The solution structure of ribosomal protein L18 from Thermus thermophilus reveals a conserved RNA-binding fold

2002 ◽  
Vol 363 (3) ◽  
pp. 553-561 ◽  
Author(s):  
Esmeralda A. WOESTENENK ◽  
George M. GONGADZE ◽  
Dmitry V. SHCHERBAKOV ◽  
Alexey V. RAK ◽  
Maria B. GARBER ◽  
...  
Keyword(s):  
Ribosomal Protein ◽  
Solution Structure ◽  
Rna Binding ◽  
Large Subunit ◽  
Thermus Thermophilus ◽  
23S Rrna ◽  
Haloarcula Marismortui ◽  
Globular Structure ◽  
High Resolution Structure ◽  
Rna Motif

We have determined the solution structure of ribosomal protein L18 from Thermus thermophilus. L18 is a 12.5kDa protein of the large subunit of the ribosome and binds to both 5S and 23S rRNA. In the uncomplexed state L18 folds to a mixed α/β globular structure with a long disordered N-terminal region. We compared our high-resolution structure with RNA-complexed L18 from Haloarcula marismortui and T. thermophilus to examine RNA-induced as well as species-dependent structural differences. We also identified T. thermophilus S11 as a structural homologue and found that the structures of the RNA-recognition sites are conserved. Important features, for instance a bulge in the RNA-contacting β-sheet, are conserved in both proteins. We suggest that the L18 fold recognizes a specific RNA motif and that the resulting RNA—protein-recognition module is tolerant to variations in sequence.

scholarly journals The solution structure of ribosomal protein L18 from Thermus thermophilus reveals a conserved RNA-binding fold

2002 ◽  
Vol 363 (3) ◽  
pp. 553 ◽  
Author(s):  
Esmeralda A. WOESTENENK ◽  
George M. GONGADZE ◽  
Dmitry V. SHCHERBAKOV ◽  
Alexey V. RAK ◽  
Maria B. GARBER ◽  
...  
Keyword(s):  
Ribosomal Protein ◽  
Solution Structure ◽  
Rna Binding ◽  
Thermus Thermophilus

Ribosomal Protein S15 from Thermus Thermophilus. Cloning, Sequencing, Overexpression of the Gene and RNA-Binding Properties of the Protein

1997 ◽  
Vol 246 (2) ◽  
pp. 291-300 ◽  
Author(s):  
Alexander Serganov ◽  
Alexey Rak ◽  
Maria Garber ◽  
Joseph Reinbolt ◽  
Bernard Ehresmann ◽  
...  
Keyword(s):  
Ribosomal Protein ◽  
Rna Binding ◽  
Thermus Thermophilus ◽  
Binding Properties ◽  
Ribosomal Protein S15

The solution structure of ribosomal protein L36 from Thermus thermophilus reveals a zinc-ribbon-like fold 1 1Edited by P. E. Wright

2000 ◽  
Vol 296 (1) ◽  
pp. 169-180 ◽  
Author(s):  
Torleif Härd ◽  
Alexey Rak ◽  
Peter Allard ◽  
Lars Kloo ◽  
Maria Garber
Keyword(s):  
Ribosomal Protein ◽  
Solution Structure ◽  
Thermus Thermophilus ◽  
Zinc Ribbon

Solution structure of the ribosomal RNA binding protein S15 from Thermus thermophilus

1997 ◽  
Vol 4 (1) ◽  
pp. 20-23 ◽  
Author(s):  
Helena Berglund ◽  
Alexey Rak ◽  
Alexander Serganov ◽  
Maria Garber ◽  
Torleif Härd
Keyword(s):  
Ribosomal Rna ◽  
Solution Structure ◽  
Rna Binding ◽  
Binding Protein ◽  
Thermus Thermophilus ◽  
Rna Binding Protein

Protein–RNA affinity of ribosomal protein L1 mutants does not correlate with the number of intermolecular interactions

