Base de dados : MEDLINE
Pesquisa : D13.444.735.757.700.650 [Categoria DeCS]
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[PMID]:29107006
[Au] Autor:Fandilolu PM; Kamble AS; Sambhare SB; Sonawane KD
[Ad] Endereço:Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, 416004, Maharashtra (M.S.), India.
[Ti] Título:Conformational preferences and structural analysis of hypermodified nucleoside, peroxywybutosine (o2yW) found at 37 position in anticodon loop of tRNA and its role in modulating UUC codon-anticodon interactions.
[So] Source:Gene;641:310-325, 2018 Jan 30.
[Is] ISSN:1879-0038
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Hypermodified bases present at 3'-adjacent (37 ) position in anticodon loop of tRNA are well known for their contribution in modulating codon-anticodon interactions. Peroxywybutosine (o2yW), a wyosine family member, is one of such tricyclic modified bases observed at the 37 position in tRNA . Conformational preferences and three-dimensional structural analysis of peroxywybutosine have not been investigated in detail at atomic level. Hence, in the present study quantum chemical semi-empirical RM1 and multiple molecular dynamics (MD) simulations have been used to study structural significance of peroxywybutosine in tRNA . Full geometry optimizations over the peroxywybutosine base have also been performed using ab-initio HF-SCF (6-31G**), DFT (B3LYP/6-31G**) and semi-empirical PM6 method to compare the salient properties. RM1 predicted most stable structure shows that the amino-carboxy-propyl side chain of o2yW remains 'distal' to the five membered imidazole ring of tricyclic guanosine. MD simulation trajectory of the isolated peroxy base showed restricted periodical fluctuations of peroxywybutosine side chain which might be helpful to maintain proper anticodon loop structure and mRNA reading frame during protein biosynthesis process. Another comparative MD simulation study of the anticodon stem loop with codon UUC showed various properties, which justify the functional implications of peroxywybutosine at 37 position along with other modified bases present in ASL of tRNA . Thus, this study presents an atomic view into the structural properties of peroxywybutosine, which can be useful to determine its role in the anticodon stem loop in context of codon-anticodon interactions and frame shift mutations.
[Mh] Termos MeSH primário: Anticódon/genética
Códon/genética
Guanosina/análogos & derivados
Nucleosídeos/genética
RNA de Transferência de Fenilalanina/genética
[Mh] Termos MeSH secundário: Anticódon/química
Códon/química
Mutação da Fase de Leitura/genética
Guanosina/química
Guanosina/genética
Conformação Molecular
Simulação de Dinâmica Molecular
Nucleosídeos/química
Biossíntese de Proteínas/genética
RNA Mensageiro/química
RNA Mensageiro/genética
RNA de Transferência de Fenilalanina/química
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Anticodon); 0 (Codon); 0 (Nucleosides); 0 (RNA, Messenger); 0 (RNA, Transfer, Phe); 12133JR80S (Guanosine); 52662-10-9 (wyosine)
[Em] Mês de entrada:1711
[Cu] Atualização por classe:171128
[Lr] Data última revisão:
171128
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171107
[St] Status:MEDLINE


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[PMID]:28657303
[Au] Autor:Leamy KA; Yennawar NH; Bevilacqua PC
[Ad] Endereço:Department of Chemistry, ‡Center for RNA Molecular Biology, §Huck Institutes of the Life Sciences, and ⊥Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States.
[Ti] Título:Cooperative RNA Folding under Cellular Conditions Arises From Both Tertiary Structure Stabilization and Secondary Structure Destabilization.
[So] Source:Biochemistry;56(27):3422-3433, 2017 Jul 11.
