Imagerie PI2

@article{,

title = {Crystal structure of glutamyl-queuosine tRNAAsp synthetase complexed with L-glutamate: structural elements mediating tRNA-independent activation of glutamate and glutamylation of tRNAAsp anticodon},

author = {M Blaise and V Olieric and C Sauter and B Lorber and B Roy and S Karmakar and R Banerjee and H D Becker and D Kern},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18602926},

isbn = {18602926},

year  = {2008},

date = {2008-01-01},

journal = {J Mol Biol},

volume = {381},

number = {5},

pages = {1224-1237},

abstract = {Glutamyl-queuosine tRNA(Asp) synthetase (Glu-Q-RS) from Escherichia coli is a paralog of the catalytic core of glutamyl-tRNA synthetase (GluRS) that catalyzes glutamylation of queuosine in the wobble position of tRNA(Asp). Despite important structural similarities, Glu-Q-RS and GluRS diverge strongly by their functional properties. The only feature common to both enzymes consists in the activation of Glu to form Glu-AMP, the intermediate of transfer RNA (tRNA) aminoacylation. However, both enzymes differ by the mechanism of selection of the cognate amino acid and by the mechanism of its activation. Whereas GluRS selects l-Glu and activates it only in the presence of the cognate tRNA(Glu), Glu-Q-RS forms Glu-AMP in the absence of tRNA. Moreover, while GluRS transfers the activated Glu to the 3' accepting end of the cognate tRNA(Glu), Glu-Q-RS transfers the activated Glu to Q34 located in the anticodon loop of the noncognate tRNA(Asp). In order to gain insight into the structural elements leading to distinct mechanisms of amino acid activation, we solved the three-dimensional structure of Glu-Q-RS complexed to Glu and compared it to the structure of the GluRS.Glu complex. Comparison of the catalytic site of Glu-Q-RS with that of GluRS, combined with binding experiments of amino acids, shows that a restricted number of residues determine distinct catalytic properties of amino acid recognition and activation by the two enzymes. Furthermore, to explore the structural basis of the distinct aminoacylation properties of the two enzymes and to understand why Glu-Q-RS glutamylates only tRNA(Asp) among the tRNAs possessing queuosine in position 34, we performed a tRNA mutational analysis to search for the elements of tRNA(Asp) that determine recognition by Glu-Q-RS. The analyses made on tRNA(Asp) and tRNA(Asn) show that the presence of a C in position 38 is crucial for glutamylation of Q34. The results are discussed in the context of the evolution and adaptation of the tRNA glutamylation system.},

note = {1089-8638 (Electronic) 

Journal Article 

Research Support, Non-U.S. Gov't},

keywords = {Adenosine Triphosphate/metabolism Amino Acid Sequence Amino Acyl-tRNA Synthetases/*chemistry Anticodon/*metabolism Base Sequence Binding Sites Catalysis Conserved Sequence Crystallography, Asp/*chemistry/genetics  Regulatory Sequences, FFRUGIER, Molecular  Molecular Sequence Data  Nucleic Acid Conformation  Nucleoside Q/*chemistry  Protein Structure, Ribonucleic Acid/*genetics  Thermus thermophilus/enzymology, Secondary  RNA, Transfer, Unité ARN, X-Ray  Escherichia coli/*enzymology  Escherichia coli Proteins/*chemistry  Glutamic Acid/*chemistry  Models},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Functional analysis of the translation factor aIF2/5B in the thermophilic archaeon Sulfolobus solfataricus},

author = {E Maone and M Di Stefano and A Berardi and D Benelli and S Marzi and A La Teana and P Londei},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17608795},

doi = {10.1111/j.1365-2958.2007.05820.x},

isbn = {17608795},

year  = {2007},

date = {2007-01-01},

journal = {Mol Microbiol},

volume = {65},

number = {3},

pages = {700-13},

abstract = {The protein IF2/eIF5B is one of the few translation initiation factors shared by all three primary domains of life (bacteria, archaea, eukarya). Despite its phylogenetic conservation, the factor is known to present marked functional divergences in the bacteria and the eukarya. In this work, the function in translation of the archaeal homologue (aIF2/5B) has been analysed in detail for the first time using a variety of in vitro assays. The results revealed that the protein is a ribosome-dependent GTPase which strongly stimulates the binding of initiator tRNA to the ribosomes even in the absence of other factors. In agreement with this finding, aIF2/5B enhances the translation of both leadered and leaderless mRNAs when expressed in a cell-free protein-synthesizing system. Moreover, the degree of functional conservation of the IF2-like factors in the archaeal and bacterial lineages was investigated by analysing the behaviour of 'chimeric' proteins produced by swapping domains between the Sulfolobus solfataricus aIF2/5B factor and the IF2 protein of the thermophilic bacterium Bacillus stearothermophilus. Beside evidencing similarities and differences between the archaeal and bacterial factors, these experiments have provided insight into the common role played by the IF2/5B proteins in all extant cells.},

note = {0950-382X (Print) 

