conformational change in substrate nucleotide phosphates. Enzyme-kinetics assays were carried out for both the D-alanine and ATP substrates and a substrate-binding mechanism was proposed for YpDDL involving conformational changes of the loops.
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Affiliation(s)
- Huyen Thi Tran
- Department of Biological Sciences, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
| | - Myoung Ki Hong
- Department of Biological Sciences, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
| | - Ho Phuong Thuy Ngo
- Department of Biological Sciences, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
| | - Kim Hung Huynh
- Department of Biological Sciences, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
| | - Yeh Jin Ahn
- Department of Life Science, Sangmyung University, 7 Hongji-dong, Jongno-gu, Seoul 110-743, Republic of Korea
| | - Zhong Wang
- Center for Cellular & Structural Biology, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Lin Woo Kang
- Department of Biological Sciences, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
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17
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The crystal structure of the D-alanine-D-alanine ligase from Acinetobacter baumannii suggests a flexible conformational change in the central domain before nucleotide binding. J Microbiol 2015; 53:776-82. [PMID: 26502962 DOI: 10.1007/s12275-015-5475-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 10/20/2015] [Accepted: 10/20/2015] [Indexed: 10/22/2022]
Abstract
Acinetobacter baumannii, which is emerging as a multidrug-resistant nosocomial pathogen, causes a number of diseases, including pneumonia, bacteremia, meningitis, and skin infections. With ATP hydrolysis, the D-alanine-D-alanine ligase (DDL) catalyzes the synthesis of D-alanyl-D-alanine, which is an essential component of bacterial peptidoglycan. In this study, we determined the crystal structure of DDL from A. baumannii (AbDDL) at a resolution of 2.2 Å. The asymmetric unit contained six protomers of AbDDL. Five protomers had a closed conformation in the central domain, while one protomer had an open conformation in the central domain. The central domain with an open conformation did not interact with crystallographic symmetry-related protomers and the conformational change of the central domain was not due to crystal packing. The central domain of AbDDL can have an ensemble of the open and closed conformations before the binding of substrate ATP. The conformational change of the central domain is important for the catalytic activity and the detail information will be useful for the development of inhibitors against AbDDL and putative antibacterial agents against A. baumannii. The AbDDL structure was compared with that of other DDLs that were in complex with potent inhibitors and the catalytic activity of AbDDL was confirmed using enzyme kinetics assays.
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18
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Tsuda T, Asami M, Koguchi Y, Kojima S. Single mutation alters the substrate specificity of L-amino acid ligase. Biochemistry 2014; 53:2650-60. [PMID: 24702628 DOI: 10.1021/bi500292b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
L-Amino acid ligase (Lal) catalyzes the formation of a dipeptide from two L-amino acids in an ATP-dependent manner and belongs to the ATP-grasp superfamily. Bacillus subtilis YwfE, the first identified Lal, produces the dipeptide antibiotic bacilysin, which consists of L-Ala and L-anticapsin. Its substrate specificity is restricted to smaller amino acids such as L-Ala for the N-terminal end of the dipeptide, whereas a wide range of hydrophobic amino acids including L-Phe and L-Met are recognized for the C-terminal end in vitro. We determined the crystal structures of YwfE with bound ADP-Mg(2+)-Pi and ADP-Mg(2+)-L-Ala at 1.9 and 2.0 Å resolutions, respectively. On the basis of these structures, we generated point mutants of residues that are considered to participate in the recognition of L-Ala and measured their ATPase activity. The conserved Arg328 is suggested to be a crucial residue for L-Ala recognition and catalysis. The mutation of Trp332 to Ala caused the enzyme to hydrolyze ATP, even in the absence of l-Ala, and the structure of this mutant protein appeared to show a cavity in the N-terminal substrate-binding pocket. These results suggest that Trp332 plays a key role in restricting the substrate specificity to smaller amino acids such as L-Ala. Moreover, Trp332 mutants can alter the substrate specificity and activity depending on the size and shape of substituted amino acids. These observations provide sufficient scope for the rational design of Lal to produce desirable dipeptides. We propose that the positioning of the conserved Arg residue in Lal is important for enantioselective recognition of L-amino acids.