[Is] ISSN:1520-4995
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:RNA folding has been studied extensively in vitro, typically under dilute solution conditions and abiologically high salt concentrations of 1 M Na or 10 mM Mg . The cellular environment is very different, with 20-40% crowding and only 10-40 mM Na , 140 mM K , and 0.5-2.0 mM Mg . As such, RNA structures and functions can be radically altered under cellular conditions. We previously reported that tRNA secondary and tertiary structures unfold together in a cooperative two-state fashion under crowded in vivo-like ionic conditions, but in a noncooperative multistate fashion under dilute in vitro ionic conditions unless in nonphysiologically high concentrations of Mg . The mechanistic basis behind these effects remains unclear, however. To address the mechanism that drives RNA folding cooperativity, we probe effects of cellular conditions on structures and stabilities of individual secondary structure fragments comprising the full-length RNA. We elucidate effects of a diverse set of crowders on tRNA secondary structural fragments and full-length tRNA at three levels: at the nucleotide level by temperature-dependent in-line probing, at the tertiary structure level by small-angle X-ray scattering, and at the global level by thermal denaturation. We conclude that cooperative RNA folding is induced by two overlapping mechanisms: increased stability and compaction of tertiary structure through effects of Mg , and decreased stability of certain secondary structure elements through the effects of molecular crowders. These findings reveal that despite having very different chemical makeups RNA and protein can both have weak secondary structures in vivo leading to cooperative folding.
[Mh] Termos MeSH primário: Modelos Moleculares
RNA Fúngico/química
RNA de Transferência de Fenilalanina/química
Saccharomyces cerevisiae/metabolismo
[Mh] Termos MeSH secundário: Algoritmos
Temperatura Alta/efeitos adversos
Magnésio/química
Peso Molecular
Desnaturação de Ácido Nucleico
Concentração Osmolar
Polietilenoglicóis/química
Dobramento de Proteína
Dobramento de RNA
Estabilidade de RNA
Espalhamento a Baixo Ângulo
Temperatura de Transição
[Pt] Tipo de publicação:COMPARATIVE STUDY; JOURNAL ARTICLE
[Nm] Nome de substância:
0 (RNA, Fungal); 0 (RNA, Transfer, Phe); 30IQX730WE (Polyethylene Glycols); I38ZP9992A (Magnesium)
[Em] Mês de entrada:1707
[Cu] Atualização por classe:170805
[Lr] Data última revisão:
170805
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170629
[St] Status:MEDLINE
[do] DOI:10.1021/acs.biochem.7b00325


  3 / 855 MEDLINE  
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[PMID]:28637321
[Au] Autor:Shin BS; Katoh T; Gutierrez E; Kim JR; Suga H; Dever TE
[Ad] Endereço:Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
[Ti] Título:Amino acid substrates impose polyamine, eIF5A, or hypusine requirement for peptide synthesis.
[So] Source:Nucleic Acids Res;45(14):8392-8402, 2017 Aug 21.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Whereas ribosomes efficiently catalyze peptide bond synthesis by most amino acids, the imino acid proline is a poor substrate for protein synthesis. Previous studies have shown that the translation factor eIF5A and its bacterial ortholog EF-P bind in the E site of the ribosome where they contact the peptidyl-tRNA in the P site and play a critical role in promoting the synthesis of polyproline peptides. Using misacylated Pro-tRNAPhe and Phe-tRNAPro, we show that the imino acid proline and not tRNAPro imposes the primary eIF5A requirement for polyproline synthesis. Though most proline analogs require eIF5A for efficient peptide synthesis, azetidine-2-caboxylic acid, a more flexible four-membered ring derivative of proline, shows relaxed eIF5A dependency, indicating that the structural rigidity of proline might contribute to the requirement for eIF5A. Finally, we examine the interplay between eIF5A and polyamines in promoting translation elongation. We show that eIF5A can obviate the polyamine requirement for general translation elongation, and that this activity is independent of the conserved hypusine modification on eIF5A. Thus, we propose that the body of eIF5A functionally substitutes for polyamines to promote general protein synthesis and that the hypusine modification on eIF5A is critically important for poor substrates like proline.
