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Sharma VK, Chhibber-Goel J, Yogavel M, Sharma A. Structural characterization of glutamyl-tRNA synthetase (GluRS) from Plasmodium falciparum. Mol Biochem Parasitol 2023; 253:111530. [PMID: 36370911 DOI: 10.1016/j.molbiopara.2022.111530] [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: 08/27/2022] [Revised: 11/05/2022] [Accepted: 11/08/2022] [Indexed: 11/11/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes in protein translation machinery that provide the charged tRNAs needed for protein synthesis. Over the past decades, aaRSs have been studied as anti-parasitic, anti-bacterial, and anti-fungal drug targets. This study focused on the cytoplasmic glutamyl-tRNA synthetase (GluRS) from Plasmodium falciparum, which belongs to class Ib in aaRSs. GluRS unlike most other aaRSs requires tRNA to activate its cognate amino acid substrate L-Glutamate (L-Glu), and fails to form an intermediate adenylate complex in the absence of tRNA. The crystal structures of the Apo, ATP, and ADP-bound forms of Plasmodium falciparum glutamyl-tRNA synthetase (PfGluRS) were solved at 2.1 Å, 2.2 Å, and 2.8 Å respectively. The structural comparison of the Apo- and ATP-bound holo-forms of PfGluRS showed considerable conformational changes in the loop regions around the ATP-binding pocket of the enzyme. Biophysical characterization of the PfGluRS showed binding of the enzyme substrates L-Gluand ATP.. The sequence and structural conservation were evident across GluRS compared to other species. The structural dissection of the PfGluRS gives insight into the critical residues involved in the binding of ATP substrate, which can be harvested to develop new antimalarial drugs.
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Affiliation(s)
- Vivek Kumar Sharma
- Molecular Medicine - Structural Parasitology, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Jyoti Chhibber-Goel
- Molecular Medicine - Structural Parasitology, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Manickam Yogavel
- Molecular Medicine - Structural Parasitology, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Amit Sharma
- Molecular Medicine - Structural Parasitology, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India.
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Datt M. Interplay of substrate polymorphism and conformational plasticity of Plasmodium tyrosyl-tRNA synthetase. Comput Biol Chem 2021; 95:107582. [PMID: 34571426 DOI: 10.1016/j.compbiolchem.2021.107582] [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: 06/16/2021] [Revised: 08/12/2021] [Accepted: 09/12/2021] [Indexed: 11/18/2022]
Abstract
Aminoacyl-tRNA synthetases are an indispensable component of ribosomal protein translational machinery and Plasmodium Tyrosyl-tRNA synthetase (PfTyrRS) is a validated drug target. This manuscript illustrates the dynamic conformational landscape of PfTyrRS in the context of substrate binding. Molecular dynamics simulations of PfTyrRS in the presence and absence of ligand show conformational heterogeneity for both the protein and the bound ligand. Diverse conformations for the evolutionarily conserved ATP binding motif (KMSKS) have been observed in both apo- and holo PfTyrRS. Further, the presented attributes of the tyrosyl-adenylate conformational sub-states in situ along with their implications on the strength of intermolecular interactions would be a pertinent benchmark for molecular design studies. In addition, an analysis of the ligand hydration pattern foregrounds the structurally conserved water-mediated inter-molecular interactions. The quantitative assessment of the conformational landscape, based on the fluctuations of the distance between the ligand binding pockets, of apo-PfTyrRS and holo-PfTyrRS highlights the nature of diversity in conformational sampling for the two cases. Evidently, the holo-PfTyrRS adopts a rather compact conformation compared to the apo-PfTyrRS. An intriguing asymmetry in the dynamics of the two monomers is contextualized with the functional asymmetry of the symmetrically dimeric PfTyrRS. Importantly, the network of non-bonded contacts in the apo- and holo- simulated ensembles has been analyzed. The graph-theoretic analysis-based novel insights concerning the nature of information flow as a function of ligation state would prove valuable in understanding PfTyrRS functions. The results presented here contend that understanding allostery in PfTyrRS is essential to astutely design structure-based inhibitors.
