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8 results on '"MESH: Nitrogenous Group Transferases"'

1. Structure-Based Site-Directed Mutagenesis of the UDP-MurNAc-Pentapeptide-Binding Cavity of the FemX Alanyl Transferase from Weissella viridescens

Author

Wladimir Sougakoff, Sabrina Biarrotte-Sorin, Claudine Mayer, Michel Arthur, Stéphane Mesnage, Antoine P. Maillard, Régis Villet, Ahmed Bouhss, Pathogenèse bactérienne et réponses cellulaires (PBRC), Biologie du Cancer et de l'Infection (BCI ), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Krebs Inst, University of Sheffield [Sheffield], Institut de biochimie et biophysique moléculaire et cellulaire (IBBMC), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Centre d'Immunologie et de Maladies Infectieuses (CIMI), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot - Paris 7 (UPD7), Centre de Recherche des Cordeliers (CRC), Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC), Université Pierre et Marie Curie - Paris 6 (UPMC)-École pratique des hautes études (EPHE), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Université Paris Diderot - Paris 7 (UPD7)-École pratique des hautes études (EPHE)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
Peptidyl transferase, Nitrogenous Group Transferases, [SDV]Life Sciences [q-bio], MESH: Catalytic Domain, Peptide, MESH: Nitrogenous Group Transferases, Biology, Microbiology, MESH: Protein Structure, Tertiary, 03 medical and health sciences, chemistry.chemical_compound, Catalytic Domain, Transferase, Binding site, Site-directed mutagenesis, Molecular Biology, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Binding Sites, Crystallography, MESH: Kinetics, 030306 microbiology, MESH: Crystallography, Mutagenesis, Enzymes and Proteins, MESH: Amino Acid Substitution, Uridine Diphosphate N-Acetylmuramic Acid, Protein Structure, Tertiary, Amino acid, carbohydrates (lipids), Kinetics, Lactobacillus, MESH: Mutagenesis, Site-Directed, Amino Acid Substitution, MESH: Binding Sites, chemistry, Biochemistry, Mutagenesis, Site-Directed, MESH: Uridine Diphosphate N-Acetylmuramic Acid, biology.protein, Peptidoglycan, MESH: Lactobacillus
Abstract

Weissella viridescens FemX (FemX Wv ) belongs to the Fem family of nonribosomal peptidyl transferases that use aminoacyl-tRNA as the amino acid donor to synthesize the peptide cross-bridge found in the peptidoglycan of many species of pathogenic gram-positive bacteria. We have recently solved the crystal structure of FemX Wv in complex with the peptidoglycan precursor UDP-MurNAc-pentapeptide and report here the site-directed mutagenesis of nine residues located in the binding cavity for this substrate. Two substitutions, Lys36Met and Arg211Met, depressed FemX Wv transferase activity below detectable levels without affecting protein folding. Analogues of UDP-MurNAc-pentapeptide lacking the phosphate groups or the C-terminal d -alanyl residues were not substrates of the enzyme. These results indicate that Lys36 and Arg211 participate in a complex hydrogen bond network that connects the C-terminal d -Ala residues to the phosphate groups of UDP-MurNAc-pentapeptide and constrains the substrate in a conformation that is essential for transferase activity.

Published
2005
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2. Crystal structure of a transfer-ribonucleoprotein particle that promotes asparagine formation

Author

Mathieu Frechin, Frédéric Fischer, Hubert Dominique Becker, Daniel Kern, Manja A. Behrens, Marc Bailly, Jan Skov Pedersen, Cristiano L. P. Oliveira, Mickaël Blaise, Søren Thirup, Department of Molecular Biology, University of Aarhus, Architecture et Réactivité de l'ARN (ARN), Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Architecture et réactivité de l'ARN (ARN), and Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS)