[Mh] Termos MeSH primário: Aminoácidos/metabolismo
Lisina/análogos & derivados
Biossíntese Peptídica
Fatores de Iniciação de Peptídeos/metabolismo
Poliaminas/metabolismo
Proteínas de Ligação a RNA/metabolismo
Proteínas de Saccharomyces cerevisiae/metabolismo
[Mh] Termos MeSH secundário: Sequência de Bases
Lisina/metabolismo
Conformação de Ácido Nucleico
Fatores de Iniciação de Peptídeos/química
Peptídeos/metabolismo
Prolina/análogos & derivados
Prolina/química
Prolina/metabolismo
RNA de Transferência de Fenilalanina/química
RNA de Transferência de Fenilalanina/metabolismo
RNA de Transferência de Prolina/química
RNA de Transferência de Prolina/metabolismo
Proteínas de Ligação a RNA/química
Ribossomos/metabolismo
Saccharomyces cerevisiae/genética
Saccharomyces cerevisiae/metabolismo
Proteínas de Saccharomyces cerevisiae/química
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Amino Acids); 0 (Peptide Initiation Factors); 0 (Peptides); 0 (Polyamines); 0 (RNA, Transfer, Phe); 0 (RNA, Transfer, Pro); 0 (RNA-Binding Proteins); 0 (Saccharomyces cerevisiae Proteins); 0 (eukaryotic translation initiation factor 5A); 25191-13-3 (polyproline); 3874VXF092 (hypusine); 9DLQ4CIU6V (Proline); K3Z4F929H6 (Lysine)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171023
[Lr] Data última revisão:
171023
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170623
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx532


  4 / 855 MEDLINE  
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[PMID]:28419689
[Au] Autor:Kartvelishvili E; Tworowski D; Vernon H; Moor N; Wang J; Wong LJ; Chrzanowska-Lightowlers Z; Safro M
[Ad] Endereço:Department of Structural Biology, Weizmann Institute of Science, Israel.
[Ti] Título:Kinetic and structural changes in HsmtPheRS, induced by pathogenic mutations in human FARS2.
[So] Source:Protein Sci;26(8):1505-1516, 2017 Aug.
[Is] ISSN:1469-896X
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Mutations in the mitochondrial aminoacyl-tRNA synthetases (mtaaRSs) can cause profound clinical presentations, and have manifested as diseases with very selective tissue specificity. To date most of the mtaaRS mutations could be phenotypically recognized, such that clinicians could identify the affected mtaaRS from the symptoms alone. Among the recently reported pathogenic variants are point mutations in FARS2 gene, encoding the human mitochondrial PheRS. Patient symptoms range from spastic paraplegia to fatal infantile Alpers encephalopathy. How clinical manifestations of these mutations relate to the changes in three-dimensional structures and kinetic characteristics remains unclear, although impaired aminoacylation has been proposed as possible etiology of diseases. Here, we report four crystal structures of HsmtPheRS mutants, and extensive MD simulations for wild-type and nine mutants to reveal the structural changes on dynamic trajectories of HsmtPheRS. Using steady-state kinetic measurements of phenylalanine activation and tRNA aminoacylation, we gained insight into the structural and kinetic effects of mitochondrial disease-related mutations in FARS2 gene.
