Abstract:The crystal structure of the isolated full-length ribosomal L1 stalk, consisting of Thermus thermophilus ribosomal protein L1 in complex with a specific 80-nucleotide fragment of 23S rRNA, has been solved for the first time at high resolution. The structure revealed details of protein-RNA interactions in the L1 stalk. Analysis of the crystal packing enabled the identification of sticky sites on the protein and the 23S rRNA which may be important for ribosome assembly and function. The structure was used to mod… Show more
“…Figure 2.Core structure of the head-to-tail double T-loop module. ( A ) Stereo view of the head-to-tail double T-loop module of 23S rRNA L1 stalk [pdb 3U4M (16)] and RNAse P [pdb 3Q1Q (12)]. ( B ) Core of the head-to-tail double T-loop module, involving the highly conserved AG..A and UG..A residues of the two T-loops (Figure 1C).…”
Section: Resultsmentioning
confidence: 99%
“…This conservation, therefore, suggests the presence of higher structural constraints connected with the formation of the module itself. A high-resolution crystal structure of the L1 stalk of T. thermophilus (16) and a crystal structure of the RNAse P of T. maritima (12) enables a detailed characterization of the core of the head-to-tail double T-loop module. The structure of this core, identical in both molecules, precisely involves all six residues with the highest overall conservation (Figure 1C).…”
The structure and function of conserved motifs constituting the apex of Stem I in T-box mRNA leaders are investigated. We point out that this apex shares striking similarities with the L1 stalk (helices 76–78) of the ribosome. A sequence and structure analysis of both elements shows that, similarly to the head of the L1 stalk, the function of the apex of Stem I lies in the docking of tRNA through a stacking interaction with the conserved G19:C56 base pair platform. The inferred structure in the apex of Stem I consists of a module of two T-loops bound together head to tail, a module that is also present in the head of the L1 stalk, but went unnoticed. Supporting the analysis, we show that a highly conserved structure in RNAse P formerly described as the J11/12–J12/11 module, which is precisely known to bind the elbow of tRNA, constitutes a third instance of this T-loop module. A structural analysis explains why six nucleotides constituting the core of this module are highly invariant among all three types of RNA. Our finding that major RNA partners of tRNA bind the elbow with a same RNA structure suggests an explanation for the origin of the tRNA L-shape.
“…Figure 2.Core structure of the head-to-tail double T-loop module. ( A ) Stereo view of the head-to-tail double T-loop module of 23S rRNA L1 stalk [pdb 3U4M (16)] and RNAse P [pdb 3Q1Q (12)]. ( B ) Core of the head-to-tail double T-loop module, involving the highly conserved AG..A and UG..A residues of the two T-loops (Figure 1C).…”
Section: Resultsmentioning
confidence: 99%
“…This conservation, therefore, suggests the presence of higher structural constraints connected with the formation of the module itself. A high-resolution crystal structure of the L1 stalk of T. thermophilus (16) and a crystal structure of the RNAse P of T. maritima (12) enables a detailed characterization of the core of the head-to-tail double T-loop module. The structure of this core, identical in both molecules, precisely involves all six residues with the highest overall conservation (Figure 1C).…”
The structure and function of conserved motifs constituting the apex of Stem I in T-box mRNA leaders are investigated. We point out that this apex shares striking similarities with the L1 stalk (helices 76–78) of the ribosome. A sequence and structure analysis of both elements shows that, similarly to the head of the L1 stalk, the function of the apex of Stem I lies in the docking of tRNA through a stacking interaction with the conserved G19:C56 base pair platform. The inferred structure in the apex of Stem I consists of a module of two T-loops bound together head to tail, a module that is also present in the head of the L1 stalk, but went unnoticed. Supporting the analysis, we show that a highly conserved structure in RNAse P formerly described as the J11/12–J12/11 module, which is precisely known to bind the elbow of tRNA, constitutes a third instance of this T-loop module. A structural analysis explains why six nucleotides constituting the core of this module are highly invariant among all three types of RNA. Our finding that major RNA partners of tRNA bind the elbow with a same RNA structure suggests an explanation for the origin of the tRNA L-shape.
“…The tongs consist of a central part formed by -sheet of domain I and two movable arms formed by loops 7-8 and 9-10. Loop 1-1 protects Similar to other L1-rRNA complexes [11,15] the protein L1 of the H. marismortui L1 stalk acts as tongs that enclose helix 77 of 23S rRNA (Figure 4). The tongs consist of a central part formed by β-sheet of domain I and two movable arms formed by loops β7-β8 and β9-β10.…”
Section: The Designed Model Of the Hmal1 Stalkmentioning
confidence: 96%
“…Nevertheless, the crystal structures of the isolated L1 stalk [11] and 70S ribosomes [5,12,13] from T. thermophilus show that helices 76 and 77 form one helical structure, while the helix 78 consists of two parts (H78a and H78b) that are approximately perpendicular to each other. The 92 nucleotide fragment of 23S rRNA from H. marismortui used in this work contains a part of long helix 76-77 topped by an approximately globular structure formed by the residual part of the L1 stalk rRNA (Figure 1b).…”
Section: Structure Of the L1-specific Rrna Fragment From H Marismortuimentioning
confidence: 99%
“…The structure was solved by molecular replacement with Phaser [18] using the structure of 80 nt fragment of 23S rRNA from T. thermophilus (PDB entry 3U4M; [11]) as a search model. Water molecules and metal ions were removed from the model.…”
Section: Data Collection and Structure Determinationmentioning
Abstract:The crystal structure of the 92-nucleotide L1-specific fragment of 23S rRNA from Haloarcula marismortui (Hma) has been determined at 3.3 Å resolution. Similar to the corresponding bacterial rRNA fragments, this structure contains joined helix 76-77 topped by an approximately globular structure formed by the residual part of the L1 stalk rRNA. The position of HmaL1 relative to the rRNA was found by its docking to the rRNA fragment using the L1-rRNA complex from Thermus thermophilus as a guide model. In spite of the anomalous negative charge of the halophilic archaeal protein, the conformation of the HmaL1-rRNA interface appeared to be very close to that observed in all known L1-rRNA complexes. The designed structure of the L1 stalk was incorporated into the H. marismortui 50S ribosomal subunit. Comparison of relative positions of L1 stalks in 50S subunits from H. marismortui and T. thermophilus made it possible to reveal the site of inflection of rRNA during the ribosome function.
L1 is a conserved protein of the large ribosomal subunit. This protein binds strongly to the specific region of the high molecular weight rRNA of the large ribosomal subunit, thus forming a conserved flexible structural element--the L1 stalk. L1 protein also regulates translation of the operon that comprises its own gene. Crystallographic data suggest that L1 interacts with RNA mainly by means of its domain I. We show here for the first time that the isolated domain I of the bacterial protein L1 of Thermus thermophilus and Escherichia coli is able to incorporate in vivo into the E. coli ribosome. Furthermore, domain I of T. thermophilus L1 can regulate expression of the L1 gene operon of Archaea in the coupled transcription-translation system in vitro, as well as the intact protein. We have identified the structural elements of domain I of the L1 protein that may be responsible for its regulatory properties.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
