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Crystal structure of a eukaryotic group II intron lariat.

Robart AR, Chan RT, Peters JK, Rajashankar KR, Toor N - Nature (2014)

Bottom Line: On the basis of structural and biochemical data, we propose that π-π' is a dynamic interaction that mediates the transition between the two steps of splicing, with η-η' serving an ancillary role.The structure also reveals a four-magnesium-ion cluster involved in both catalysis and positioning of the 5' end.Given the evolutionary relationship between group II and nuclear introns, it is likely that this active site configuration exists in the spliceosome as well.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA.

ABSTRACT
The formation of branched lariat RNA is an evolutionarily conserved feature of splicing reactions for both group II and spliceosomal introns. The lariat is important for the fidelity of 5' splice-site selection and consists of a 2'-5' phosphodiester bond between a bulged adenosine and the 5' end of the intron. To gain insight into this ubiquitous intramolecular linkage, we determined the crystal structure of a eukaryotic group IIB intron in the lariat form at 3.7 Å. This revealed that two tandem tetraloop-receptor interactions, η-η' and π-π', place domain VI in the core to position the lariat bond in the post-catalytic state. On the basis of structural and biochemical data, we propose that π-π' is a dynamic interaction that mediates the transition between the two steps of splicing, with η-η' serving an ancillary role. The structure also reveals a four-magnesium-ion cluster involved in both catalysis and positioning of the 5' end. Given the evolutionary relationship between group II and nuclear introns, it is likely that this active site configuration exists in the spliceosome as well.

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Companion to Fig. 2 showing the location of the individual tertiary interactions relative to the overall structure.
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Figure 10: Companion to Fig. 2 showing the location of the individual tertiary interactions relative to the overall structure.

Mentions: One of the most highly conserved tertiary contacts in group II introns is the κ-κ’ interaction between the base of the catalytic DV stem and domain I (DI)16. The conserved κ sequence GAA, nucleotide A171 from near the κ region, and residues from a GUAAC pentaloop in DIII converge to form a pentuple adenosine base stack (underlined residues) that inserts into the minor groove at the base of DV; rigidly placing the active site into the DI scaffold (Fig. 2a; Extended Data Fig. 5a).


Crystal structure of a eukaryotic group II intron lariat.

Robart AR, Chan RT, Peters JK, Rajashankar KR, Toor N - Nature (2014)

Companion to Fig. 2 showing the location of the individual tertiary interactions relative to the overall structure.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4197185&req=5

Figure 10: Companion to Fig. 2 showing the location of the individual tertiary interactions relative to the overall structure.
Mentions: One of the most highly conserved tertiary contacts in group II introns is the κ-κ’ interaction between the base of the catalytic DV stem and domain I (DI)16. The conserved κ sequence GAA, nucleotide A171 from near the κ region, and residues from a GUAAC pentaloop in DIII converge to form a pentuple adenosine base stack (underlined residues) that inserts into the minor groove at the base of DV; rigidly placing the active site into the DI scaffold (Fig. 2a; Extended Data Fig. 5a).

Bottom Line: On the basis of structural and biochemical data, we propose that π-π' is a dynamic interaction that mediates the transition between the two steps of splicing, with η-η' serving an ancillary role.The structure also reveals a four-magnesium-ion cluster involved in both catalysis and positioning of the 5' end.Given the evolutionary relationship between group II and nuclear introns, it is likely that this active site configuration exists in the spliceosome as well.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA.

ABSTRACT
The formation of branched lariat RNA is an evolutionarily conserved feature of splicing reactions for both group II and spliceosomal introns. The lariat is important for the fidelity of 5' splice-site selection and consists of a 2'-5' phosphodiester bond between a bulged adenosine and the 5' end of the intron. To gain insight into this ubiquitous intramolecular linkage, we determined the crystal structure of a eukaryotic group IIB intron in the lariat form at 3.7 Å. This revealed that two tandem tetraloop-receptor interactions, η-η' and π-π', place domain VI in the core to position the lariat bond in the post-catalytic state. On the basis of structural and biochemical data, we propose that π-π' is a dynamic interaction that mediates the transition between the two steps of splicing, with η-η' serving an ancillary role. The structure also reveals a four-magnesium-ion cluster involved in both catalysis and positioning of the 5' end. Given the evolutionary relationship between group II and nuclear introns, it is likely that this active site configuration exists in the spliceosome as well.

Show MeSH