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Affiliation(s)
- Manish Datt
- Biological and Life Sciences Division, School of Arts and Sciences, Ahmedabad University, Ahmedabad, Gujarat - 380009, India.
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Mishra S, Malhotra N, Kumari S, Sato M, Kikuchi H, Yogavel M, Sharma A. Conformational heterogeneity in apo and drug-bound structures of Toxoplasma gondii prolyl-tRNA synthetase. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2019; 75:714-724. [PMID: 31702585 DOI: 10.1107/s2053230x19014808] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/01/2019] [Indexed: 11/11/2022]
Abstract
Prolyl-tRNA synthetase (PRS) is a member of the aminoacyl-tRNA synthetase family that drives protein translation in cells. The apicomplexan PRSs are validated targets of febrifugine (FF) and its halogenated derivative halofuginone (HF). PRSs are of great interest for drug development against Plasmodium falciparum and Toxoplasma gondii. In this study, structures of apo and FF-bound T. gondii (TgPRS) are revealed and the dynamic nature of the conformational changes that occur upon FF binding is unraveled. In addition, this study highlights significant conformational plasticity within two different crystal structures of apo PRSs but not within drug-bound PRSs. The apo PRSs exist in multi-conformational states and manifest pseudo-dimeric structures. In contrast, when FF is bound the PRS dimer adopts a highly symmetrical architecture. It is shown that TgPRS does not display extant fold switching, in contrast to P. falciparum PRS, despite having over 65% sequence identity. Finally, structure-comparison analyses suggest the utility of r.m.s.d. per residue (r.m.s.d./res) as a robust tool to detect structural alterations even when the r.m.s.d. is low. Apo TgPRS reveals FF/HF-induced rigidity and this work has implications for drug-design studies that rely on the apo structures of target proteins.
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Affiliation(s)
- Siddhartha Mishra
- Structural Parasitology, International Centre for Genetic Engineering and Biotechnology, New Delhi, Aruna Asaf Ali Marg, New Delhi, Delhi 110067, India
| | - Nipun Malhotra
- Structural Parasitology, International Centre for Genetic Engineering and Biotechnology, New Delhi, Aruna Asaf Ali Marg, New Delhi, Delhi 110067, India
| | - Shreya Kumari
- Structural Parasitology, International Centre for Genetic Engineering and Biotechnology, New Delhi, Aruna Asaf Ali Marg, New Delhi, Delhi 110067, India
| | - Mizuki Sato
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Haruhisa Kikuchi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Manickam Yogavel
- Structural Parasitology, International Centre for Genetic Engineering and Biotechnology, New Delhi, Aruna Asaf Ali Marg, New Delhi, Delhi 110067, India
| | - Amit Sharma
- Structural Parasitology, International Centre for Genetic Engineering and Biotechnology, New Delhi, Aruna Asaf Ali Marg, New Delhi, Delhi 110067, India
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Nachiappan M, Jain V, Sharma A, Yogavel M, Jeyakanthan J. Structural and functional analysis of Glutaminyl-tRNA synthetase (TtGlnRS) from Thermus thermophilus HB8 and its complexes. Int J Biol Macromol 2018; 120:1379-1386. [DOI: 10.1016/j.ijbiomac.2018.09.115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 09/19/2018] [Accepted: 09/19/2018] [Indexed: 10/28/2022]
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Wang W, Qin B, Wojdyla JA, Wang M, Gao X, Cui S. Structural characterization of free-state and product-state Mycobacterium tuberculosis methionyl-tRNA synthetase reveals an induced-fit ligand-recognition mechanism. IUCRJ 2018; 5:478-490. [PMID: 30002848 PMCID: PMC6038951 DOI: 10.1107/s2052252518008217] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 06/04/2018] [Indexed: 06/08/2023]
Abstract
Mycobacterium tuberculosis (MTB) caused 10.4 million cases of tuberculosis and 1.7 million deaths in 2016. The incidence of multidrug-resistant and extensively drug-resistant MTB is becoming an increasing threat to public health and the development of novel anti-MTB drugs is urgently needed. Methionyl-tRNA synthetase (MetRS) is considered to be a valuable drug target. However, structural characterization of M. tuberculosis MetRS (MtMetRS) was lacking for decades, thus hampering drug design. Here, two high-resolution crystal structures of MtMetRS are reported: the free-state structure (apo form; 1.9 Å resolution) and a structure with the intermediate product methionyl-adenylate (Met-AMP) bound (2.4 Å resolution). It was found that free-state MtMetRS adopts a previously unseen conformation that has never been observed in other MetRS homologues. The pockets for methionine and AMP are not formed in free-state MtMetRS, suggesting that it is in a nonproductive conformation. Combining these findings suggests that MtMetRS employs an induced-fit mechanism in ligand binding. By comparison with the structure of human cytosolic MetRS, additional pockets specific to MtMetRS that could be used for anti-MTB drug design were located.