Subjects
MESH: Asparagine, Stereochemistry, Protein Conformation, [SDV]Life Sciences [q-bio], MESH: RNA, Transfer, Asn, Nitrogenous Group Transferases, MESH: Thermus thermophilus, MESH: Nitrogenous Group Transferases, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, MESH: Protein Conformation, Protein structure, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Asparagine, Molecular Biology, ComputingMilieux_MISCELLANEOUS, MESH: Crystallization, 030304 developmental biology, Ribonucleoprotein, Glutamine amidotransferase, 0303 health sciences, General Immunology and Microbiology, biology, RNA, Transfer, Asn, General Neuroscience, Thermus thermophilus, 030302 biochemistry & molecular biology, Ribonucleoprotein particle, Active site, biology.organism_classification, MESH: Ribonucleoproteins, MESH: Transfer RNA Aminoacylation, Biochemistry, Ribonucleoproteins, Transfer RNA, biology.protein, Transfer RNA Aminoacylation, Crystallization
Abstract

International audience; Four out of the 22 aminoacyl-tRNAs (aa-tRNAs) are systematically or alternatively synthesized by an indirect, two-step route requiring an initial mischarging of the tRNA followed by tRNA-dependent conversion of the non-cognate amino acid. During tRNA-dependent asparagine formation, tRNA(Asn) promotes assembly of a ribonucleoprotein particle called transamidosome that allows channelling of the aa-tRNA from non-discriminating aspartyl-tRNA synthetase active site to the GatCAB amidotransferase site. The crystal structure of the Thermus thermophilus transamidosome determined at 3 A resolution reveals a particle formed by two GatCABs, two dimeric ND-AspRSs and four tRNAs(Asn) molecules. In the complex, only two tRNAs are bound in a functional state, whereas the two other ones act as an RNA scaffold enabling release of the asparaginyl-tRNA(Asn) without dissociation of the complex. We propose that the crystal structure represents a transient state of the transamidation reaction. The transamidosome constitutes a transfer-ribonucleoprotein particle in which tRNAs serve the function of both substrate and structural foundation for a large molecular machine.

Published
2010
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3. Translating organellar glutamine codons: a case by case scenario?

Author

Mathieu Frechin, Hubert Dominique Becker, Anne-Marie Duchêne, Architecture et Réactivité de l'ARN (ARN), Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie moléculaire des plantes (IBMP), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Génétique moléculaire, génomique, microbiologie (GMGM), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), and Martin, Isabelle

Subjects
Chloroplasts, Glutamine, Nitrogenous Group Transferases, MESH: Plants, MESH: Nitrogenous Group Transferases, Mitochondrion, Genome, Cytosol, 0302 clinical medicine, RNA, Transfer, MESH: Cytosol, MESH: Animals, ComputingMilieux_MISCELLANEOUS, chemistry.chemical_classification, 0303 health sciences, biology, MESH: Codon, MESH: Glutamate-tRNA Ligase, Plants, Mitochondria, Amino acid, Biochemistry, 030220 oncology & carcinogenesis, Transfer RNA, Eukaryote, MESH: Mitochondria, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Models, Biological, Amino Acyl-tRNA Synthetases, 03 medical and health sciences, Organelle, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, RNA, Messenger, MESH: Amino Acyl-tRNA Synthetases, Codon, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, Molecular Biology, Gene, tRNA, 030304 developmental biology, Glutamine amidotransferase, MESH: RNA, Messenger, MESH: Glutamine, MESH: Chloroplasts, MESH: Models, Biological, Cell Biology, biology.organism_classification, MESH: RNA, Transfer, Glutamate-tRNA Ligase, chemistry
Abstract

