NMR characterisation of a highly conserved secondary structural RNA motif of Halobacterium halobium 23S rRNA

2013 ◽  
Vol 11 (20) ◽  
pp. 3382 ◽  
Author(s):  
John King ◽  
Christos Shammas ◽  
Misbah Nareen ◽  
Moreno Lelli ◽  
Vasudevan Ramesh
Keyword(s):  
23S Rrna ◽  
Halobacterium Halobium ◽  
Rna Motif

scholarly journals Interaction of Avilamycin with Ribosomes and Resistance Caused by Mutations in 23S rRNA

2002 ◽  
Vol 46 (11) ◽  
pp. 3339-3342 ◽  
Author(s):  
Christine B. Kofoed ◽  
Birte Vester
Keyword(s):  
Binding Site ◽  
Initiation Factor ◽  
23S Rrna ◽  
Cross Resistance ◽  
Halobacterium Halobium ◽  
Growth Promoter ◽  
A Site ◽  
Domain V ◽  
Trna Binding ◽  
Selection Of

ABSTRACT The antibiotic growth promoter avilamycin inhibits protein synthesis by binding to bacterial ribosomes. Here the binding site is further characterized on Escherichia coli ribosomes. The drug interacts with domain V of 23S rRNA, giving a chemical footprint at nucleotides A2482 and A2534. Selection of avilamycin-resistant Halobacterium halobium cells revealed mutations in helix 89 of 23S rRNA. Furthermore, mutations in helices 89 and 91, which have previously been shown to confer resistance to evernimicin, give cross-resistance to avilamycin. These data place the binding site of avilamycin on 23S rRNA close to the elbow of A-site tRNA. It is inferred that avilamycin interacts with the ribosomes at the ribosomal A-site interfering with initiation factor IF2 and tRNA binding in a manner similar to evernimicin.

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.

Nomenclature Abstract for Halobacterium halobium (Petter 1931) Elazari-Volcani 1957 (Approved Lists 1980).

2003 ◽  
Author(s):  
Charles Thomas Parker ◽  
Sarah Wigley ◽  
George M Garrity ◽  
Dorothea Taylor
Keyword(s):  
Halobacterium Halobium

Structures of Artificially Designed RNA Nanoarchitectures at Near-Atomic Resolution

2020 ◽  
Author(s):  
Di Liu ◽  
Yaming Shao ◽  
Joseph A. Piccirilli ◽  
Yossi Weizmann
Keyword(s):  
Nucleic Acid ◽  
High Resolution ◽  
Single Strand ◽  
Atomic Resolution ◽  
Rna Motifs ◽  
X Ray ◽  
Structural Details ◽  
Rna Motif

<p>Though advances in nanotechnology have enabled the construction of synthetic nucleic acid based nanoarchitectures with ever-increasing complexity for various applications, high-resolution structures are lacking due to the difficulty of obtaining good diffracting crystals. Here we report the design of RNA nanostructures based on homooligomerizable tiles from an RNA single-strand for X-ray determination. Three structures are solved to near-atomic resolution: a 2D parallelogram, an unexpectedly formed 3D nanobracelet, and a 3D nanocage. Structural details of their constituent motifs—such as kissing loops, branched kissing-loops and T-junctions—that resemble natural RNA motifs and resisted X-ray determination are revealed. This work unveils the largely unexplored potential of crystallography in gaining high-resolution feedback for nanostructure design and suggests a novel route to investigate RNA motif structures by configuring them into nanoarchitectures.</p>

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