0950-382X (Linking) 

Journal Article 

Research Support, Non-U.S. Gov't},

keywords = {Archaeal  Hydrolysis  Peptide Chain Initiation, Met/metabolism  Recombinant Fusion Proteins/metabolism  Ribosomes/metabolism  Sulfolobus solfataricus/genetics/*metabolism, Molecular  Conserved Sequence  GTP Phosphohydrolases/metabolism  Gene Expression  Genes, ROMBY, Secondary  RNA, Transfer, Translational  Peptide Initiation Factors/chemistry/isolation & purification/*metabolism  Protein Binding  *Protein Biosynthesis  Protein Structure, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Specific recognition of rpsO mRNA and 16S rRNA by Escherichia coli ribosomal protein S15 relies on both mimicry and site differentiation},

author = {N Mathy and O Pellegrini and A Serganov and D J Patel and C Ehresmann and C Portier},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15101974},

isbn = {15101974},

year  = {2004},

date = {2004-01-01},

journal = {Mol Microbiol},

volume = {52},

number = {3},

pages = {661-675},

abstract = {The ribosomal protein S15 binds to 16S rRNA, during ribosome assembly, and to its own mRNA (rpsO mRNA), affecting autocontrol of its expression. In both cases, the RNA binding site is bipartite with a common subsite consisting of a G*U/G-C motif. The second subsite is located in a three-way junction in 16S rRNA and in the distal part of a stem forming a pseudoknot in Escherichia coli rpsO mRNA. To determine the extent of mimicry between these two RNA targets, we determined which amino acids interact with rpsO mRNA. A plasmid carrying rpsO (the S15 gene) was mutagenized and introduced into a strain lacking S15 and harbouring an rpsO-lacZ translational fusion. Analysis of deregulated mutants shows that each subsite of rpsO mRNA is recognized by a set of amino acids known to interact with 16S rRNA. In addition to the G*U/G-C motif, which is recognized by the same amino acids in both targets, the other subsite interacts with amino acids also involved in contacts with helix H22 of 16S rRNA, in the region adjacent to the three-way junction. However, specific S15-rpsO mRNA interactions can also be found, probably with A(-46) in loop L1 of the pseudoknot, demonstrating that mimicry between the two targets is limited.},

note = {0950-382x 

Journal Article},

keywords = {16S/chemistry/genetics/*metabolism  Recombinant Fusion Proteins/metabolism  Ribosomal Proteins/chemistry/*genetics/*metabolism  Sequence Alignment  Support, Bacterial  Models, EHRESMANN  Amino Acid Sequence  Base Sequence  Escherichia coli Proteins/chemistry/genetics/*metabolism  Gene Expression Regulation, Messenger/metabolism  RNA, Molecular  *Molecular Mimicry  Molecular Sequence Data  Mutagenesis, Non-U.S. Gov't  Support, P.H.S., Ribosomal, Secondary  RNA, Site-Directed  Nucleic Acid Conformation  Protein Structure, U.S. Gov't, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Crystal structure of paromomycin docked into the eubacterial ribosomal decoding A site},

author = {Q Vicens and E Westhof},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11587639},