[Mh] Termos MeSH primário: Esclerose Cerebral Difusa de Schilder/genética
Proteínas Mitocondriais/química
Mutação
Paraplegia/genética
Fenilalanina-tRNA Ligase/química
RNA de Transferência de Fenilalanina/química
[Mh] Termos MeSH secundário: Adolescente
Motivos de Aminoácidos
Aminoacilação
Sítios de Ligação
Pré-Escolar
Cristalografia por Raios X
Esclerose Cerebral Difusa de Schilder/diagnóstico
Esclerose Cerebral Difusa de Schilder/metabolismo
Esclerose Cerebral Difusa de Schilder/patologia
Feminino
Seres Humanos
Cinética
Masculino
Mitocôndrias/genética
Mitocôndrias/metabolismo
Mitocôndrias/patologia
Proteínas Mitocondriais/genética
Proteínas Mitocondriais/metabolismo
Simulação de Dinâmica Molecular
Paraplegia/diagnóstico
Paraplegia/metabolismo
Paraplegia/patologia
Fenilalanina-tRNA Ligase/genética
Fenilalanina-tRNA Ligase/metabolismo
Ligação Proteica
Conformação Proteica em alfa-Hélice
Conformação Proteica em Folha beta
Domínios e Motivos de Interação entre Proteínas
RNA de Transferência de Fenilalanina/metabolismo
Alinhamento de Sequência
Especificidade por Substrato
Termodinâmica
[Pt] Tipo de publicação:CASE REPORTS; JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Mitochondrial Proteins); 0 (RNA, Transfer, Phe); EC 6.1.1.20 (FARS2 protein, human); EC 6.1.1.20 (Phenylalanine-tRNA Ligase)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170824
[Lr] Data última revisão:
170824
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170419
[St] Status:MEDLINE
[do] DOI:10.1002/pro.3176


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[PMID]:28168297
[Au] Autor:Mohler K; Mann R; Bullwinkle TJ; Hopkins K; Hwang L; Reynolds NM; Gassaway B; Aerni HR; Rinehart J; Polymenis M; Faull K; Ibba M
[Ad] Endereço:Department of Microbiology, The Ohio State University, 318 West 12th Avenue, Columbus, OH 43210, USA.
[Ti] Título:Editing of misaminoacylated tRNA controls the sensitivity of amino acid stress responses in Saccharomyces cerevisiae.
[So] Source:Nucleic Acids Res;45(7):3985-3996, 2017 Apr 20.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Amino acid starvation activates the protein kinase Gcn2p, leading to changes in gene expression and translation. Gcn2p is activated by deacylated tRNA, which accumulates when tRNA aminoacylation is limited by lack of substrates or inhibition of synthesis. Pairing of amino acids and deacylated tRNAs is catalyzed by aminoacyl-tRNA synthetases, which use quality control pathways to maintain substrate specificity. Phenylalanyl-tRNA synthetase (PheRS) maintains specificity via an editing pathway that targets non-cognate Tyr-tRNAPhe. While the primary role of aaRS editing is to prevent misaminoacylation, we demonstrate editing of misaminoacylated tRNA is also required for detection of amino acid starvation by Gcn2p. Ablation of PheRS editing caused accumulation of Tyr-tRNAPhe (5%), but not deacylated tRNAPhe during amino acid starvation, limiting Gcn2p kinase activity and suppressing Gcn4p-dependent gene expression. While the PheRS-editing ablated strain grew 50% slower and displayed a 27-fold increase in the rate of mistranslation of Phe codons as Tyr compared to wild type, the increase in mistranslation was insufficient to activate an unfolded protein stress response. These findings show that during amino acid starvation a primary role of aaRS quality control is to help the cell mount an effective stress response, independent of the role of editing in maintaining translational accuracy.
[Mh] Termos MeSH primário: Fenilalanina-tRNA Ligase/metabolismo
Edição de RNA
RNA de Transferência de Fenilalanina/metabolismo
Saccharomyces cerevisiae/metabolismo
Aminoacilação de RNA de Transferência
Resposta a Proteínas não Dobradas
[Mh] Termos MeSH secundário: Aminoácidos/metabolismo
Fenilalanina/metabolismo
Aminoacil-RNA de Transferência/metabolismo
Saccharomyces cerevisiae/enzimologia
Saccharomyces cerevisiae/genética
Saccharomyces cerevisiae/crescimento & desenvolvimento
Estresse Fisiológico
Tirosina/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Amino Acids); 0 (RNA, Transfer, Amino Acyl); 0 (RNA, Transfer, Phe); 42HK56048U (Tyrosine); 47E5O17Y3R (Phenylalanine); EC 6.1.1.20 (Phenylalanine-tRNA Ligase)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171114
[Lr] Data última revisão:
171114
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170208
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx077


  6 / 855 MEDLINE  
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[PMID]:28082677
[Au] Autor:Zaganelli S; Rebelo-Guiomar P; Maundrell K; Rozanska A; Pierredon S; Powell CA; Jourdain AA; Hulo N; Lightowlers RN; Chrzanowska-Lightowlers ZM; Minczuk M; Martinou JC
[Ad] Endereço:From the Department of Cell Biology, University of Geneva, 30 quai Ernest-Ansermet, 1211 Genève 4, Switzerland.