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Affiliation(s)
- Takeo Tsuda
- Department of Life Science, Faculty of Science, Gakushuin University , 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
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19
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Doan TTN, Kim JK, Ngo HPT, Tran HT, Cha SS, Min Chung K, Huynh KH, Ahn YJ, Kang LW. Crystal structures of d-alanine-d-alanine ligase from Xanthomonas oryzae pv. oryzae alone and in complex with nucleotides. Arch Biochem Biophys 2014; 545:92-9. [PMID: 24440607 DOI: 10.1016/j.abb.2014.01.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 01/04/2014] [Accepted: 01/09/2014] [Indexed: 10/25/2022]
Abstract
D-Alanine-D-alanine ligase (DDL) catalyzes the biosynthesis of d-alanyl-d-alanine, an essential bacterial peptidoglycan precursor, and is an important drug target for the development of antibacterials. We determined four different crystal structures of DDL from Xanthomonas oryzae pv. oryzae (Xoo) causing Bacteria Blight (BB), which include apo, ADP-bound, ATP-bound, and AMPPNP-bound structures at the resolution between 2.3 and 2.0 Å. Similarly with other DDLs, the active site of XoDDL is formed by three loops from three domains at the center of enzyme. Compared with d-alanyl-d-alanine and ATP-bound TtDDL structure, the γ-phosphate of ATP in XoDDL structure was shifted outside toward solution. We swapped the ω-loop (loop3) of XoDDL with those of Escherichia coli and Helicobacter pylori DDLs, and measured the enzymatic kinetics of wild-type XoDDL and two mutant XoDDLs with the swapped ω-loops. Results showed that the direct interactions between ω-loop and other two loops are essential for the active ATP conformation for D-ala-phosphate formation.
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Affiliation(s)
- Thanh Thi Ngoc Doan
- Department of Advanced Technology Fusion, Konkuk University, Hwayang dong, Gwangjin-gu, Seoul 143-01, Republic of Korea
| | - Jin-Kwang Kim
- Department of Advanced Technology Fusion, Konkuk University, Hwayang dong, Gwangjin-gu, Seoul 143-01, Republic of Korea
| | - Ho-Phuong-Thuy Ngo
- Department of Biological Sciences, Konkuk University, Seoul 143-701, Republic of Korea
| | - Huyen-Thi Tran
- Department of Biological Sciences, Konkuk University, Seoul 143-701, Republic of Korea
| | - Sun-Shin Cha
- Marine Biotechnology Research Division, Korea Institute of Ocean Science and Technology, Ansan 426-744, Republic of Korea
| | - Kyung Min Chung
- Department of Microbiology and Immunology, Chonbuk National University Medical School, Jeonju, Jeonbuk 561-756, Republic of Korea
| | - Kim-Hung Huynh
- Department of Biological Sciences, Konkuk University, Seoul 143-701, Republic of Korea
| | - Yeh-Jin Ahn
- Department of Green Life Science, College of Convergence, Sangmyung University, 7 Hongji-dong, Jongno-gu, Seoul 110-743, Republic of Korea
| | - Lin-Woo Kang
- Department of Biological Sciences, Konkuk University, Seoul 143-701, Republic of Korea; Institute for Cellular and Structural Bioloy, Sun Yat-Sen University, Guangzhou, People's Republic of China.