2015 ◽  
Vol 71 (2) ◽  
pp. 376-386 ◽  
Author(s):  
Svetlana Tishchenko ◽  
Olga Kostareva ◽  
Azat Gabdulkhakov ◽  
Alisa Mikhaylina ◽  
Ekaterina Nikonova ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Ribosomal Protein ◽  
Rna Binding ◽  
Function Analysis ◽  
Ribosomal Subunit ◽  
23S Rrna ◽  
Wild Type ◽  
Type Protein ◽  
Wild Type Protein ◽  
Ribosomal Protein L1

Ribosomal protein L1, as part of the L1 stalk of the 50S ribosomal subunit, is implicated in directing tRNA movement through the ribosome during translocation. High-resolution crystal structures of four mutants (T217V, T217A, M218L and G219V) of the ribosomal protein L1 fromThermus thermophilus(TthL1) in complex with a specific 80 nt fragment of 23S rRNA and the structures of two of these mutants (T217V and G219V) in the RNA-unbound form are reported in this work. All mutations are located in the highly conserved triad Thr-Met-Gly, which is responsible for about 17% of all protein–RNA hydrogen bonds and 50% of solvent-inaccessible intermolecular hydrogen bonds. In the mutated proteins without bound RNA the RNA-binding regions show substantial conformational changes. On the other hand, in the complexes with RNA the structures of the RNA-binding surfaces in all studied mutants are very similar to the structure of the wild-type protein in complex with RNA. This shows that formation of the RNA complexes restores the distorted surfaces of the mutant proteins to a conformation characteristic of the wild-type protein complex. Domain I of the mutated TthL1 and helix 77 of 23S rRNA form a rigid body identical to that found in the complex of wild-type TthL1 with RNA, suggesting that the observed relative orientation is conserved and is probably important for ribosome function. Analysis of the complex structures and the kinetic data show that the number of intermolecular contacts and hydrogen bonds in the RNA–protein contact area does not correlate with the affinity of the protein for RNA and cannot be used as a measure of affinity.

scholarly journals Mutations in the Bacterial Ribosomal Protein L3 and Their Association with Antibiotic Resistance

2015 ◽  
Vol 59 (6) ◽  
pp. 3518-3528 ◽  
Author(s):  
Rasmus N. Klitgaard ◽  
Eleni Ntokou ◽  
Katrine Nørgaard ◽  
Daniel Biltoft ◽  
Lykke H. Hansen ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Ribosomal Protein ◽  
Large Subunit ◽  
23S Rrna ◽  
Wild Type ◽  
Growth Data ◽  
Content Type ◽  
E Coli ◽  
Ribosomal Protein L3 ◽  
The Impact

ABSTRACTDifferent groups of antibiotics bind to the peptidyl transferase center (PTC) in the large subunit of the bacterial ribosome. Resistance to these groups of antibiotics has often been linked with mutations or methylations of the 23S rRNA. In recent years, there has been a rise in the number of studies where mutations have been found in the ribosomal protein L3 in bacterial strains resistant to PTC-targeting antibiotics but there is often no evidence that these mutations actually confer antibiotic resistance. In this study, a plasmid exchange system was used to replace plasmid-carried wild-type genes with mutated L3 genes in a chromosomal L3 deletion strain. In this way, the essential L3 gene is available for the bacteria while allowing replacement of the wild type with mutated L3 genes. This enables investigation of the effect of single mutations inEscherichia coliwithout a wild-type L3 background. Ten plasmid-carried mutated L3 genes were constructed, and their effect on growth and antibiotic susceptibility was investigated. Additionally, computational modeling of the impact of L3 mutations inE. coliwas used to assess changes in 50S structure and antibiotic binding. All mutations are placed in the loops of L3 near the PTC. Growth data show that 9 of the 10 mutations were well accepted inE. coli, although some of them came with a fitness cost. Only one of the mutants exhibited reduced susceptibility to linezolid, while five exhibited reduced susceptibility to tiamulin.