International audience; Aminoacyl-tRNAs are generally formed by direct attachment of an amino acid to tRNAs by aminoacyl-tRNA synthetases, but glutaminyl-tRNA (Q-tRNA) is an exception to this rule. Glutaminyl-tRNA(Gln) (Q-tRNA(Q)) is formed by this direct pathway in the eukaryotic cytosol and in a small subset of bacteria, but is formed by an indirect transamidation pathway in most bacteria and archaea. To date it is almost impossible to predict what pathway generates organellar Q-tRNA(Q) in a given eukaryote. All eukaryotic genomes sequenced so far, display a single glutaminyl-tRNA synthetase (QRS) gene which is at least responsible for the cytosolic QRS activity, as well as a gene coding for a mitochondrial ortholog of the essential GatB subunit of the tRNA-dependent amidotransferase (AdT). Indeed, QRS activity was found in protozoan mitochondria while AdT activity was characterized in plant organelles. The pathway for Q-tRNA(Q) synthesis in yeast and mammals mitochondria is still questionable.

Published
2009
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4. tRNA-dependent asparagine formation in prokaryotes: Characterization, isolation and structural and functional analysis of a ribonucleoprotein particle generating Asn-tRNAAsn

Author

Bernard Lorber, Hubert Dominique Becker, Catherine Birck, Marzanna Deniziak, Hervé Roy, Mickaël Blaise, Daniel Kern, Marc Bailly, Architecture et réactivité de l'ARN (ARN), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de génétique et biologie moléculaire et cellulaire (IGBMC), Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Louis Pasteur - Strasbourg I

Subjects
MESH: Asparagine, Light, Operon, Nitrogenous Group Transferases, MESH: RNA, Transfer, Asn, [SDV]Life Sciences [q-bio], MESH: Nitrogenous Group Transferases, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Scattering, Radiation, TRNA aminoacylation, Transfer RNA Aminoacylation, MESH: Scattering, Radiation, Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Glutamine amidotransferase, Ribonucleoprotein, MESH: Crystallization, MESH: Prokaryotic Cells, 0303 health sciences, RNA, Transfer, Asn, biology, 030302 biochemistry & molecular biology, MESH: Ultracentrifugation, Ribonucleoprotein particle, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Thermus thermophilus, biology.organism_classification, MESH: Light, MESH: Ribonucleoproteins, MESH: Transfer RNA Aminoacylation, Prokaryotic Cells, Ribonucleoproteins, Biochemistry, Transfer RNA, Asparagine, Crystallization, Ultracentrifugation
Abstract

In some living organisms the 20 aa-tRNA species participating in protein synthesis are not charged by a complete set of 20 aminoacyl-tRNA synthetases. In prokaryotes, the deficiency of asparaginyl- and/or glutaminyl-tRNA synthetases is compensated by another aminoacyl-tRNA synthetase of relaxed specificity that mischarges the orphan tRNA and by an enzyme that converts the amino acid into that homologous to the tRNA. In Thermus thermophilus Asn-tRNA(Asn) is formed indirectly via a two-step pathway whereby tRNA(Asn) is mischarged with Asp that will subsequently be amidated into Asn by an amidotransferase. The non-discriminating aspartyl-tRNA synthetase, the trimeric GatCAB tRNA-dependent amidotransferase and the tRNA(Asn) promoting this pathway assemble into a ribonucleoprotein particle termed transamidosome. This article deals with the methods and techniques employed to clone the genes encoding the enzymes and the tRNA involved in this pathway, to express them in Escherichia coli, to isolate them on a large scale, and to transcribe and produce mg quantities of pure tRNA(Asn)in vitro. The approaches designed especially for this system include (i) clustering of the ORFs encoding the subunits of the heterotrimeric GatCAB that are sprinkled in the genome into an artificial operon, and (ii) the self-cleavage of the tRNA(Asn) transcript starting with U in 5' position through fusion with a hammerhead ribozyme. Further, the crystallization of the free enzymes is described and the characterization of their assembly with tRNA(Asn) into a ribonucleoprotein particle, as well as the investigation of the catalytic mechanism of Asn-tRNA(Asn) formation by the complex are reported.