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20
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Bouvier G, Duclert-Savatier N, Desdouits N, Meziane-Cherif D, Blondel A, Courvalin P, Nilges M, Malliavin TE. Functional Motions Modulating VanA Ligand Binding Unraveled by Self-Organizing Maps. J Chem Inf Model 2014; 54:289-301. [DOI: 10.1021/ci400354b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guillaume Bouvier
- Département
de Biologie Structurale et Chimie, Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3825, 25, rue du Dr Roux, 75015 Paris, France
| | - Nathalie Duclert-Savatier
- Département
de Biologie Structurale et Chimie, Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3825, 25, rue du Dr Roux, 75015 Paris, France
| | - Nathan Desdouits
- Département
de Biologie Structurale et Chimie, Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3825, 25, rue du Dr Roux, 75015 Paris, France
| | - Djalal Meziane-Cherif
- Institut
Pasteur,
Unité des Agents Antibactériens, 25, rue du Dr Roux, 75015 Paris, France
| | - Arnaud Blondel
- Département
de Biologie Structurale et Chimie, Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3825, 25, rue du Dr Roux, 75015 Paris, France
| | - Patrice Courvalin
- Institut
Pasteur,
Unité des Agents Antibactériens, 25, rue du Dr Roux, 75015 Paris, France
| | - Michael Nilges
- Département
de Biologie Structurale et Chimie, Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3825, 25, rue du Dr Roux, 75015 Paris, France
| | - Thérèse E. Malliavin
- Département
de Biologie Structurale et Chimie, Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3825, 25, rue du Dr Roux, 75015 Paris, France
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21
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Prosser GA, de Carvalho LPS. Kinetic mechanism and inhibition of Mycobacterium tuberculosis D-alanine:D-alanine ligase by the antibiotic D-cycloserine. FEBS J 2013; 280:1150-66. [PMID: 23286234 DOI: 10.1111/febs.12108] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 12/17/2012] [Accepted: 12/19/2012] [Indexed: 11/30/2022]
Abstract
D-cycloserine (DCS) is an antibiotic that is currently used in second-line treatment of tuberculosis. DCS is a structural analogue of D-alanine, and targets two enzymes involved in the cytosolic stages of peptidoglycan synthesis: alanine racemase (Alr) and D-alanine:D-alanine ligase (Ddl). The mechanisms of inhibition of DCS have been well-assessed using Alr and Ddl enzymes from various bacterial species, but little is known regarding the interactions of DCS with the mycobacterial orthologues of these enzymes. We have over-expressed and purified recombinant Mycobacterium tuberculosis Ddl (MtDdl; Rv2981c), and report a kinetic examination of the enzyme with both its native substrate and DCS. MtDdl is activated by K(+), follows an ordered ter ter mechanism and displays distinct affinities for D-Ala at each D-Ala binding site (K(m,D-Ala1) = 0.075 mm, K(m,D-Ala2) = 3.6 mm). ATP is the first substrate to bind and is necessary for subsequent binding of D-alanine or DCS. The pH dependence of MtDdl kinetic parameters indicate that general base chemistry is involved in the catalytic step. DCS was found to competitively inhibit D-Ala binding at both MtDdl D-Ala sites with equal affinity (K(i,DCS1) = 14 μm, K(i,DCS2) = 25 μm); however, each enzyme active site can only accommodate a single DCS molecule at a given time. The pH dependence of K(i,DCS2) revealed a loss of DCS binding affinity at high pH (pK(a) = 7.5), suggesting that DCS binds optimally in the zwitterionic form. The results of this study may assist in the design and development of novel Ddl-specific inhibitors for use as anti-mycobacterial agents.
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Affiliation(s)
- Gareth A Prosser
- Mycobacterial Research Division, Medical Research Council National Institute for Medical Research, London, UK
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22
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Kobayashi E, Yura K, Nagai Y. Distinct Conformation of ATP Molecule in Solution and on Protein. Biophysics (Nagoya-shi) 2013; 9:1-12. [PMID: 27493535 PMCID: PMC4629688 DOI: 10.2142/biophysics.9.1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Accepted: 12/12/2012] [Indexed: 12/01/2022] Open
Abstract
Adenosine triphosphate (ATP) is a versatile molecule used mainly for energy and a phosphate source. The hydrolysis of γ phosphate initiates the reactions and these reactions almost always start when ATP binds to protein. Therefore, there should be a mechanism to prevent spontaneous hydrolysis reaction and a mechanism to lead ATP to a pure energy source or to a phosphate source. To address these questions, we extensively analyzed the effect of protein to ATP conformation based on the sampling of the ATP solution conformations obtained from molecular dynamics simulation and the sampling of ATP structures bound to protein found in a protein structure database. The comparison revealed mainly the following three points; 1) The ribose ring in ATP molecule, which puckers in many ways in solution, tends to assume either C2′ exo or C2′ endo when it binds to protein. 2) The adenine ring in ATP molecule, which takes open-book motion with the two ring structures, has two distinct structures when ATP binds to protein. 3) The glycosyl-bond and the bond between phosphate and the ribose have unique torsion angles, when ATP binds to protein. The combination of torsion angles found in protein-bound forms is under-represented in ATP molecule in water. These findings suggest that ATP-binding protein exerts forces on ATP molecule to assume a conformation that is rarely found in solution, and that this conformation change should be a trigger for the reactions on ATP molecule.