[Ti] Título:The Pseudouridine Synthase RPUSD4 Is an Essential Component of Mitochondrial RNA Granules.
[So] Source:J Biol Chem;292(11):4519-4532, 2017 Mar 17.
[Is] ISSN:1083-351X
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Mitochondrial gene expression is a fundamental process that is largely dependent on nuclear-encoded proteins. Several steps of mitochondrial RNA processing and maturation, including RNA post-transcriptional modification, appear to be spatially organized into distinct foci, which we have previously termed mitochondrial RNA granules (MRGs). Although an increasing number of proteins have been localized to MRGs, a comprehensive analysis of the proteome of these structures is still lacking. Here, we have applied a microscopy-based approach that has allowed us to identify novel components of the MRG proteome. Among these, we have focused our attention on RPUSD4, an uncharacterized mitochondrial putative pseudouridine synthase. We show that RPUSD4 depletion leads to a severe reduction of the steady-state level of the 16S mitochondrial (mt) rRNA with defects in the biogenesis of the mitoribosome large subunit and consequently in mitochondrial translation. We report that RPUSD4 binds 16S mt-rRNA, mt-tRNA , and mt-tRNA , and we demonstrate that it is responsible for pseudouridylation of the latter. These data provide new insights into the relevance of RNA pseudouridylation in mitochondrial gene expression.
[Mh] Termos MeSH primário: Transferases Intramoleculares/metabolismo
RNA/metabolismo
[Mh] Termos MeSH secundário: Linhagem Celular
Seres Humanos
Transferases Intramoleculares/análise
Transferases Intramoleculares/genética
Mitocôndrias/genética
Mitocôndrias/metabolismo
Proteínas Mitocondriais/metabolismo
Transporte Proteico
Interferência de RNA
RNA Ribossômico 16S/metabolismo
RNA Interferente Pequeno/genética
RNA de Transferência de Metionina/metabolismo
RNA de Transferência de Fenilalanina/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Mitochondrial Proteins); 0 (RNA, Ribosomal, 16S); 0 (RNA, Small Interfering); 0 (RNA, Transfer, Met); 0 (RNA, Transfer, Phe); 0 (RNA, mitochondrial); 63231-63-0 (RNA); EC 5.4.- (Intramolecular Transferases); EC 5.4.99.- (pseudouridine synthases)
[Em] Mês de entrada:1706
[Cu] Atualização por classe:170606
[Lr] Data última revisão:
170606
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170114
[St] Status:MEDLINE
[do] DOI:10.1074/jbc.M116.771105


  7 / 855 MEDLINE  
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[PMID]:28003514
[Au] Autor:Han L; Marcus E; D'Silva S; Phizicky EM
[Ad] Endereço:Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA.
[Ti] Título: Trm140 has two recognition modes for 3-methylcytidine modification of the anticodon loop of tRNA substrates.
[So] Source:RNA;23(3):406-419, 2017 Mar.