isbn = {11587639},

year  = {2001},

date = {2001-01-01},

journal = {Structure},

volume = {9},

number = {8},

pages = {647-658},

abstract = {BACKGROUND: Aminoglycoside antibiotics interfere with translation in both gram-positive and gram-negative bacteria by binding to the tRNA decoding A site of the 16S ribosomal RNA. RESULTS: Crystals of complexes between oligoribonucleotides incorporating the sequence of the ribosomal A site of Escherichia coli and the aminoglycoside paromomycin have been solved at 2.5 A resolution. Each RNA fragment contains two A sites inserted between Watson-Crick pairs. The paromomycin molecules interact in an enlarged deep groove created by two bulging and one unpaired adenines. In both sites, hydroxyl and ammonium side chains of the antibiotic form 13 direct hydrogen bonds to bases and backbone atoms of the A site. In the best-defined site, 8 water molecules mediate 12 other hydrogen bonds between the RNA and the antibiotics. Ring I of paromomycin stacks over base G1491 and forms pseudo-Watson-Crick contacts with A1408. Both the hydroxyl group and one ammonium group of ring II form direct and water-mediated hydrogen bonds to the U1495oU1406 pair. The bulging conformation of the two adenines A1492 and A1493 is stabilized by hydrogen bonds between phosphate oxygens and atoms of rings I and II. The hydrophilic sites of the bulging A1492 and A1493 contact the shallow groove of G=C pairs in a symmetrical complex. CONCLUSIONS: Water molecules participate in the binding specificity by exploiting the antibiotic hydration shell and the typical RNA water hydration patterns. The observed contacts rationalize the protection, mutation, and resistance data. The crystal packing mimics the intermolecular contacts induced by aminoglycoside binding in the ribosome.},

note = {0969-2126 

Journal Article},

keywords = {16S/*chemistry  Ribosomes/*chemistry  Spectrometry, Amino Acid Motifs  Anti-Bacterial Agents/chemistry  Base Sequence  Binding Sites  Crystallography, Mass, Matrix-Assisted Laser Desorption-Ionization  Support, Molecular  Molecular Sequence Data  Mutation  Paromomycin/*chemistry  Protein Structure, Non-U.S. Gov't  Tobramycin/chemistry  Water/chemistry, Ribosomal, Secondary  RNA, Unité ARN, X-Ray  Escherichia coli/metabolism  Magnetic Resonance Spectroscopy  Models},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Detailed analysis of RNA-protein interactions within the ribosomal protein S8-rRNA complex from the archaeon Methanococcus jannaschii},

author = {S Tishchenko and A Nikulin and N Fomenkova and N Nevskaya and O Nikonov and P Dumas and H Moine and B Ehresmann and C Ehresmann and W Piendl and V Lamzin and M Garber and S Nikonov},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11478863},

isbn = {11478863},

year  = {2001},

date = {2001-01-01},

journal = {J Mol Biol},

volume = {311},

number = {2},

pages = {311-324},

abstract = {The crystal structure of ribosomal protein S8 bound to its target 16 S rRNA from a hyperthermophilic archaeon Methanococcus jannaschii has been determined at 2.6 A resolution. The protein interacts with the minor groove of helix H21 at two sites located one helical turn apart, with S8 forming a bridge over the RNA major groove. The specificity of binding is essentially provided by the C-terminal domain of S8 and the highly conserved nucleotide core, characterized by two dinucleotide platforms, facing each other. The first platform (A595-A596), which is the less phylogenetically and structurally constrained, does not directly contact the protein but has an important shaping role in inducing cross-strand stacking interactions. The second platform (U641-A642) is specifically recognized by the protein. The universally conserved A642 plays a pivotal role by ensuring the cohesion of the complex organization of the core through an array of hydrogen bonds, including the G597-C643-U641 base triple. In addition, A642 provides the unique base-specific interaction with the conserved Ser105, while the Thr106 - Thr107 peptide link is stacked on its purine ring. Noteworthy, the specific recognition of this tripeptide (Thr-Ser-Thr/Ser) is parallel to the recognition of an RNA tetraloop by a dinucleotide platform in the P4-P6 ribozyme domain of group I intron. This suggests a general dual role of dinucleotide platforms in recognition of RNA or peptide motifs. One prominent feature is that conserved side-chain amino acids, as well as conserved bases, are essentially involved in maintaining tertiary folds. The specificity of binding is mainly driven by shape complementarity, which is increased by the hydrophobic part of side-chains. The remarkable similarity of this complex with its homologue in the T. thermophilus 30 S subunit indicates a conserved interaction mode between Archaea and Bacteria.},