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Affiliation(s)
- Eri Kobayashi
- Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo 112-8610, Japan
| | - Kei Yura
- Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo 112-8610, Japan; Center for Informational Biology, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo 112-8610, Japan; Center for Simulation Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo 112-8610, Japan
| | - Yoshinori Nagai
- Faculty of Political Science and Economics, Kokushikan University, 4-28-1, Setagaya, Tokyo 154-8515, Japan
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Quitterer F, List A, Beck P, Bacher A, Groll M. Biosynthesis of the 22nd genetically encoded amino acid pyrrolysine: structure and reaction mechanism of PylC at 1.5Å resolution. J Mol Biol 2012; 424:270-82. [PMID: 22985965 DOI: 10.1016/j.jmb.2012.09.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 08/21/2012] [Accepted: 09/05/2012] [Indexed: 11/25/2022]
Abstract
The second step in the biosynthesis of the 22nd genetically encoded amino acid pyrrolysine (Pyl) is catalyzed by PylC that forms the pseudopeptide L-lysine-N(ε)-3R-methyl-D-ornithine. Here, we present six crystal structures of the monomeric active ligase in complex with substrates, reaction intermediates, and products including ATP, the non-hydrolyzable ATP analogue 5'-adenylyl-β-γ-imidodiphosphate, ADP, D-ornithine (D-Orn), L-lysine (Lys), phosphorylated D-Orn, L-lysine-N(ε)-D-ornithine, inorganic phosphate, carbonate, and Mg(2+). The overall structure of PylC reveals similarities to the superfamily of ATP-grasp enzymes; however, there exist unique structural and functional features for a topological control of successive substrate entry and product release. Furthermore, the presented high-resolution structures provide detailed insights into the reaction mechanism of isopeptide bond formation starting with phosphorylation of D-Orn by transfer of a phosphate moiety from activated ATP. The binding of Lys to the enzyme complex is then followed by an S(N)2 reaction resulting in L-lysine-N(ε)-D-ornithine and inorganic phosphate. Surprisingly, PylC harbors two adenine nucleotides bound at the active site, what has not been observed in any ATP-grasp protein analyzed to date. Whereas one ATP molecule is involved in catalysis, the second adenine nucleotide functions as a selective anchor for the C- and N-terminus of the Lys substrate and is responsible for protein stability as shown by mutagenesis.
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Affiliation(s)
- Felix Quitterer
- Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Garching D-85747, Germany
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Meziane-Cherif D, Saul FA, Haouz A, Courvalin P. Structural and functional characterization of VanG D-Ala:D-Ser ligase associated with vancomycin resistance in Enterococcus faecalis. J Biol Chem 2012; 287:37583-92. [PMID: 22969085 DOI: 10.1074/jbc.m112.405522] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
d-Alanyl:d-lactate (d-Ala:d-Lac) and d-alanyl:d-serine ligases are key enzymes in vancomycin resistance of Gram-positive cocci. They catalyze a critical step in the synthesis of modified peptidoglycan precursors that are low binding affinity targets for vancomycin. The structure of the d-Ala:d-Lac ligase VanA led to the understanding of the molecular basis for its specificity, but that of d-Ala:d-Ser ligases had not been determined. We have investigated the enzymatic kinetics of the d-Ala:d-Ser ligase VanG from Enterococcus faecalis and solved its crystal structure in complex with ADP. The overall structure of VanG is similar to that of VanA but has significant differences mainly in the N-terminal and central domains. Based on reported mutagenesis data and comparison of the VanG and VanA structures, we show that residues Asp-243, Phe-252, and Arg-324 are molecular determinants for d-Ser selectivity. These residues are conserved in both enzymes and explain why VanA also displays d-Ala:d-Ser ligase activity, albeit with low catalytic efficiency in comparison with VanG. These observations suggest that d-Ala:d-Lac and d-Ala:d-Ser enzymes have evolved from a common ancestral d-Ala:d-X ligase. The crystal structure of VanG showed an unusual interaction between two dimers involving residues of the omega loop that are deeply anchored in the active site. We constructed an octapeptide mimicking the omega loop and found that it selectively inhibits VanG and VanA but not Staphylococcus aureus d-Ala:d-Ala ligase. This study provides additional insight into the molecular evolution of d-Ala:d-X ligases and could contribute to the development of new structure-based inhibitors of vancomycin resistance enzymes.