Published
2008
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5. Dual-targeted tRNA-dependent amidotransferase ensures both mitochondrial and chloroplastic Gln-tRNAGln synthesis in plants

Author

Daniel Kern, Laurence Maréchal-Drouard, Anne-Marie Duchêne, Claire Pujol, Marc Bailly, Hubert Dominique Becker, Institut de biologie moléculaire des plantes (IBMP), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Architecture et réactivité de l'ARN (ARN), and Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS)

Subjects
Cell Extracts, MESH: Protein Transport, Chloroplasts, MESH: Mitochondria, Glutamine, Nitrogenous Group Transferases, Protein subunit, Arabidopsis, MESH: Nitrogenous Group Transferases, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, RNA, Transfer, Amino Acyl, Mitochondrion, Biology, MESH: Solanum tuberosum, 03 medical and health sciences, Cytosol, MESH: Cytosol, MESH: Cell Extracts, MESH: RNA, Transfer, Amino Acyl, Glutamate—tRNA ligase, MESH: Arabidopsis, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Solanum tuberosum, 030304 developmental biology, Glutamine amidotransferase, chemistry.chemical_classification, 0303 health sciences, MESH: Glutamine, Multidisciplinary, MESH: Chloroplasts, MESH: Glutamate-tRNA Ligase, 030302 biochemistry & molecular biology, Biological Sciences, MESH: Protein Subunits, Mitochondria, Amino acid, Chloroplast, Glutamate-tRNA Ligase, Protein Subunits, Protein Transport, Biochemistry, chemistry, Transfer RNA
Abstract

Aminoacyl-tRNAs are generally formed by direct attachment of an amino acid to tRNAs by aminoacyl-tRNA synthetases, but Gln-tRNA is an exception to this rule. Gln-tRNA Gln is formed by this direct pathway in the eukaryotic cytosol and in protists or fungi mitochondria but is formed by an indirect transamidation pathway in most of bacteria, archaea, and chloroplasts. We show here that the formation of Gln-tRNA Gln is also achieved by the indirect pathway in plant mitochondria. The mitochondrial-encoded tRNA Gln , which is the only tRNA Gln present in mitochondria, is first charged with glutamate by a nondiscriminating GluRS, then is converted into Gln-tRNA Gln by a tRNA-dependent amidotransferase (AdT). The three subunits GatA, GatB, and GatC are imported into mitochondria and assemble into a functional GatCAB AdT. Moreover, the mitochondrial pathway of Gln-tRNA Gln formation is shared with chloroplasts as both the GluRS, and the three AdT subunits are dual-imported into mitochondria and chloroplasts.

Published
2008
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6. Structural basis of RNA-dependent recruitment of glutamine to the genetic code

Author

Yuko Nakamura, Osamu Nureki, Sylvain Blanquet, Hiroyuki Oshikane, Shuya Fukai, Dieter Söll, Kelly Sheppard, Yves Mechulam, R. Lynn Sherrer, Ryuichiro Ishitani, Tomoyuki Numata, Michel Panvert, Liang Feng, Emmanuelle Schmitt, Department of biological information-Tokyo Institute of Technology (DBI), Tokyo Institute of Technology [Tokyo] (TITECH), Department of Molecular Biophysics and Biochemistry-Yale (DMBB), Yale University [New Haven], Laboratoire de Biochimie de l'Ecole polytechnique (BIOC), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), and CNRS-Ecole Polytechnique