note = {0022-2836 

Journal Article},

keywords = {16S/*chemistry/genetics/*metabolism  RNA-Binding Proteins/chemistry/metabolism  Ribosomal Proteins/*chemistry/*metabolism  Ribosomes/chemistry/genetics/metabolism  Sequence Alignment  Substrate Specificity  Support, Amino Acid Sequence  Archaeal Proteins/chemistry/metabolism  Bacteria/chemistry/genetics  Base Sequence  Binding Sites  Conserved Sequence/genetics  Crystallography, Archaeal/chemistry/genetics/metabolism  RNA, Molecular  Human  Hydrogen Bonding  Methanococcus/*chemistry/*genetics  Models, Molecular  Molecular Sequence Data  Nucleic Acid Conformation  Protein Binding  Protein Structure, Non-U.S. Gov't, Ribosomal, Secondary  RNA, Unité ARN, X-Ray  Evolution},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {The free yeast aspartyl-tRNA synthetase differs from the tRNA(Asp)-complexed enzyme by structural changes in the catalytic site, hinge region, and anticodon-binding domain},

author = {C Sauter and B Lorber and J Cavarelli and D Moras and R Giege},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10873455},

isbn = {10873455},

year  = {2000},

date = {2000-01-01},

journal = {J Mol Biol},

volume = {299},

number = {5},

pages = {1313-1324},

abstract = {Aminoacyl-tRNA synthetases catalyze the specific charging of amino acid residues on tRNAs. Accurate recognition of a tRNA by its synthetase is achieved through sequence and structural signalling. It has been shown that tRNAs undergo large conformational changes upon binding to enzymes, but little is known about the conformational rearrangements in tRNA-bound synthetases. To address this issue the crystal structure of the dimeric class II aspartyl-tRNA synthetase (AspRS) from yeast was solved in its free form and compared to that of the protein associated to the cognate tRNA(Asp). The use of an enzyme truncated in N terminus improved the crystal quality and allowed us to solve and refine the structure of free AspRS at 2.3 A resolution. For the first time, snapshots are available for the different macromolecular states belonging to the same tRNA aminoacylation system, comprising the free forms for tRNA and enzyme, and their complex. Overall, the synthetase is less affected by the association than the tRNA, although significant local changes occur. They concern a rotation of the anticodon binding domain and a movement in the hinge region which connects the anticodon binding and active-site domains in the AspRS subunit. The most dramatic differences are observed in two evolutionary conserved loops. Both are in the neighborhood of the catalytic site and are of importance for ligand binding. The combination of this structural analysis with mutagenesis and enzymology data points to a tRNA binding process that starts by a recognition event between the tRNA anticodon loop and the synthetase anticodon binding module.},

note = {0022-2836 

Journal Article},

keywords = {Anticodon/chemistry/genetics/*metabolism  Aspartate-tRNA Ligase/*chemistry/genetics/*metabolism  Binding Sites  Catalytic Domain  Conserved Sequence/genetics  Crystallization  Crystallography, Asp/chemistry/genetics/*metabolism  Rotation  Sequence Deletion/genetics  Support, Fungal/chemistry/genetics/metabolism  RNA, Molecular  Molecular Sequence Data  Movement  Nucleic Acid Conformation  Protein Structure, Non-U.S. Gov't  Yeasts/*enzymology/genetics, Secondary  RNA, Transfer, Unité ARN, X-Ray  Models},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {The ribosomal protein S8 from Thermus thermophilus VK1. Sequencing of the gene, overexpression of the protein in Escherichia coli and interaction with rRNA},

author = {V Vysotskaya and S Tischenko and M Garber and D Kern and M Mougel and C Ehresmann and B Ehresmann},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7519982},

isbn = {7519982},

year  = {1994},

date = {1994-01-01},

journal = {Eur J Biochem},

volume = {223},

number = {2},

pages = {437-445},

abstract = {The gene of the ribosomal protein S8 from Thermus thermophilus VK1 has been isolated from a genomic library by hybridization of an oligonucleotide coding for the N-terminal amino acid sequence of the protein, amplified by PCR and sequenced. Nucleotide sequence reveals an open reading frame coding for a protein of 138 amino acid residues (M(r) 15,839). The codon usage shows that 94% of the codons possess G or C in the third position, and agrees with the preferential usage of codons of high G+C content in the bacteria of the genus Thermus. The amino acid sequence of the protein shows 48% identity with the protein from Escherichia coli. Ribosomal protein S8 from T. thermophilus has been expressed in E. coli under the control of the T7 promoter and purified to homogeneity by heat treatment of the extract followed by cation-exchange chromatography. Conditions were defined in which T. thermophilus protein S8 binds specifically an homologous 16S rRNA fragment containing the putative S8 binding site with an apparent association constant of 5 x 10(7) M-1. The overexpressed protein binds the rRNA with the same affinity as that extracted from T. thermophilus, indicating that the thermophilic protein is correctly folded in E. coli. The specificity of this binding is dependent on the ionic strength. The protein S8 from T. thermophilus recognizes the E. coli rRNA binding sites as efficiently as the S8 protein from E. coli. This result agrees with sequence comparisons of the S8 binding site on the small subunit rRNA from E. coli and from T. thermophilus, showing strong similarities in the regions involved in the interaction. It suggests that the structural features responsible for the recognition are conserved in the mesophilic and thermophilic eubacteria, despite structural peculiarities in the thermophilic partners conferring thermostability.},