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Affiliation(s)
- Wei Wang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Science, No. 9 Dong Dan San Tiao, Dong Cheng Qu, Beijing 100730, People’s Republic of China
| | - Bo Qin
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Science, No. 9 Dong Dan San Tiao, Dong Cheng Qu, Beijing 100730, People’s Republic of China
| | | | - Meitian Wang
- Paul Scherrer Institute, Swiss Light Source, CH-5232 Villigen, Switzerland
| | - Xiaopan Gao
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Science, No. 9 Dong Dan San Tiao, Dong Cheng Qu, Beijing 100730, People’s Republic of China
| | - Sheng Cui
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Science, No. 9 Dong Dan San Tiao, Dong Cheng Qu, Beijing 100730, People’s Republic of China
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Negi A, Bhandari N, Shyamlal BRK, Chaudhary S. Inverse docking based screening and identification of protein targets for Cassiarin alkaloids against Plasmodium falciparum. Saudi Pharm J 2018; 26:546-567. [PMID: 29844728 PMCID: PMC5961758 DOI: 10.1016/j.jsps.2018.01.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 01/31/2018] [Indexed: 12/21/2022] Open
Abstract
Various reports have shown Cassiarin alkaloids, selective in vitro activities against various strains of Plasmodium falciparum with low cytotoxicity, which indicates their possible candidature as antimalarial drug. However, poor recognition of their protein targets and molecular binding behaviour, certainly limits their exploration as antimalarial drug candidature. To address this, we utilises inverse screening, based on three different docking methodologies in order to find their most putative protein targets. In our study, we screened 1047 protein structures from protein data bank, which belongs to 147 different proteins. Our investigation identified 16 protein targets for Cassiarins. In few cases of identified protein targets, the binding site was poorly studied, which encouraged us to perform comparative sequence and structural studies with their homologous proteins, like as in case of Kelch motif associated protein, Armadillo repeats only protein and Methionine aminopeptidase 1b. In our study, we also found Tryptophanyl-tRNA synthetase and 1-Deoxy-D-Xylose-5-phosphate reductoisomerase proteins are the most common targets for Cassiarins.