Subjects
Models, Molecular, MESH: Protein Structure, Quaternary, Acylation, Glutamine, Nitrogenous Group Transferases, Mutant, MESH: Protein Structure, Secondary, MESH: Catalytic Domain, RNA, Archaeal, MESH: Nitrogenous Group Transferases, Crystallography, X-Ray, Protein Structure, Secondary, MESH: Protein Structure, Tertiary, Adenosine Triphosphate, Catalytic Domain, RNA, Transfer, Gln, MESH: Adenosine Triphosphate, MESH: Magnesium, Magnesium, MESH: Ammonia, Multidisciplinary, biology, Glutaminase, MESH: RNA, Transfer, Gln, Genetic code, MESH: Nucleic Acid Conformation, Biochemistry, Genetic Code, Transfer RNA, Dimerization, MESH: Models, Molecular, Methanobacteriaceae, MESH: Mutation, Stereochemistry, MESH: Computer Simulation, Ammonia, Anticodon, MESH: Anticodon, Computer Simulation, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: Hydrogen Bonding, Protein Structure, Quaternary, Glutamine amidotransferase, MESH: Acylation, MESH: Glutamine, Binding Sites, MESH: Methanobacteriaceae, RNA, Hydrogen Bonding, biology.organism_classification, MESH: Crystallography, X-Ray, MESH: Genetic Code, Protein Structure, Tertiary, MESH: Binding Sites, MESH: Dimerization, Mutation, Nucleic Acid Conformation, MESH: RNA, Archaeal, Archaea
Abstract

Glutaminyl–transfer RNA (Gln-tRNA Gln ) in archaea is synthesized in a pretranslational amidation of misacylated Glu-tRNA Gln by the heterodimeric Glu-tRNA Gln amidotransferase GatDE. Here we report the crystal structure of the Methanothermobacter thermautotrophicus GatDE complexed to tRNA Gln at 3.15 angstroms resolution. Biochemical analysis of GatDE and of tRNA Gln mutants characterized the catalytic centers for the enzyme's three reactions (glutaminase, kinase, and amidotransferase activity). A 40 angstrom–long channel for ammonia transport connects the active sites in GatD and GatE. tRNA Gln recognition by indirect readout based on shape complementarity of the D loop suggests an early anticodon-independent RNA-based mechanism for adding glutamine to the genetic code.

Published
2006
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7. Structural basis for tRNA-dependent amidotransferase function

Author

Emmanuelle Schmitt, Yves Mechulam, Michel Panvert, Sylvain Blanquet, Laboratoire de Biochimie de l'Ecole polytechnique (BIOC), and Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)

Subjects
Models, Molecular, Threonine, Protein Folding, Pyrococcus abyssi, MESH: Sequence Homology, Amino Acid, Nitrogenous Group Transferases, MESH: Protein Structure, Secondary, RNA, Archaeal, MESH: Amino Acid Sequence, MESH: Nitrogenous Group Transferases, Crystallography, X-Ray, Protein Structure, Secondary, MESH: Protein Structure, Tertiary, RNA, Transfer, X-Ray Diffraction, Structural Biology, RNA, Transfer, Gln, Protein biosynthesis, MESH: Threonine, MESH: Pyrococcus abyssi, Conserved Sequence, chemistry.chemical_classification, MESH: Conserved Sequence, MESH: Glutamate-tRNA Ligase, MESH: X-Ray Diffraction, MESH: RNA, Transfer, Gln, MESH: Protein Subunits, Amino acid, RNA, Bacterial, Biochemistry, MESH: Protein Biosynthesis, Transfer RNA, MESH: RNA, Bacterial, Dimerization, MESH: Models, Molecular, MESH: Protein Folding, Molecular Sequence Data, Biology, Amino Acyl-tRNA Synthetases, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, MESH: Amino Acyl-tRNA Synthetases, Molecular Biology, Glutamine amidotransferase, Binding Sites, MESH: Molecular Sequence Data, Sequence Homology, Amino Acid, biology.organism_classification, Lyase, MESH: RNA, Transfer, MESH: Crystallography, X-Ray, TRNA binding, Protein Structure, Tertiary, Glutamate-tRNA Ligase, Protein Subunits, chemistry, MESH: Binding Sites, MESH: Dimerization, Protein Biosynthesis, MESH: RNA, Archaeal
Abstract