[Is] ISSN:1469-9001
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The 3-methylcytidine (m C) modification is ubiquitous in eukaryotic tRNA, widely found at C in the anticodon loop of tRNA , tRNA , and some tRNA species, as well as in the variable loop (V-loop) of certain tRNA species. In the yeast , formation of m C requires Trm140 for six tRNA substrates, including three tRNA species and three tRNA species, whereas in , two Trm140 homologs are used, one for tRNA and one for tRNA The occurrence of a single Trm140 homolog is conserved broadly among Ascomycota, whereas multiple Trm140-related homologs are found in metazoans and other fungi. We investigate here how Trm140 protein recognizes its six tRNA substrates. We show that Trm140 has two modes of tRNA substrate recognition. Trm140 recognizes G -U -t A of the anticodon loop of tRNA substrates, and this sequence is an identity element because it can be used to direct m C modification of tRNA However, Trm140 recognition of tRNA substrates is different, since their anticodons do not share G -U and do not have any nucleotides in common. Rather, specificity of Trm140 for tRNA is achieved by seryl-tRNA synthetase and the distinctive tRNA V-loop, as well as by t A and i A We provide evidence that all of these components are important in vivo and that seryl-tRNA synthetase greatly stimulates m C modification of tRNA and tRNA in vitro. In addition, our results show that Trm140 binding is a significant driving force for tRNA modification and suggest separate contributions from each recognition element for the modification.
[Mh] Termos MeSH primário: Anticódon/química
Citidina/análogos & derivados
Proteínas dos Microfilamentos/metabolismo
RNA de Transferência de Serina/química
Proteínas de Saccharomyces cerevisiae/metabolismo
Saccharomyces cerevisiae/metabolismo
tRNA Metiltransferases/metabolismo
[Mh] Termos MeSH secundário: Anticódon/metabolismo
Sequência de Bases
Sítios de Ligação
Clonagem Molecular
Citidina/genética
Citidina/metabolismo
Escherichia coli/genética
Escherichia coli/metabolismo
Expressão Gênica
Proteínas dos Microfilamentos/genética
Conformação de Ácido Nucleico
Ligação Proteica
Biossíntese de Proteínas
Domínios Proteicos
RNA de Transferência de Fenilalanina/química
RNA de Transferência de Fenilalanina/genética
RNA de Transferência de Fenilalanina/metabolismo
RNA de Transferência de Serina/genética
RNA de Transferência de Serina/metabolismo
RNA de Transferência de Treonina/química
RNA de Transferência de Treonina/genética
RNA de Transferência de Treonina/metabolismo
Proteínas Recombinantes/genética
Proteínas Recombinantes/metabolismo
Saccharomyces cerevisiae/genética
Proteínas de Saccharomyces cerevisiae/genética
Especificidade por Substrato
tRNA Metiltransferases/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (ABP140 protein, S cerevisiae); 0 (Anticodon); 0 (Microfilament Proteins); 0 (RNA, Transfer, Phe); 0 (RNA, Transfer, Ser); 0 (RNA, Transfer, Thr); 0 (Recombinant Proteins); 0 (Saccharomyces cerevisiae Proteins); 2140-64-9 (3-methylcytidine); 5CSZ8459RP (Cytidine); EC 2.1.1.- (tRNA Methyltransferases)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170908
[Lr] Data última revisão:
170908
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161223
[St] Status:MEDLINE
[do] DOI:10.1261/rna.059667.116


  8 / 855 MEDLINE  
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[PMID]:27852927
[Au] Autor:Urbonavicius J; Rutkiene R; Lopato A; Tauraite D; Stankeviciute J; Aucynaite A; Kaliniene L; van Tilbeurgh H; Meskys R
[Ad] Endereço:Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius 10222, Lithuania.
[Ti] Título:Evolution of tRNAPhe:imG2 methyltransferases involved in the biosynthesis of wyosine derivatives in Archaea.
[So] Source:RNA;22(12):1871-1883, 2016 Dec.
