Pfister P, Hobbie S, Vicens Q, Bottger E C, Westhof E
The molecular basis for A-site mutations conferring aminoglycoside resistance: relationship between ribosomal susceptibility and X-ray crystal structures Article de journal
Dans: Chembiochem, vol. 4, no. 10, p. 1078-1088, 2003, ISBN: 14523926, (1439-4227 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Aminoglycosides/*pharmacology Anti-Bacterial Agents/*pharmacology Binding Sites Comparative Study Crystallography, Bacterial/genetics Ribosomes/*chemistry/drug effects/metabolism Species Specificity Structure-Activity Relationship Support, Molecular Mutagenesis, Non-U.S. Gov't, Site-Directed Nucleic Acid Conformation Oligonucleotides/chemistry/metabolism Plasmids Point Mutation/drug effects RNA, Unité ARN, WESTHOF, X-Ray Drug Design Drug Resistance Escherichia coli/genetics/metabolism Hemagglutinins Models
@article{,
title = {The molecular basis for A-site mutations conferring aminoglycoside resistance: relationship between ribosomal susceptibility and X-ray crystal structures},
author = {P Pfister and S Hobbie and Q Vicens and E C Bottger and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14523926},
isbn = {14523926},
year = {2003},
date = {2003-01-01},
journal = {Chembiochem},
volume = {4},
number = {10},
pages = {1078-1088},
abstract = {Aminoglycoside antibiotics target the 16S ribosomal RNA (rRNA) bacterial A site and induce misreading of the genetic code. Point mutations of the ribosomal A site may confer resistance to aminoglycoside antibiotics. The influence of bacterial mutations (introduced by site-directed mutagenesis) on ribosomal drug susceptibility was investigated in vivo by determination of minimal inhibitory concentrations. To determine the origin of the various resistance phenotypes at a molecular level, the in vivo results were compared with the previously published crystal structures of paromomycin, tobramycin, and geneticin bound to oligonucleotides containing the minimal A site. Two regions appear crucial for binding in the A site: the single adenine residue at position 1408 and the non-Watson-Crick U1406.U1495 pair. The effects of mutations at those positions are modulated by the nature of the substituent at position 6' (either hydroxy or ammonium group) on ring I, by the number of positive charges on the antibiotic, and by the linkage between rings I and III (either 4,5 or 4,6). In particular, the analysis demonstrates: 1) that the C1409-G1491 to A1409-U1491 polymorphism (observed in 15 % of bacteria) is not associated with resistance, which indicates that it does not affect the stacking of ring I on residue 1491, 2) that the high-level resistance to 6'-NH3+ aminoglycosides exhibited by the A1408G mutation most probably results from the inability of ring I forming a pseudo base pair with G1408, which prevents its insertion inside the A site helix, and 3) that mutations of the uracil residues forming the U1406.U1495 pair either to cytosine or to adenine residues mostly confer low to moderate levels of drug resistance, whereas the U1406C/U1495A double mutation confers high-level resistance (except for neomycin), which suggests that aminoglycoside binding to the wild-type A site and its functional consequences strongly depend on a particular geometry of the U1406.U1495 pair. The relationships between the resistance phenotypes observed in vivo and the interactions described at the molecular level define the biological importance of the different structural interactions observed by X-ray crystallography studies.},
note = {1439-4227
Journal Article},
keywords = {Aminoglycosides/*pharmacology Anti-Bacterial Agents/*pharmacology Binding Sites Comparative Study Crystallography, Bacterial/genetics Ribosomes/*chemistry/drug effects/metabolism Species Specificity Structure-Activity Relationship Support, Molecular Mutagenesis, Non-U.S. Gov't, Site-Directed Nucleic Acid Conformation Oligonucleotides/chemistry/metabolism Plasmids Point Mutation/drug effects RNA, Unité ARN, WESTHOF, X-Ray Drug Design Drug Resistance Escherichia coli/genetics/metabolism Hemagglutinins Models},
pubstate = {published},
tppubtype = {article}
}
Paillart J C, Westhof E, Ehresmann C, Ehresmann B, Marquet R
Non-canonical interactions in a kissing loop complex: the dimerization initiation site of HIV-1 genomic RNA Article de journal
Dans: J Mol Biol, vol. 270, no. 1, p. 36-49, 1997, ISBN: 9231899, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Dimerization HIV-1/*genetics Kinetics Models, MARQUET, Molecular Mutagenesis, Non-U.S. Gov't, PAILLART, Site-Directed Nucleic Acid Conformation Purines/chemistry RNA, Unité ARN, Viral/*chemistry/genetics/*metabolism Support
@article{,
title = {Non-canonical interactions in a kissing loop complex: the dimerization initiation site of HIV-1 genomic RNA},
author = {J C Paillart and E Westhof and C Ehresmann and B Ehresmann and R Marquet},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9231899},
isbn = {9231899},
year = {1997},
date = {1997-01-01},
journal = {J Mol Biol},