International audience; Besides direct charging of tRNAs by aminoacyl-tRNA synthetases, indirect routes also ensure attachment of some amino acids onto tRNA. Such routes may explain how new amino acids entered into protein synthesis. In archaea and in most bacteria, tRNA(Gln) is first misaminoacylated by glutamyl-tRNA synthetase. Glu-tRNA(Gln) is then matured into Gln-tRNA(Gln) by a tRNA-dependent amidotransferase. We report the structure of a tRNA-dependent amidotransferase-that of GatDE from Pyrococcus abyssi. The 3.0 A resolution crystal structure shows a tetramer with two GatD molecules as the core and two GatE molecules at the periphery. The fold of GatE cannot be related to that of any tRNA binding enzyme. The ammonium donor site on GatD and the tRNA site on GatE are markedly distant. Comparison of GatD and L-asparaginase structures shows how the motion of a beta hairpin region containing a crucial catalytic threonine may control the overall reaction cycle of GatDE.

Published
2005
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8. Crystal Structures of Weissella viridescens FemX and Its Complex with UDP-MurNAc-Pentapeptide: Insights into FemABX Family Substrates Recognition

Author

Claudine Mayer, Sabrina Biarrotte-Sorin, Jean Delettré, Wladimir Sougakoff, Antoine P. Maillard, Michel Arthur, Pathogenèse bactérienne et réponses cellulaires (PBRC), Biologie du Cancer et de l'Infection (BCI ), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de minéralogie, cristallographie de Paris (LMCP), Université Pierre et Marie Curie - Paris 6 (UPMC)-IPG PARIS-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Centre d'Immunologie et de Maladies Infectieuses (CIMI), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC), Centre de Recherche des Cordeliers (CRC), Université Pierre et Marie Curie - Paris 6 (UPMC)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Diderot - Paris 7 (UPD7), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Institut de Physique du Globe de Paris (IPG Paris)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Université Paris Diderot - Paris 7 (UPD7)-École pratique des hautes études (EPHE)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
Models, Molecular, Protein family, Stereochemistry, MESH: Sequence Homology, Amino Acid, Nitrogenous Group Transferases, [SDV]Life Sciences [q-bio], Molecular Sequence Data, MESH: Amino Acid Sequence, MESH: Nitrogenous Group Transferases, Biology, Crystallography, X-Ray, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, MESH: Protein Structure, Tertiary, Bacterial Proteins, Structural Biology, MESH: Leuconostoc, Transferase, Amino Acid Sequence, Binding site, Molecular Biology, MESH: Bacterial Proteins, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, DNA ligase, MESH: Molecular Sequence Data, Sequence Homology, Amino Acid, 010405 organic chemistry, MESH: Crystallography, X-Ray, Uridine Diphosphate N-Acetylmuramic Acid, Protein Structure, Tertiary, 0104 chemical sciences, Amino acid, carbohydrates (lipids), chemistry, Biochemistry, Docking (molecular), Transfer RNA, MESH: Uridine Diphosphate N-Acetylmuramic Acid, Peptidoglycan, Leuconostoc, MESH: Models, Molecular
Abstract

International audience; Members of the FemABX protein family are novel therapeutic targets, as they are involved in the synthesis of the bacterial cell wall. They catalyze the addition of amino acid(s) on the peptidoglycan precursor using aminoacylated tRNA as a substrate. We report here the high-resolution structure of Weissella viridescens L-alanine transferase FemX and its complex with the UDP-MurNAc-pentapeptide. This is the first structure example of a FemABX family member that does not possess a coiled-coil domain. FemX consists of two structurally equivalent domains, separated by a cleft containing the binding site of the UDP-MurNAc-pentapeptide and a long channel that traverses one of the two domains. Our structural studies bring new insights into the evolution of the FemABX and the related GNAT superfamilies, shed light on the recognition site of the aminoacylated tRNA in Fem proteins, and allowed manual docking of the acceptor end of the alanyl-tRNAAla.

Published
2004
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