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Affiliation(s)
- Arvind Negi
- School of Chemistry, National University of Ireland, University Road, Galway H91 TK33, Ireland
| | - Nitisha Bhandari
- School of Biotechnology, Graphic Era University, Dehradun, Bell Road, Society Area, Clement Town, Dehradun, Uttarakhand 248002, India
| | - Bharti Rajesh Kumar Shyamlal
- Laboratory of Organic and Medicinal Chemistry, Department of Chemistry, National Institute of Technology Jaipur, Jawaharlal Nehru Marg, Jaipur 302017, India
| | - Sandeep Chaudhary
- Laboratory of Organic and Medicinal Chemistry, Department of Chemistry, National Institute of Technology Jaipur, Jawaharlal Nehru Marg, Jaipur 302017, India
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Manickam Y, Chaturvedi R, Babbar P, Malhotra N, Jain V, Sharma A. Drug targeting of one or more aminoacyl-tRNA synthetase in the malaria parasite Plasmodium falciparum. Drug Discov Today 2018; 23:1233-1240. [PMID: 29408369 DOI: 10.1016/j.drudis.2018.01.050] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/02/2018] [Accepted: 01/29/2018] [Indexed: 11/28/2022]
Abstract
Malaria remains a major infectious disease and, despite incidence reduction, it threatens resurgence in drug-resistant forms. Antimalarial drugs remain the mainstay of therapeutic options and hence there is a constant need to identify and validate new druggable targets. Plasmodium falciparum aminoacyl-tRNA synthetases (Pf-aaRSs) drive protein translation and are potent targets for development of next-generation antimalarials. Here, we detail advances made in structural-biology-based investigations in Pf-aaRSs and discuss their distribution of druggable pockets. This review establishes a platform for systematic experimental dissection of malarial parasite aaRSs as a new focus for sustained drug development efforts against malaria.
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Affiliation(s)
- Yogavel Manickam
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India
| | - Rini Chaturvedi
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India
| | - Palak Babbar
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India
| | - Nipun Malhotra
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India
| | - Vitul Jain
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India; Present address: Division of Structural Biology, Wellcome Trust Centre for Human Genetics, The Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Amit Sharma
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India.
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Na I, DeForte S, Stojanovski BM, Ferreira GC, Uversky VN. Molecular dynamics analysis of the structural and dynamic properties of the functionally enhanced hepta-variant of mouse 5-aminolevulinate synthase. J Biomol Struct Dyn 2017; 36:152-165. [PMID: 27928941 DOI: 10.1080/07391102.2016.1269688] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Heme biosynthesis, a complex, multistage, and tightly controlled process, starts with 5-aminolevulinate (ALA) production, which, in metazoa and certain bacteria, is a reaction catalyzed by 5-aminolevulinate synthase (ALAS), a pyridoxal 5'-phosphate (PLP)-dependent enzyme. Functional aberrations in ALAS are associated with several human diseases. ALAS can adopt open and closed conformations, with segmental rearrangements of a C-terminal, 16-amino acid loop and an α-helix regulating accessibility to the ALAS active site. Of the murine erythroid ALAS (mALAS2) forms previously engineered to assess the role of the flexible C-terminal loop versus mALAS2 function one stood out due to its impressive gain in catalytic power. To elucidate how the simultaneously introduced seven mutations of this activity-enhanced variant affected structural and dynamic properties of mALAS2, we conducted extensive molecular dynamics simulation analysis of the dimeric forms of wild-type mALAS2, hepta-variant and Rhodobacter capsulatus ALAS (aka R. capsulatus HemA). This analysis revealed that the seven simultaneous mutations in the C-terminal loop, which extends over the active site of the enzyme, caused the bacterial and murine proteins to adopt different conformations. Specifically, a new β-strand in the mutated 'loop' led to interaction with two preexisting β-strands and formation of an anti-parallel three-stranded β-sheet, which likely endowed the murine hepta-variant a more 'stable' open conformation than that of wild-type mALAS2, consistent with a kinetic mechanism involving a faster closed-to-open conformation transition and product release for the mutated than wild-type enzyme. Further, the dynamic behavior of the mALAS2 protomers was strikingly different in the two dimeric forms.
