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@article{,

title = {Molecular modeling of the three-dimensional structure of the bacterial RNase P holoenzyme},

author = {H Y Tsai and B Masquida and R Biswas and E Westhof and V Gopalan},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12507471},

isbn = {12507471},

year  = {2003},

date = {2003-01-01},

journal = {J Mol Biol},

volume = {325},

number = {4},

pages = {661-675},

abstract = {Bacterial ribonuclease P (RNase P), an enzyme involved in tRNA maturation, consists of a catalytic RNA subunit and a protein cofactor. Comparative phylogenetic analysis and molecular modeling have been employed to derive secondary and tertiary structure models of the RNA subunits from Escherichia coli (type A) and Bacillus subtilis (type B) RNase P. The tertiary structure of the protein subunit of B.subtilis and Staphylococcus aureus RNase P has recently been determined. However, an understanding of the structure of the RNase P holoenzyme (i.e. the ribonucleoprotein complex) is lacking. We have now used an EDTA-Fe-based footprinting approach to generate information about RNA-protein contact sites in E.coli RNase P. The footprinting data, together with results from other biochemical and biophysical studies, have furnished distance constraints, which in turn have enabled us to build three-dimensional models of both type A and B versions of the bacterial RNase P holoenzyme in the absence and presence of its precursor tRNA substrate. These models are consistent with results from previous studies and provide both structural and mechanistic insights into the functioning of this unique catalytic RNP complex.},

note = {0022-2836 

Journal Article},

keywords = {Amino Acid Sequence  Base Sequence  Catalytic Domain  Computer Simulation  Cysteine/chemistry  DNA Footprinting  DNA, Bacterial/chemistry/genetics/metabolism  RNA, Bacterial/genetics  Edetic Acid  Endoribonucleases/*chemistry/genetics/metabolism  Escherichia coli/*enzymology/genetics  Evolution, Catalytic/*chemistry/genetics/metabolism  Ribonuclease P  Support, Molecular  Ferrous Compounds  Holoenzymes/chemistry/genetics/metabolism  Hydroxyl Radical/chemistry  Models, Molecular  Molecular Sequence Data  Mutagenesis, Non-P.H.S.  Support, P.H.S., Site-Directed  Nucleic Acid Conformation  Protein Subunits  RNA, U.S. Gov't, Unité ARN, WESTHOF},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Proline-dependent oligomerization with arm exchange},

author = {M Bergdoll and M H Remy and C Cagnon and J M Masson and P Dumas},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9083108},

isbn = {9083108},

year  = {1997},

date = {1997-01-01},

journal = {Structure},

volume = {5},

number = {3},

pages = {391-401},

abstract = {BACKGROUND: Oligomerization is often necessary for protein activity or regulation and its efficiency is fundamental for the cell. The quaternary structure of a large number of oligomers consists of protomers tightly anchored to each other by exchanged arms or swapped domains. However, nothing is known about how the arms can be kept in a favourable conformation before such an oligomerization. RESULTS: Upon examination of such quaternary structures, we observe an extremely frequent occurrence of proline residues at the point where the arm leaves the protomer. Sequence alignment and site-directed mutagenesis confirm the importance of these prolines. The conservation of these residues at the hinge regions can be explained by the constraints that they impose on polypeptide conformation and dynamics: by rigidifying the mainchain, prolines favour extended conformations of arms thus favouring oligomerization, and may prevent interaction of the arms with the core of the protomer. CONCLUSIONS: Hinge prolines can be considered as 'quaternary structure helpers'. The presence of a proline should be considered when searching for a determinant of oligomerization with arm exchange and could be used to engineer synthetic oligomers or to displace a monomers to oligomers equilibrium by mutation of this proline residue.},

note = {0969-2126 

Journal Article},

keywords = {*Acetyltransferases  Amino Acid Sequence  Animals  Aspartate Aminotransferases/chemistry  Bacterial Proteins/chemistry  Cattle  Chickens  Comparative Study  *Dimerization  Human  Mitochondria, Heart/enzymology  Models, Molecular  Molecular Sequence Data  Mutagenesis, Pancreatic/chemistry  Sequence Alignment  Viral Structural Proteins/chemistry, Site-Directed  Na(+)-K(+)-Exchanging ATPase/chemistry  Plant Viruses/chemistry  Proline/*physiology  Protein Binding  *Protein Conformation  *Protein Folding  Pyrophosphatases/chemistry  Ribonuclease, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {A three-dimensional model of hepatitis delta virus ribozyme based on biochemical and mutational analyses},

author = {N K Tanner and S Schaff and G Thill and E Petit-Koskas and A M Crain-Denoyelle and E Westhof},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7922369},

isbn = {7922369},

year  = {1994},

date = {1994-01-01},

journal = {Curr Biol},

volume = {4},

number = {6},

pages = {488-498},

abstract = {BACKGROUND: Hepatitis delta virus (HDV), which has a single-stranded RNA genome about 1700 nucleotides long, is a satellite virus of hepatitis B, and is associated with a high incidence of fulminant hepatitis and death in infected humans. Like certain pathogenic subviral RNAs that infect plants, HDV RNA features a closed-circular conformation, a rolling-circle mechanism of replication and RNA-catalyzed self-cleaving reactions of both genomic and anti-genomic strands in vitro. The catalytic domains cannot be folded into either the hammerhead or hairpin secondary-structure motifs that have been found in other self-cleaving RNAs. RESULTS: A pseudoknot secondary-structure model has been suggested for the catalytic domain (ribozyme) of HDV RNA. We conducted extensive mutational analyses of regions of the HDV ribozyme predicted in this model to be single stranded, and found that several of them are important for catalytic activity. We used these data, sequence comparisons between different isolates and previously published structural analyses to produce a computer graphic model of the three-dimensional architecture of the HDV ribozyme. CONCLUSIONS: Our model supports the pseudoknotted structure and rationalizes several observations relating to the lengths of the various stems and the sequence requirements of the single-stranded regions. It also provides insight into the catalytic mechanism of the HDV ribozyme. We specifically propose that residues C75, U20 and C21 form the basis of the catalytic region and are close to the cleavable phosphate.},