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Hrast M, Vehar B, Turk S, Konc J, Gobec S, Janežič D. Function of the d-Alanine:d-Alanine Ligase Lid Loop: A Molecular Modeling and Bioactivity Study. J Med Chem 2012; 55:6849-56. [DOI: 10.1021/jm3006965] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martina Hrast
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7,
SI-1000 Ljubljana, Slovenia
| | - Blaž Vehar
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Samo Turk
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7,
SI-1000 Ljubljana, Slovenia
| | - Janez Konc
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7,
SI-1000 Ljubljana, Slovenia
| | - Dušanka Janežič
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
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Shomura Y, Hinokuchi E, Ikeda H, Senoo A, Takahashi Y, Saito JI, Komori H, Shibata N, Yonetani Y, Higuchi Y. Structural and enzymatic characterization of BacD, an L-amino acid dipeptide ligase from Bacillus subtilis. Protein Sci 2012; 21:707-16. [PMID: 22407814 PMCID: PMC3403468 DOI: 10.1002/pro.2058] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 02/26/2012] [Accepted: 02/29/2012] [Indexed: 11/06/2022]
Abstract
BacD is an ATP-dependent dipeptide ligase responsible for the biosynthesis of L-alanyl-L-anticapsin, a precursor of an antibiotic produced by Bacillus spp. In contrast to the well-studied and phylogenetically related D-alanine: D-alanine ligase (Ddl), BacD synthesizes dipeptides using L-amino acids as substrates and has a low substrate specificity in vitro. The enzyme is of great interest because of its potential application in industrial protein engineering for the environmentally friendly biological production of useful peptide compounds, such as physiologically active peptides, artificial sweeteners and antibiotics, but the determinants of its substrate specificity and its catalytic mechanism have not yet been established due to a lack of structural information. In this study, we report the crystal structure of BacD in complex with ADP and an intermediate analog, phosphorylated phosphinate L-alanyl-L-phenylalanine, refined to 2.5-Å resolution. The complex structure reveals that ADP and two magnesium ions bind in a manner similar to that of Ddl. However, the dipeptide orientation is reversed, and, concomitantly, the entrance to the amino acid binding cavity differs in position. Enzymatic characterization of two mutants, Y265F and S185A, demonstrates that these conserved residues are not catalytic residues at least in the reaction where L-phenylalanine is used as a substrate. On the basis of the biochemical and the structural data, we propose a reaction scheme and a catalytic mechanism for BacD.