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Affiliation(s)
- Insung Na
- a Department of Molecular Medicine , Morsani College of Medicine, University of South Florida , Tampa , FL 33612 , USA
| | - Shelly DeForte
- a Department of Molecular Medicine , Morsani College of Medicine, University of South Florida , Tampa , FL 33612 , USA
| | - Bosko M Stojanovski
- a Department of Molecular Medicine , Morsani College of Medicine, University of South Florida , Tampa , FL 33612 , USA
| | - Gloria C Ferreira
- a Department of Molecular Medicine , Morsani College of Medicine, University of South Florida , Tampa , FL 33612 , USA.,b Department of Chemistry , College of Arts and Sciences, University of South Florida , Tampa , FL 33612 , USA
| | - Vladimir N Uversky
- a Department of Molecular Medicine , Morsani College of Medicine, University of South Florida , Tampa , FL 33612 , USA.,c USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine , University of South Florida , Tampa , Florida 33612 , USA.,d Laboratory of Structural Dynamics, Stability and Folding of Proteins , Institute of Cytology, Russian Academy of Sciences , St. Petersburg , Russia
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Kravchuk VO, Savytskyi OV, Odynets KO, Mykuliak VV, Kornelyuk AI. Computational modeling and molecular dynamics simulations of mammalian cytoplasmic tyrosyl-tRNA synthetase and its complexes with substrates. J Biomol Struct Dyn 2016; 35:2772-2788. [PMID: 27615678 DOI: 10.1080/07391102.2016.1235512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Cytoplasmic tyrosyl-tRNA synthetase (TyrRS) is one of the key enzymes of protein biosynthesis. TyrRSs of pathogenic organisms have gained attention as potential targets for drug development. Identifying structural differences between various TyrRSs will facilitate the development of specific inhibitors for the TyrRSs of pathogenic organisms. However, there is a deficiency in structural data for mammalian cytoplasmic TyrRS in complexes with substrates. In this work, we constructed spatial structure of full-length Bos taurus TyrRS (BtTyrRS) and its complexes with substrates using the set of computational modeling techniques. Special attention was paid to BtTyrRS complexes with substrates [L-tyrosine, K+ and ATP:Mg2+] and intermediate products [tyrosyl-adenylate (Tyr-AMP), K+ and PPi:Mg2+] with the different catalytic loop conformations. In order to analyze their dynamical properties, we performed 100 ns of molecular dynamics (MD) simulations. MD simulations revealed new structural data concerning the tyrosine activation reaction in mammalian TyrRS. Formation of strong interaction between Lys154 and γ-phosphate suggests the additional role of CP1 insertion as an important factor for ATP binding. The presence of a potassium-binding pocket within the active site of mammalian TyrRS compensates the absence of the second lysine in the KMSKS motif. Our data provide new details concerning a role of K+ ions at different stages of the first step of the tyrosylation reaction, including the coordination of substrates and involvement in the PPi releasing. The results of this work suggest that differences between ATP-binding sites of mammalian and bacterial TyrRSs are meaningful and could be exploited in the drug design.
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Affiliation(s)
- Vladyslav O Kravchuk
- a Department of Protein Engineering and Bioinformatics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150, Akademika Zabolotnogo Str., Kyiv , 03143 , Ukraine.,b Department of Biotechnology , National Aviation University , 1, Kosmonavta Komarova Str., Kyiv , 03058 , Ukraine
| | - Oleksandr V Savytskyi
- a Department of Protein Engineering and Bioinformatics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150, Akademika Zabolotnogo Str., Kyiv , 03143 , Ukraine
| | - Konstantin O Odynets
- a Department of Protein Engineering and Bioinformatics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150, Akademika Zabolotnogo Str., Kyiv , 03143 , Ukraine
| | - Vasyl V Mykuliak
- a Department of Protein Engineering and Bioinformatics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150, Akademika Zabolotnogo Str., Kyiv , 03143 , Ukraine.,c Institute of High Technologies , Taras Shevchenko National University of Kyiv , 64, Volodymyrs'ka Str., Kyiv , 01601 , Ukraine
| | - Alexander I Kornelyuk
- a Department of Protein Engineering and Bioinformatics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150, Akademika Zabolotnogo Str., Kyiv , 03143 , Ukraine.,c Institute of High Technologies , Taras Shevchenko National University of Kyiv , 64, Volodymyrs'ka Str., Kyiv , 01601 , Ukraine