volume = {270},
number = {1},
pages = {36-49},
abstract = {Retroviruses encapsidate two molecules of genomic RNA that are noncovalently linked close to their 5' ends in a region called the dimer linkage structure (DLS). The dimerization initiation site (DIS) of human immunodeficiency virus type 1 (HIV-1) constitutes the essential part of the DLS in vitro and is crucial for efficient HIV-1 replication in cell culture. We previously identified the DIS as a hairpin structure, located upstream of the major splice donor site, that contains in the loop a six-nucleotide self-complementary sequence preceded and followed by two and one purines, respectively. Two RNA monomers form a kissing loop complex via intermolecular interactions of the six nucleotide self-complementary sequence. Here, we introduced compensatory mutations in the self-complementary sequence and/or a mutation in the flanking purines. We determined the kinetics of dimerization, the thermal stabilities and the apparent equilibrium dissociation constants of wild-type and mutant dimers and used chemical probing to obtain structural information. Our results demonstrate the importance of the 5'-flanking purine and of the two central bases of the self-complementary sequence in the dimerization process. The experimental data are rationalized by triple interactions between these residues in the deep groove of the kissing helix and are incorporated into a three-dimensional model of the kissing loop dimer. In addition, chemical probing and molecular modeling favor the existence of a non-canonical interaction between the conserved adenine residues at the first and last positions in the DIS loop. Furthermore, we show that destabilization of the kissing loop complex at the DIS can be compensated by interactions involving sequences located downstream of the splice donor site of the HIV-1 genomic RNA.},
note = {0022-2836
Journal Article},
keywords = {Dimerization HIV-1/*genetics Kinetics Models, MARQUET, Molecular Mutagenesis, Non-U.S. Gov't, PAILLART, Site-Directed Nucleic Acid Conformation Purines/chemistry RNA, Unité ARN, Viral/*chemistry/genetics/*metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Eriani G, Cavarelli J, Martin F, Dirheimer G, Moras D, Gangloff J
Role of dimerization in yeast aspartyl-tRNA synthetase and importance of the class II invariant proline Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 90, no. 22, p. 10816-10820, 1993, ISBN: 8248175, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Asp/metabolism Saccharomyces cerevisiae/chemistry Structure-Activity Relationship Support, Aspartate-tRNA Ligase/*chemistry Fungal Proteins/chemistry Kinetics Macromolecular Systems Models, ERIANI, Molecular Mutagenesis, Non-U.S. Gov't, Site-Directed Proline/chemistry Protein Binding Protein Conformation RNA, Transfer, Unité ARN
@article{,
title = {Role of dimerization in yeast aspartyl-tRNA synthetase and importance of the class II invariant proline},
author = {G Eriani and J Cavarelli and F Martin and G Dirheimer and D Moras and J Gangloff},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8248175},
isbn = {8248175},
year = {1993},
date = {1993-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {90},
number = {22},
pages = {10816-10820},
abstract = {Cytoplasmic aspartyl-tRNA synthetase (AspRS; EC 6.1.1.12) from yeast is, as are most class II synthetases, an alpha 2 dimer. The only invariant amino acid in signature motif 1 of this class is Pro-273; this residue is located at the dimer interface. To understand the role of Pro-273 in the conserved dimeric configuration, we tested the effect of a Pro-273-->Gly (P273G) substitution on the catalytic properties of homo- and heterodimeric AspRS. Heterodimers of AspRS were produced in vivo by overexpression of their respective subunit variants from plasmid-encoded genes and purified to homogeneity in one HPLC step. The homodimer containing the P273G shows an 80% inactivation of the enzyme and an affinity decrease for its cognate tRNA(Asp) of one order of magnitude. The P273G-mutated subunit recovered wild-type enzymatic properties when associated with a native subunit or a monomer otherwise inactivated having an intact dimeric interface domain. These results, which can be explained by the crystal structure of the native enzyme complexed with its substrates, confirm the structural importance of Pro-273 for dimerization and clearly establish the functional interdependence of the AspRS subunits. More generally, the dimeric conformation may be a structural prerequisite for the activity of mononucleotide binding sites constructed from antiparallel beta strands.},
note = {0027-8424
Journal Article},
keywords = {Asp/metabolism Saccharomyces cerevisiae/chemistry Structure-Activity Relationship Support, Aspartate-tRNA Ligase/*chemistry Fungal Proteins/chemistry Kinetics Macromolecular Systems Models, ERIANI, Molecular Mutagenesis, Non-U.S. Gov't, Site-Directed Proline/chemistry Protein Binding Protein Conformation RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}