scholarly journals Crystallographic analysis of archaeal ribosomal protein L11

2015 ◽  
Vol 71 (8) ◽  
pp. 1083-1087 ◽  
Author(s):  
Ivan Mitroshin ◽  
Maria Garber ◽  
Azat Gabdulkhakov
Keyword(s):  
Ribosomal Protein ◽  
Rna Binding ◽  
Crystallographic Analysis ◽  
23S Rrna ◽  
Data Sets ◽  
Peptide Antibiotics ◽  
Orthorhombic Space Group ◽  
Terminal Domain ◽  
Dispersion Data ◽  
Ribosomal Protein L11

Ribosomal protein L11 is an important part of the GTPase-associated centre in ribosomes of all organisms. L11 is a highly conserved two-domain ribosomal protein. The C-terminal domain of L11 is an RNA-binding domain that binds to a fragment of 23S rRNA and stabilizes its structure. The complex between L11 and 23S rRNA is involved in the GTPase activity of the translation elongation and release factors. Bacterial and archaeal L11–rRNA complexes are targets for peptide antibiotics of the thiazole class. To date, there is no complete structure of archaeal L11 owing to the mobility of the N-terminal domain of the protein. Here, the crystallization and X-ray analysis of the ribosomal protein L11 fromMethanococcus jannaschiiare reported. Crystals of the native protein and its selenomethionine derivative belonged to the orthorhombic space groupI222 and were suitable for structural studies. Native and single-wavelength anomalous dispersion data sets have been collected and determination of the structure is in progress.

scholarly journals Crystal structure of the RNA binding ribosomal protein L1 from Thermus thermophilus.

1996 ◽  
Vol 15 (6) ◽  
pp. 1350-1359 ◽  
Author(s):  
S. Nikonov ◽  
N. Nevskaya ◽  
I. Eliseikina ◽  
N. Fomenkova ◽  
A. Nikulin ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Ribosomal Protein ◽  
Rna Binding ◽  
Thermus Thermophilus ◽  
Ribosomal Protein L1

Rapid evolution in sequence and length of the nuclear-located gene for mitochondrial L2 ribosomal protein in cereals

Genome ◽  
2006 ◽  
Vol 49 (3) ◽  
pp. 275-281 ◽  
Author(s):  
Selvi Subramanian ◽  
Linda Bonen
Keyword(s):  
Amino Acids ◽  
Ribosomal Protein ◽  
Ribosomal Rna ◽  
Ribosomal Proteins ◽  
Rna Binding ◽  
Large Subunit ◽  
Rapid Evolution ◽  
Comparative Sequence Analysis ◽  
Marchantia Polymorpha ◽  
Peptidyl Transferase

The L2 ribosomal protein is typically one of the most conserved proteins in the ribosome and is universally present in bacterial, archaeal, and eukaryotic cytosolic and organellar ribosomes. It is usually 260–270 amino acids long and its binding to the large-subunit ribosomal RNA near the peptidyl transferase center is mediated by a β-barrel RNA-binding domain with 10 β strands. In the diverse land plants Marchantia polymorpha (liverwort) and Oryza sativa (rice), the mitochondrial-encoded L2 ribosomal protein is about 500 amino acids long owing to a centrally located expansion containing the β3–β4 strand region. We have determined that, in wheat, the functional rpl2 gene has been trans ferred to the nucleus and much of the plant-specific internal insert has been deleted. Its mRNA is only 1.2 kb, and two expressed copies in wheat encode proteins of 318 and 319 amino acids, so they are considerably shorter than the maize nuclear-located rpl2 gene of 448 codons. Comparative sequence analysis of cereal mitochondrial L2 ribosomal proteins indicates that the mid region has undergone unexpectedly rapid evolution during the last 60 million years.Key words: mitochondria, ribosomal protein, plants, evolutionary gene transfer.

Solution structure of the ribosomal protein S19 from Thermus thermophilus 1 1Edited by P. E. Wright

1999 ◽  
Vol 292 (5) ◽  
pp. 1071-1081 ◽  
Author(s):  
Magnus Helgstrand ◽  
Alexey V Rak ◽  
Peter Allard ◽  
Natalia Davydova ◽  
Maria B Garber ◽  
...  
Keyword(s):  
Ribosomal Protein ◽  
Solution Structure ◽  
Thermus Thermophilus ◽  
Ribosomal Protein S19
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