A chemical phylogeny of group I introns based upon interference mapping of a bacterial ribozyme 1 1Edited by D. Draper

Strauss-Soukup, Juliane K.; Strobel, Scott A.

doi:10.1006/jmbi.2000.4056

Cited by 46 publications

(75 citation statements)

References 80 publications

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“…These bands were compressed and the real extent of protection was difficult to quantify. The model is also consistent with nucleotide analog interference data (38). Discussion 3D Model of the Azoarcus Intron.…”

Section: D Model Of the Azoarcus Ribozymesupporting

confidence: 78%

“…Deviations from A-form geometry around internal loops in P6 and P8 and a sharp bend between stems P7 and P9.0 cause the two helical domains to twist around each other, maximizing the buried surface area. The extensive helical packing predicted by our model is largely consistent with the positions of 2Ј OH modifications that interfere with catalytic activity (38).…”

Section: D Model Of the Azoarcus Ribozymesupporting

confidence: 76%

“…Group I introns share a common core structure that contains the active site (14), but differ in the architecture of peripheral tertiary interactions among subfamilies (33). Nucleotide analog interference showed that the active site of the Azoarcus IC3 intron shares many features with the IC1 intron from T. thermophila (38). Interactions that organize the interface between the P3-P7 and P4-P6 domains include a central triple helix (14), a base triple that joins J8͞7 and P4 (39), and contacts between L9 and P5 (40).…”

Section: D Model Of the Azoarcus Ribozymementioning

confidence: 99%

“…It has been proposed that a shorter J8͞7 is compensated by the extension of J2͞3 in the Azoarcus intron (38). In the Tetrahymena intron, P1 is 6 bp and is proposed to dock orthogonally to P2 and P2.1 helices (33,41).…”

Section: D Model Of the Azoarcus Ribozymementioning

confidence: 99%

“…In our model of the Azoarcus intron, the 3-bp P1 helix stacks on top of P2. As a consequence, the sugar edge of A166 of J8͞7 interacts with the first base pairs of P2 (type II A-minor motif or cis sugar-sugar pair), whereas A167 of J8͞7 binds to C(Ϫ3) of P1 (type I A-minor motif or trans sugar-sugar pair) as seen in the Tetrahymena intron (38,42). After our model was constructed, we learned that interference from a carbon at position 3 of A166 is suppressed by a 2Ј deoxy substitution at C12 in P2, consistent with the pair modeled between these residues (43).…”

Section: D Model Of the Azoarcus Ribozymementioning

confidence: 99%

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Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme

Rangan

Masquida

Westhof

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

136

166

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Compact but non-native intermediates have been implicated in the hierarchical folding of several large RNAs, but there is little information on their structure. In this article, ribonuclease and hydroxyl radical cleavage protection assays showed that base pairing of core helices stabilize a compact state of a small group I ribozyme from Azoarcus pre-tRNA ile . Base pairing of the ribozyme core requires 10-fold less Mg 2؉ than stable tertiary interactions, indicating that assembly of helices in the catalytic core represents a distinct phase that precedes the formation of native tertiary structure. Tertiary folding occurs in <100 ms at 37°C. Such rapid folding is unprecedented among group I ribozymes and illustrates the association between structural complexity and folding time. A 3D model of the Azoarcus ribozyme was constructed by identifying homologous sequence motifs in rRNA. The model reveals distinct structural features, such as a large interface between the P4 -P6 and P3-P9 domains, that may explain the unusual stability of the Azoarcus ribozyme and the cooperativity of folding.RNA modeling ͉ RNA structure ͉ metal ions ͉ hydroxyl radical footprinting T he assembly of RNA into functional structures underlies many steps in gene expression and regulation. Recent work has outlined the Mg 2ϩ -dependent folding pathways of large ribozymes (1, 2). Experimental and theoretical results suggest that the initial association of divalent cations induces collapse of the extended RNA chain into more compact structures that favor formation of tertiary interactions (3-8). The structure of the compact intermediates and the extent to which these interactions lead to the native conformation are not yet characterized.On the one hand, individual domains of the Tetrahymena group I ribozyme and the catalytic domain of RNase P fold on a time scale (10-100 ms) similar to the initial collapse transitions of the ribozyme (6, 9, 10). On the other hand, nonspecific collapse results in an ensemble of native and non-native conformations. Many larger RNAs, such as the Tetrahymena group I and Bacillus subtilis RNase P ribozymes, fold slowly in vitro because a large fraction of the RNA population becomes trapped in misfolded intermediates (11,12). An important question is whether RNAs with a simpler 3D architecture are more likely to fold directly to the native structure, as expected from theoretical models (4). Furthermore, we want to know whether the likelihood of misfolding can be predicted from the specificity of counterion-induced collapse.We investigated the Mg 2ϩ -dependent equilibrium folding pathway and constructed a 3D model of the Azoarcus group I intron. The 205-nt group IC3 intron in the pre-tRNA ile of the Azoarcus bacterium is the smallest known self-splicing group I intron (13). It retains the conserved catalytic core common to all group I introns, but lacks the peripheral domains that stabilize folding intermediates of the larger Tetrahymena intron (14).We observed two macroscopic folding transitions in the Azoarcus ribozyme...

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Section: D Model Of the Azoarcus Ribozymesupporting

confidence: 78%

Section: D Model Of the Azoarcus Ribozymesupporting

confidence: 76%

Section: D Model Of the Azoarcus Ribozymementioning

confidence: 99%

Section: D Model Of the Azoarcus Ribozymementioning

confidence: 99%

Section: D Model Of the Azoarcus Ribozymementioning

confidence: 99%

See 3 more Smart Citations

Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme

Rangan

Masquida

Westhof

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

136

166

View full text Add to dashboard Cite

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Nucleotide Analog Interference Mapping and Suppression: Specific Applications in Studies of RNA Tertiary Structure, Dynamic Helicase Mechanism and RNA–Protein Interactions

Fedorova¹,

Boudvillain²,

Kawaola³

et al. 2005

Handbook of RNA Biochemistry

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Structure and Function Converge To Identify a Hydrogen Bond in a Group I Ribozyme Active Site

et al. 2009

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The determination of how enzymes achieve their catalytic power requires an understanding of how structural motifs are used to position functional groups of enzymes and substrates within active sites. The recent explosion of RNA crystal structures provides an extraordinary opportunity to delve deeply into the relationship between ribozyme structure and function. The Tetrahymena group I ribozyme provides an attractive system for such studies because of the wealth of structural information, with ten crystal structures of group I introns solved in the past

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A chemical phylogeny of group I introns based upon interference mapping of a bacterial ribozyme 1 1Edited by D. Draper

Cited by 46 publications

References 80 publications

Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme

Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme

Nucleotide Analog Interference Mapping and Suppression: Specific Applications in Studies of RNA Tertiary Structure, Dynamic Helicase Mechanism and RNA–Protein Interactions

Structure and Function Converge To Identify a Hydrogen Bond in a Group I Ribozyme Active Site

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