note = {0960-9822 

Journal Article},

keywords = {Base Sequence  DNA, Catalytic/*chemistry/genetics/metabolism  RNA, Molecular  Molecular Sequence Data  Mutagenesis, Non-U.S. Gov't, Nucleic Acid  Support, Site-Directed  Nucleic Acid Conformation  RNA, Unité ARN, Viral/chemistry/genetics/metabolism  Sequence Homology, Viral/genetics  Hepatitis Delta Virus/*enzymology/genetics  Human  Kinetics  Models},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Crystal structure and site-directed mutagenesis of a bleomycin resistance protein and their significance for drug sequestering},

author = {P Dumas and M Bergdoll and C Cagnon and J M Masson},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7516875},

isbn = {7516875},

year  = {1994},

date = {1994-01-01},

journal = {EMBO J},

volume = {13},

number = {11},

pages = {2483-2492},

abstract = {The antibiotic bleomycin, a strong DNA cutting agent, is naturally produced by actinomycetes which have developed a resistance mechanism against such a lethal compound. The crystal structure, at 2.3 A resolution, of a bleomycin resistance protein of 14 kDa reveals a structure in two halves with the same alpha/beta fold despite no sequence similarity. The crystal packing shows compact dimers with a hydrophobic interface and involved in mutual chain exchange. Two independent solution studies (analytical centrifugation and light scattering) showed that this dimeric form is not a packing artefact but is indeed the functional one. Furthermore, light scattering also showed that one dimer binds two antibiotic molecules as expected. A crevice located at the dimer interface, as well as the results of a site-directed mutagenesis study, led to a model wherein two bleomycin molecules are completely sequestered by one dimer. This provides a novel insight into antibiotic resistance due to drug sequestering, and probably also into drug transport and excretion.},

note = {0261-4189 

Journal Article},

keywords = {*Acetyltransferases  Amino Acid Sequence  Bacterial Proteins/*chemistry/genetics/isolation & purification/metabolism  Base Sequence  Binding Sites  Bleomycin/*metabolism/pharmacology  Crystallization  Crystallography, Bacterial/*genetics  Models, Microbial/genetics  Genes, Molecular  Molecular Sequence Data  Mutagenesis, Non-U.S. Gov't, Secondary  Recombinant Fusion Proteins/isolation & purification  Structure-Activity Relationship  Support, Site-Directed  Protein Conformation  Protein Structure, Structural, Unité ARN, X-Ray  Drug Resistance},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Binding of the yeast tRNA(Met) anticodon by the cognate methionyl-tRNA synthetase involves at least two independent peptide regions},

author = {L Despons and B Senger and F Fasiolo and P Walter},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1602489},

isbn = {1602489},

year  = {1992},

date = {1992-01-01},

journal = {J Mol Biol},

volume = {225},

number = {3},

pages = {897-907},

abstract = {As for Escherichia coli methionine tRNAs, the anticodon triplet of yeast tRNA(Met) plays an important role in the recognition by the yeast methionyl-tRNA synthetase (MetRS), indicating that this determinant for methionine identity is conserved in yeast. Efficient aminoacylation of the E. coli tRNA(Met) transcript by the heterologous yeast methionine enzyme also suggests conservation of the protein determinants that interact with the CAU anticodon sequence. We have analysed by site-directed mutagenesis the peptide region 655 to 663 of the yeast MetRS that is equivalent to the anticodon binding region of the E. coli methionine enzyme. Only one change, converting Leu658 into Ala significantly reduced tRNA aminoacylation. Semi-conservative substitutions of L658 allow a correlation to be drawn between side-chain volume of the hydrophobic residue at this site and activity. The analysis of the L658A mutant shows that Km is mainly affected. This suggests that the peptide region 655 to 663 contributes partially to the binding of the anticodon, since separate mutational analysis of the anticodon bases shows that kcat is the most critical parameter in the recognition of tRNA(Met) by the yeast synthetase. We have analysed the role of peptide region (583-GNLVNR-588) that is spatially close to the region 655 to 663. Replacements of residues N584 and R588 reduces significantly the kcat of aminoacylation. The peptide region 583-GNLVNR-588 is highly conserved in all MetRS so far sequenced. We therefore propose that the hydrogen donor/acceptor amino acid residues within this region are the most critical protein determinants for the positive selection of the methionine tRNAs.},

note = {0022-2836 

Journal Article},

keywords = {Amino Acid Sequence  Anticodon/*metabolism  Binding Sites  Kinetics  Methionine-tRNA Ligase/*metabolism  Models, Met/*metabolism  Saccharomyces cerevisiae/enzymology  Structure-Activity Relationship  Support, Molecular  Molecular Sequence Data  Mutagenesis, Non-U.S. Gov't, Site-Directed  Protein Conformation  RNA, Transfer, Unité ARN},

pubstate = {published},

tppubtype = {article}

}