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Structural characterization of antibiotic self-immunity tRNA synthetase in plant tumour biocontrol agent. Nat Commun 2016; 7:12928. [PMID: 27713402 PMCID: PMC5059758 DOI: 10.1038/ncomms12928] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 08/16/2016] [Indexed: 01/08/2023] Open
Abstract
Antibiotic-producing microbes evolved self-resistance mechanisms to avoid suicide. The biocontrol Agrobacterium radiobacter K84 secretes the Trojan Horse antibiotic agrocin 84 that is selectively transported into the plant pathogen A. tumefaciens and processed into the toxin TM84. We previously showed that TM84 employs a unique tRNA-dependent mechanism to inhibit leucyl-tRNA synthetase (LeuRS), while the TM84-producer prevents self-poisoning by expressing a resistant LeuRS AgnB2. We now identify a mechanism by which the antibiotic-producing microbe resists its own toxin. Using a combination of structural, biochemical and biophysical approaches, we show that AgnB2 evolved structural changes so as to resist the antibiotic by eliminating the tRNA-dependence of TM84 binding. Mutagenesis of key resistance determinants results in mutants adopting an antibiotic-sensitive phenotype. This study illuminates the evolution of resistance in self-immunity genes and provides mechanistic insights into a fascinating tRNA-dependent antibiotic with applications for the development of anti-infectives and the prevention of biocontrol emasculation.
The bacterium Agrobacterium radiobacter K84 secretes an antibiotic that is transported into the plant pathogen A. tumefaciens and processed into the toxin TM84. Here, the authors identify a mechanism whereby the antibiotic-producing microbe resists its own toxin.
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Datt M, Sharma A. Evolutionary and structural annotation of disease-associated mutations in human aminoacyl-tRNA synthetases. BMC Genomics 2014; 15:1063. [PMID: 25476837 PMCID: PMC4298046 DOI: 10.1186/1471-2164-15-1063] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 11/20/2014] [Indexed: 11/10/2022] Open
Abstract
Background Mutation(s) in proteins are a natural byproduct of evolution but can also cause serious diseases. Aminoacyl-tRNA synthetases (aaRSs) are indispensable components of all cellular protein translational machineries, and in humans they drive translation in both cytoplasm and mitochondria. Mutations in aaRSs have been implicated in a plethora of diseases including neurological conditions, metabolic disorders and cancer. Results We have developed an algorithmic approach for genome-wide analyses of sequence substitutions that combines evolutionary, structural and functional information. This pipeline enabled us to super-annotate human aaRS mutations and analyze their linkage to health disorders. Our data suggest that in some but not all cases, aaRS mutations occur in functional and structural sectors where they can manifest their pathological effects by altering enzyme activity or causing structural instability. Further, mutations appear in both solvent exposed and buried regions of aaRSs indicating that these alterations could lead to dysfunctional enzymes resulting in abnormal protein translation routines by affecting inter-molecular interactions or by disruption of non-bonded interactions. Overall, the prevalence of mutations is much higher in mitochondrial aaRSs, and the two most often mutated aaRSs are mitochondrial glutamyl-tRNA synthetase and dual localized glycyl-tRNA synthetase. Out of 63 mutations annotated in this work, only 12 (~20%) were observed in regions that could directly affect aminoacylation activity via either binding to ATP/amino-acid, tRNA or by involvement in dimerization. Mutations in structural cores or at potential biomolecular interfaces account for ~55% mutations while remaining mutations (~25%) remain structurally un-annotated. Conclusion This work provides a comprehensive structural framework within which most defective human aaRSs have been structurally analyzed. The methodology described here could be employed to annotate mutations in other protein families in a high-throughput manner. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1063) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Amit Sharma
- Structural and Computational Biology group, International Center for Genetic Engineering and Biotechnology, New Delhi 110067, India.
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