[Is] ISSN:1469-9001
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Tricyclic wyosine derivatives are found at position 37 of eukaryotic and archaeal tRNA In Archaea, the intermediate imG-14 is targeted by three different enzymes that catalyze the formation of yW-86, imG, and imG2. We have suggested previously that a peculiar methyltransferase (aTrm5a/Taw22) likely catalyzes two distinct reactions: N -methylation of guanosine to yield m G; and C -methylation of imG-14 to yield imG2. Here we show that the recombinant aTrm5a/Taw22-like enzymes from both Pyrococcus abyssi and Nanoarchaeum equitans indeed possess such dual specificity. We also show that substitutions of individual conservative amino acids of P. abyssi Taw22 (P260N, E173A, and R174A) have a differential effect on the formation of m G/imG2, while replacement of R134, F165, E213, and P262 with alanine abolishes the formation of both derivatives of G37. We further demonstrate that aTrm5a-type enzyme SSO2439 from Sulfolobus solfataricus, which has no N -methyltransferase activity, exhibits C -methyltransferase activity, thereby producing imG2 from imG-14. We thus suggest renaming such aTrm5a methyltransferases as Taw21 to distinguish between monofunctional and bifunctional aTrm5a enzymes.
[Mh] Termos MeSH primário: Archaea/metabolismo
Guanosina/análogos & derivados
Metiltransferases/metabolismo
RNA de Transferência de Fenilalanina/metabolismo
[Mh] Termos MeSH secundário: Sequência de Aminoácidos
Guanosina/biossíntese
Metiltransferases/química
RNA de Transferência de Fenilalanina/química
Homologia de Sequência de Aminoácidos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (RNA, Transfer, Phe); 12133JR80S (Guanosine); 52662-10-9 (wyosine); EC 2.1.1.- (Methyltransferases)
[Em] Mês de entrada:1707
[Cu] Atualização por classe:170706
[Lr] Data última revisão:
170706
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161118
[St] Status:MEDLINE


  9 / 855 MEDLINE  
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[PMID]:27289446
[Au] Autor:Basu P; Payghan PV; Ghoshal N; Suresh Kumar G
[Ad] Endereço:Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India.
[Ti] Título:Structural and thermodynamic analysis of the binding of tRNA(phe) by the putative anticancer alkaloid chelerythrine: Spectroscopy, calorimetry and molecular docking studies.
[So] Source:J Photochem Photobiol B;161:335-44, 2016 Aug.
[Is] ISSN:1873-2682
[Cp] País de publicação:Switzerland
[La] Idioma:eng
[Ab] Resumo:The interaction of the putative anticancer alkaloid chelerythrine with tRNA(phe) was characterized by spectroscopy, calorimetry and molecular docking studies. The charged iminium form of chelerythrine binds with tRNA(phe) in a cooperative mode with a binding affinity value of (4.06±0.01)×10(5)M(-1). The neutral alkanolamine form does not bind to tRNA(phe) but in the presence of high concentration of tRNA(phe) this form gets converted to the iminium form and then binds with tRNA(phe). The partial intercalative mode of binding of chelerythrine to the tRNA(phe) was characterized from the steady state anisotropy, iodide ion-induced fluorescence quenching and viscosity measurements. Chelerythrine binding induced conformational perturbations in tRNA(phe) as observed from the circular dichroism spectroscopy. The strong binding was also supported by the ethidium bromide displacement assay. The binding was favoured by both enthalpy and entropy contributions. Although the binding was dependent on the [Na(+)], non-electrostatic forces contributed predominantly to the Gibbs energy change. The negative value of the heat capacity change proposed the involvement of hydrophobic forces in the binding. Molecular docking study was carried out to decipher the details of the recognition of tRNA(phe) by chelerythrine. The study provided insights about the chelerythrine binding pockets on tRNA(phe) and marked the necessary interactions for binding of chelerythrine molecule. Partially intercalative mode of the alkaloid binding was supported by docking studies. In total, docking studies corroborated well with our experiential observations. The structural and thermodynamic results of chelerythrine binding to tRNA(phe) may be helpful to develop new RNA therapeutic agents.
