Metal Ion Stabilization of the U-Turn of the A37 N6-Dimethylallyl-Modified Anticodon Stem−Loop of Escherichia coli tRNAPhe

Cabello-Villegas, Javier; Tworowska, Izabela; Nikonowicz, Edward P.

doi:10.1021/bi0353676

Cited by 32 publications

(47 citation statements)

References 56 publications

(112 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In agreement with previous NMR studies of U-turn structures (Schweisguth and Moore 1997;Sundaram et al 2000;Cabello-Villegas et al 2004), unusually large chemical shift changes were associated with the formation of a canonical U-turn structure in SLV Mg for two specific NMR signals, the 31 P resonance of U696 39-phosphate (39-P) and the 15 N resonance of A698 N7 (Campbell and Legault 2005;Campbell et al 2006). The detection of unusual 31 P and 15 N chemical shifts in SLV RNA fragments was therefore used to identify the formation of a canonical U-turn fold for the mutants being functionally characterized in this study (Fig.…”

Section: +supporting

confidence: 92%

Role of SLV in SLI substrate recognition by the Neurospora VS ribozyme

Bouchard¹,

Lacroix‐Labonté²,

Desjardins³

et al. 2008

RNA

View full text Add to dashboard Cite

Substrate recognition by the VS ribozyme involves a magnesium-dependent loop/loop interaction between the SLI substrate and the SLV hairpin from the catalytic domain. Recent NMR studies of SLV demonstrated that magnesium ions stabilize a U-turn loop structure and trigger a conformational change for the extruded loop residue U700, suggesting a role for U700 in SLI recognition. Here, we kinetically characterized VS ribozyme mutants to evaluate the contribution of U700 and other SLV loop residues to SLI recognition. To help interpret the kinetic data, we structurally characterized the SLV mutants by NMR spectroscopy and generated a three-dimensional model of the SLI/SLV complex by homology modeling with MC-Sym. We demonstrated that the mutation of U700 by A, C, or G does not significantly affect ribozyme activity, whereas deletion of U700 dramatically impairs this activity. The U700 backbone is likely important for SLI recognition, but does not appear to be required for either the structural integrity of the SLV loop or for direct interactions with SLI. Thus, deletion of U700 may affect other aspects of SLI recognition, such as magnesium ion binding and SLV loop dynamics. As part of our NMR studies, we developed a convenient assay based on detection of unusual 31 P and 15 N N7 chemical shifts to probe the formation of U-turn structures in RNAs. Our model of the SLI/SLV complex, which is compatible with biochemical data, leads us to propose novel interactions at the loop I/loop V interface.

show abstract

Section: +supporting

confidence: 92%

Role of SLV in SLI substrate recognition by the Neurospora VS ribozyme

Bouchard¹,

Lacroix‐Labonté²,

Desjardins³

et al. 2008

RNA

View full text Add to dashboard Cite

show abstract

“…2a). The tight backbone turn in the anticodon loop mimic seems to be stabilized by a bound cation that docks in an electronegative pocket formed by both phosphates and base functional groups, consistent with the observation that cations also interact within tRNA anticodon loops 27 (Fig. 2c).…”

Section: Specific Interactions and Structures Are Critical For Functionsupporting