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Affiliation(s)
- Yasuhito Shomura
- Department of Life Science, Graduate School of Life Science, University of Hyogo3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- Biometal Science Laboratory, RIKEN SPring-8 Center1-1-1 Koto, Sayo-gun, Sayo-cho, Hyogo 679-5148, Japan
| | - Emi Hinokuchi
- Department of Life Science, Graduate School of Life Science, University of Hyogo3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Hajime Ikeda
- Bioprocess Development Center, Kyowa Hakko Bio Co., Ltd.2 Miyukigaoka, Tsukuba-shi, Ibaraki 305-0841, Japan
| | - Akihiro Senoo
- Bioprocess Development Center, Kyowa Hakko Bio Co., Ltd.2 Miyukigaoka, Tsukuba-shi, Ibaraki 305-0841, Japan
| | - Yuichi Takahashi
- Drug Discovery Research Laboratories, Kyowa Hakko Kirin Co., Ltd.1188 Shimotogari, Nagaizumi-cho, Suntou-gun, Shizuoka 411-8731, Japan
| | - Jun-ichi Saito
- Drug Discovery Research Laboratories, Kyowa Hakko Kirin Co., Ltd.1188 Shimotogari, Nagaizumi-cho, Suntou-gun, Shizuoka 411-8731, Japan
| | - Hirofumi Komori
- Department of Life Science, Graduate School of Life Science, University of Hyogo3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- Biometal Science Laboratory, RIKEN SPring-8 Center1-1-1 Koto, Sayo-gun, Sayo-cho, Hyogo 679-5148, Japan
| | - Naoki Shibata
- Department of Life Science, Graduate School of Life Science, University of Hyogo3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- Biometal Science Laboratory, RIKEN SPring-8 Center1-1-1 Koto, Sayo-gun, Sayo-cho, Hyogo 679-5148, Japan
| | - Yoshiyuki Yonetani
- Bioprocess Development Center, Kyowa Hakko Bio Co., Ltd.2 Miyukigaoka, Tsukuba-shi, Ibaraki 305-0841, Japan
| | - Yoshiki Higuchi
- Department of Life Science, Graduate School of Life Science, University of Hyogo3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- Biometal Science Laboratory, RIKEN SPring-8 Center1-1-1 Koto, Sayo-gun, Sayo-cho, Hyogo 679-5148, Japan
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Wang Z, Yan S, Liu C, Chen F, Wang T. Proteomic analysis reveals an aflatoxin-triggered immune response in cotyledons of Arachis hypogaea infected with Aspergillus flavus. J Proteome Res 2012; 11:2739-53. [PMID: 22424419 DOI: 10.1021/pr201105d] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
An immune response is triggered in host cells when host receptors recognize conserved molecular motifs, pathogen-associated molecular patterns (PAMPs), such as β-glucans, and chitin at the cell surface of a pathogen. Effector-triggered immunity occurs when pathogens deliver effectors into the host cell to suppress the first immune signaling. Using a differential proteomic approach, we identified an array of proteins responding to aflatoxins in cotyledons of peanut (Arachis hypogaea) infected with aflatoxin-producing (toxigenic) but not nonaflatoxin-producing (atoxigenic) strains of Aspergillus flavus. These proteins are involved in immune signaling and PAMP perception, DNA and RNA stabilization, induction of defense, innate immunity, hypersensitive response, biosynthesis of phytoalexins, cell wall responses, peptidoglycan assembly, penetration resistance, condensed tannin synthesis, detoxification, and metabolic regulation. Gene expression analysis confirmed the differential abundance of proteins in peanut cotyledons supplemented with aflatoxins, with or without infection with the atoxigenic strain. Similarly, peanut germination and A. flavus growth were altered in response to aflatoxin B1. These findings show an additional immunity initiated by aflatoxins. With the PAMP- and effector-triggered immune responses, this immunity constitutes the third immune response of the immune system in peanut cotyledon cells. The system is also a three-grade coevolution of plant-pathogen interaction.
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Affiliation(s)
- Zizhang Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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Sun T, Hayakawa K, Fraser ME. ADP-Mg2+ bound to the ATP-grasp domain of ATP-citrate lyase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1168-72. [PMID: 22102020 PMCID: PMC3212355 DOI: 10.1107/s1744309111028363] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 07/15/2011] [Indexed: 04/10/2023]
Abstract
Human ATP-citrate lyase (EC 2.3.3.8) is the cytoplasmic enzyme that catalyzes the production of acetyl-CoA from citrate, CoA and ATP. The amino-terminal portion of the enzyme, containing residues 1-817, was crystallized in the presence of tartrate, ATP and magnesium ions. The crystals diffracted to 2.3 Å resolution. The structure shows ADP-Mg(2+) bound to the domain that possesses the ATP-grasp fold. The structure demonstrates that this crystal form could be used to investigate the structures of complexes with inhibitors of ATP-citrate lyase that bind at either the citrate- or ATP-binding site.