[Mh] Termos MeSH primário: Benzofenantridinas/metabolismo
RNA de Transferência de Fenilalanina/metabolismo
[Mh] Termos MeSH secundário: Alcaloides/química
Alcaloides/metabolismo
Antineoplásicos/química
Antineoplásicos/metabolismo
Benzofenantridinas/química
Sítios de Ligação
Calorimetria
Dicroísmo Circular
Simulação de Acoplamento Molecular
Conformação de Ácido Nucleico
Concentração Osmolar
RNA de Transferência de Fenilalanina/química
Espectrometria de Fluorescência
Termodinâmica
Viscosidade
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Alkaloids); 0 (Antineoplastic Agents); 0 (Benzophenanthridines); 0 (RNA, Transfer, Phe); E3B045W6X0 (chelerythrine)
[Em] Mês de entrada:1703
[Cu] Atualização por classe:170313
[Lr] Data última revisão:
170313
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160613
[St] Status:MEDLINE


  10 / 855 MEDLINE  
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[PMID]:27226603
[Au] Autor:Moghal A; Hwang L; Faull K; Ibba M
[Ad] Endereço:From the Ohio State Biochemistry Program, Department of Microbiology, The Ohio State University, Columbus, Ohio 43210 and.
[Ti] Título:Multiple Quality Control Pathways Limit Non-protein Amino Acid Use by Yeast Cytoplasmic Phenylalanyl-tRNA Synthetase.
[So] Source:J Biol Chem;291(30):15796-805, 2016 07 22.
[Is] ISSN:1083-351X
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Non-protein amino acids, particularly isomers of the proteinogenic amino acids, present a threat to proteome integrity if they are mistakenly inserted into proteins. Quality control during aminoacyl-tRNA synthesis reduces non-protein amino acid incorporation by both substrate discrimination and proofreading. For example phenylalanyl-tRNA synthetase (PheRS) proofreads the non-protein hydroxylated phenylalanine derivative m-Tyr after its attachment to tRNA(Phe) We now show in Saccharomyces cerevisiae that PheRS misacylation of tRNA(Phe) with the more abundant Phe oxidation product o-Tyr is limited by kinetic discrimination against o-Tyr-AMP in the transfer step followed by o-Tyr-AMP release from the synthetic active site. This selective rejection of a non-protein aminoacyl-adenylate is in addition to known kinetic discrimination against certain non-cognates in the activation step as well as catalytic hydrolysis of mispaired aminoacyl-tRNA(Phe) species. We also report an unexpected resistance to cytotoxicity by a S. cerevisiae mutant with ablated post-transfer editing activity when supplemented with o-Tyr, cognate Phe, or Ala, the latter of which is not a substrate for activation by this enzyme. Our phenotypic, metabolomic, and kinetic analyses indicate at least three modes of discrimination against non-protein amino acids by S. cerevisiae PheRS and support a non-canonical role for SccytoPheRS post-transfer editing in response to amino acid stress.
[Mh] Termos MeSH primário: Fenilalanina-tRNA Ligase/metabolismo
Proteínas de Saccharomyces cerevisiae/metabolismo
Saccharomyces cerevisiae/enzimologia
[Mh] Termos MeSH secundário: Acilação
Monofosfato de Adenosina/genética
Monofosfato de Adenosina/metabolismo
Alanina/genética
Alanina/metabolismo
Mutação
Fenilalanina/genética
Fenilalanina/metabolismo
Fenilalanina-tRNA Ligase/genética
RNA Fúngico/genética
RNA Fúngico/metabolismo
RNA de Transferência de Fenilalanina/genética
RNA de Transferência de Fenilalanina/metabolismo
Saccharomyces cerevisiae/genética
Proteínas de Saccharomyces cerevisiae/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.
[Nm] Nome de substância:
0 (RNA, Fungal); 0 (RNA, Transfer, Phe); 0 (Saccharomyces cerevisiae Proteins); 415SHH325A (Adenosine Monophosphate); 47E5O17Y3R (Phenylalanine); EC 6.1.1.20 (Phenylalanine-tRNA Ligase); OF5P57N2ZX (Alanine)
[Em] Mês de entrada:1705
[Cu] Atualização por classe:171113
[Lr] Data última revisão:
171113
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160527
[St] Status:MEDLINE
[do] DOI:10.1074/jbc.M116.726828



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