confidence: 84%

tRNA–mRNA mimicry drives translation initiation from a viral IRES

Costantino

Pfingsten²,

Rambo

et al. 2007

Nat Struct Mol Biol

144

244

View full text Add to dashboard Cite

Internal ribosome entry site (IRES) RNAs initiate protein synthesis in eukaryotic cells by a noncanonical cap-independent mechanism. IRESes are critical for many pathogenic viruses, but efforts to understand their function are complicated by the diversity of IRES sequences as well as by limited high-resolution structural information. The intergenic region (IGR) IRESes of the Dicistroviridae viruses are powerful model systems to begin to understand IRES function. Here we present the crystal structure of a Dicistroviridae IGR IRES domain that interacts with the ribosome's decoding groove. We find that this RNA domain precisely mimics the transfer RNA anticodonmessenger RNA codon interaction, and its modeled orientation on the ribosome helps explain translocation without peptide bond formation. When combined with a previous structure, this work completes the first high-resolution description of an IRES RNA and provides insight into how RNAs can manipulate complex biological machines.Canonical eukaryotic translation initiation is a complex, multistep process in which a modified nucleotide cap on the 5′ end of the mRNA is necessary for protein factor-dependent recruitment of the 40S (small) ribosomal subunit 1 . The subunit scans the message and recognizes the AUG initiation codon, which leads to GTP hydrolysis, initiation factor protein release, and 60S (large) subunit binding to form the 80S ribosome-mRNA complex. The assembled 80S ribosome, containing an initiator tRNA in the P site, begins translation through eukaryotic elongation factor (eEF) 1A-mediated delivery of an aminoacylated tRNA into the A site. Subsequent peptide bond formation in the ribosome's peptidyl transferase site is followed by eEF 2-catalyzed translocation, and the ribosome enters the elongation phase of protein synthesis (Fig. 1a). Thus, canonical cap-dependent translation initiation is driven by the action of many protein factors and begins in the P site from an AUG codon in good context; then translocation occurs after the initial peptide bond is made.In contrast to the canonical cap-dependent pathway, an important alternate mechanism is internal initiation of translation. This mechanism depends on specific cis-acting RNA sequences called IRESes 2,3 . There is great diversity in IRES sequence, secondary structure and requirements for protein factors, but all IRESes recruit, position and activate the proteinmaking machinery without recognizing the cap or the 5′ end of the mRNA. IRESes are critical for the infection of many pathogenic viruses and may be important regulatory elements in gene expression 2 . Insight into the mechanism of many IRESes has been provided by a variety of approaches, but details of their RNA structure-based function remain incomplete. (refs. 4-6 ), and both contact the ribosome over the E site and through the large subunit's L1 stalk 4,5,7,8 . Furthermore, cryo-EM reconstructions of these IRES RNAs bound to the ribosome indicate that both may undergo subtle structural rearrangement during the course of preini...

show abstract

“…Of course formation of a loop with reversal of strand orientation represents a topological problem by itself, which results in added constraints to the phosphodiester backbone. The size of the loop, stacking interactions within and outside the loop, the geometry of the closing base pair, and the presence of modified residues or metal ions can all play a role in defining the most stable loop fold (65,67,68). In the cases of the 690 loop and the 16S-like UGAA tetraloop, the loop sequences are the same, therefore the sizes of the loop are the same, and ionic conditions for structure determination are also comparable.…”

Section: Discussionmentioning

confidence: 99%

Nuclear Magnetic Resonance Structure of the Varkud Satellite Ribozyme Stem−Loop V RNA and Magnesium-Ion Binding from Chemical-Shift Mapping^,

Campbell

Legault

2005

Biochemistry

View full text Add to dashboard Cite

An important step in the substrate recognition of the Neurospora Varkud Satellite (VS) ribozyme is the formation of a magnesium-dependent loop/loop interaction between the terminal loops of stem-loops I and V. We have studied the structure of stem-loop V by nuclear magnetic resonance spectroscopy and shown that it adopts a U-turn conformation, a common motif found in RNA. Structural comparisons indicate that the U-turn of stem-loop V fulfills some but not all of the structural characteristics found in canonical U-turn structures. This U-turn conformation exposes the Watson-Crick faces of the bases within stem-loop V (G697, A698, and C699) and makes them accessible for interaction with stem-loop I. Using chemical-shift mapping, we show that magnesium ions interact with the loop of the isolated stem-loop V and induce a conformational change that may be important for interaction with stem-loop I. This study expands our understanding of the role of U-turn motifs in RNA structure and function and provides insights into the mechanism of substrate recognition in the VS ribozyme.

show abstract

Metal Ion Stabilization of the U-Turn of the A₃₇ N⁶-Dimethylallyl-Modified Anticodon Stem−Loop of Escherichia coli tRNA^Phe

Cited by 32 publications

References 56 publications

Role of SLV in SLI substrate recognition by the Neurospora VS ribozyme

Role of SLV in SLI substrate recognition by the Neurospora VS ribozyme

tRNA–mRNA mimicry drives translation initiation from a viral IRES

Nuclear Magnetic Resonance Structure of the Varkud Satellite Ribozyme Stem−Loop V RNA and Magnesium-Ion Binding from Chemical-Shift Mapping^,

Contact Info

Product

Resources

About

Metal Ion Stabilization of the U-Turn of the A37 N6-Dimethylallyl-Modified Anticodon Stem−Loop of Escherichia coli tRNAPhe

Cited by 32 publications

References 56 publications

Role of SLV in SLI substrate recognition by the Neurospora VS ribozyme

Role of SLV in SLI substrate recognition by the Neurospora VS ribozyme

tRNA–mRNA mimicry drives translation initiation from a viral IRES

Nuclear Magnetic Resonance Structure of the Varkud Satellite Ribozyme Stem−Loop V RNA and Magnesium-Ion Binding from Chemical-Shift Mapping,

Contact Info

Product

Resources

About

Metal Ion Stabilization of the U-Turn of the A₃₇ N⁶-Dimethylallyl-Modified Anticodon Stem−Loop of Escherichia coli tRNA^Phe

Nuclear Magnetic Resonance Structure of the Varkud Satellite Ribozyme Stem−Loop V RNA and Magnesium-Ion Binding from Chemical-Shift Mapping^,