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Affiliation(s)
- Tianjun Sun
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Koto Hayakawa
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Marie E. Fraser
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
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Molecular basis of vancomycin dependence in VanA-type Staphylococcus aureus VRSA-9. J Bacteriol 2010; 192:5465-71. [PMID: 20729361 DOI: 10.1128/jb.00613-10] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The vancomycin-resistant Staphylococcus aureus VRSA-9 clinical isolate was partially dependent on glycopeptide for growth. The responsible vanA operon had the same organization as that of Tn1546 and was located on a plasmid. The chromosomal D-Ala:D-Ala ligase (ddl) gene had two point mutations that led to Q260K and A283E substitutions, resulting in a 200-fold decrease in enzymatic activity compared to that of the wild-type strain VRSA-6. To gain insight into the mechanism of enzyme impairment, we determined the crystal structure of VRSA-9 Ddl and showed that the A283E mutation induces new ion pair/hydrogen bond interactions, leading to an asymmetric rearrangement of side chains in the dimer interface. The Q260K substitution is located in an exposed external loop and did not induce any significant conformational change. The VRSA-9 strain was susceptible to oxacillin due to synthesis of pentadepsipeptide precursors ending in D-alanyl-D-lactate which are not substrates for the β-lactam-resistant penicillin binding protein PBP2'. Comparison with the partially vancomycin-dependent VRSA-7, whose Ddl is 5-fold less efficient than that of VRSA-9, indicated that the levels of vancomycin dependence and susceptibility to β-lactams correlate with the degree of Ddl impairment. Ddl drug targeting could therefore be an effective strategy against vancomycin-resistant S. aureus.
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30
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Welin M, Grossmann JG, Flodin S, Nyman T, Stenmark P, Trésaugues L, Kotenyova T, Johansson I, Nordlund P, Lehtiö L. Structural studies of tri-functional human GART. Nucleic Acids Res 2010; 38:7308-19. [PMID: 20631005 PMCID: PMC2978367 DOI: 10.1093/nar/gkq595] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Human purine de novo synthesis pathway contains several multi-functional enzymes, one of which, tri-functional GART, contains three enzymatic activities in a single polypeptide chain. We have solved structures of two domains bearing separate catalytic functions: glycinamide ribonucleotide synthetase and aminoimidazole ribonucleotide synthetase. Structures are compared with those of homologous enzymes from prokaryotes and analyzed in terms of the catalytic mechanism. We also report small angle X-ray scattering models for the full-length protein. These models are consistent with the enzyme forming a dimer through the middle domain. The protein has an approximate seesaw geometry where terminal enzyme units display high mobility owing to flexible linker segments. This resilient seesaw shape may facilitate internal substrate/product transfer or forwarding to other enzymes in the pathway.
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Affiliation(s)
- Martin Welin
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-17177 Stockholm, Sweden
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31
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Batson S, Rea D, Fülöp V, Roper DI. Crystallization and preliminary X-ray analysis of a D-alanyl-D-alanine ligase (EcDdlB) from Escherichia coli. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:405-8. [PMID: 20383009 DOI: 10.1107/s1744309110003970] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2009] [Accepted: 02/01/2010] [Indexed: 11/11/2022]
Abstract
A recombinant form of Escherichia coli DdlB (EcDdlB) has been prepared and cocrystallized with ADP and D-alanyl-D-alanine to represent the ternary complex of EcDdlB. Furthermore, EcDdlB has been cocrystallized under the same conditions with the ligands ATP and D-alanyl-D-alanine, representing the product-inhibited complex. The crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 53.0, b = 97.6, c = 109.5 A and a = 51.2, b = 97.8, c = 110.1 A, respectively, and both contained two molecules in the asymmetric unit. Complete data sets were collected to 1.5 and 1.4 A resolution, respectively, from single crystals under cryogenic conditions using synchrotron radiation.
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Affiliation(s)
- Sarah Batson
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, England
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