note = {0014-2956 

Journal Article},

keywords = {16S/*metabolism  Recombinant Proteins/metabolism  Ribosomal Proteins/chemistry/*genetics/isolation & purification/metabolism  Sequence Alignment  Support, Amino Acid Sequence  Base Sequence  Blotting, Bacterial  Molecular Sequence Data  Molecular Weight  Nucleic Acid Hybridization  Polymerase Chain Reaction  Promoter Regions (Genetics)  Protein Binding  Protein Structure, Bacterial/chemistry/genetics/isolation & purification  Escherichia coli/genetics/metabolism  *Gene Expression  *Genes, Bacterial/metabolism  RNA, Genetic, Molecular  DNA, Non-U.S. Gov't  Thermus thermophilus/*genetics  Transcription, Ribosomal, Secondary  RNA, Southern  Cloning, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Translational regulation of the Escherichia coli threonyl-tRNA synthetase gene: structural and functional importance of the thrS operator domains},

author = {C Brunel and P Romby and H Moine and J Caillet and M Grunberg-Manago and M Springer and B Ehresmann and C Ehresmann},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8199252},

isbn = {8199252},

year  = {1993},

date = {1993-01-01},

journal = {Biochimie},

volume = {75},

number = {12},

pages = {1167-1179},

abstract = {Previous work showed that E coli threonyl-tRNA synthetase (ThrRS) binds to the leader region of its own mRNA and represses its translation by blocking ribosome binding. The operator consists of four distinct domains, one of them (domain 2) sharing structural analogies with the anticodon arm of the E coli tRNA(Thr). The regulation specificity can be switched by using tRNA identity rules, suggesting that the operator could be recognized by ThrRS as a tRNA-like structure. In the present paper, we investigated the relative contribution of the four domains to the regulation process by using deletions and point mutations. This was achieved by testing the effects of the mutations on RNA conformation (by probing experiments), on ThrRS recognition (by footprinting experiments and measure of the competition with tRNA(Thr) for aminoacylation), on ribosome binding and ribosome/ThrRS competition (by toeprinting experiments). It turns out that: i) the four domains are structurally and functionally independent; ii) domain 2 is essential for regulation and contains the major structural determinants for ThrRS binding; iii) domain 4 is involved in control and ThrRS recognition, but to a lesser degree than domain 2. However, the previously described analogies with the acceptor-like stem are not functionally significant. How it is recognized by ThrRS remains to be resolved; iv) domain 1, which contains the ribosome loading site, is not involved in ThrRS recognition. The binding of ThrRS probably masks the ribosome binding site by steric hindrance and not by direct contacts. This is only achieved when ThrRS interacts with both domains 2 and 4; and v) the unpaired domain 3, which connects domains 2 and 4, is not directly involved in ThrRS recognition. It should serve as an articulation to provide an appropriate spacing between domains 2 and 4. Furthermore, it is possibly involved in ribosome binding.},

note = {0300-9084 

Journal Article},

keywords = {Bacterial/*genetics  Molecular Sequence Data  Mutation  Nucleic Acid Conformation  *Operator Regions (Genetics)  Point Mutation  Protein Structure, Base Sequence  Escherichia coli/*enzymology/genetics  Gene Deletion  Gene Expression Regulation, Genetic, Messenger/chemistry/metabolism  RNA, Met/chemistry/metabolism  Ribosomes/metabolism  Structure-Activity Relationship  Support, Non-U.S. Gov't  Threonine-tRNA Ligase/chemistry/*genetics/metabolism  Translation, ROMBY, Secondary  RNA, Transfer, Unité ARN},

pubstate = {published},

tppubtype = {article}

}