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Branch site bulge conformations in domain 6 determine functional sugar puckers in group II intron splicing.


ABSTRACT: Although group II intron ribozymes are intensively studied the question how structural dynamics affects splicing catalysis has remained elusive. We report for the first time that the group II intron domain 6 exists in a secondary structure equilibrium between a single- and a two-nucleotide bulge conformation, which is directly linked to a switch between sugar puckers of the branch site adenosine. Our study determined a functional sugar pucker equilibrium between the transesterification active C2'-endo conformation of the branch site adenosine in the 1nt bulge and an inactive C3'-endo state in the 2nt bulge fold, allowing the group II intron to switch its activity from the branching to the exon ligation step. Our detailed NMR spectroscopic investigation identified magnesium (II) ions and the branching reaction as regulators of the equilibrium populations. The tuneable secondary structure/sugar pucker equilibrium supports a conformational selection mechanism to up- and downregulate catalytically active and inactive states of the branch site adenosine to orchestrate the multi-step splicing process. The conformational dynamics of group II intron domain 6 is also proposed to be a key aspect for the directionality selection in reversible splicing.

SUBMITTER: Plangger R 

PROVIDER: S-EPMC6868427 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

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Branch site bulge conformations in domain 6 determine functional sugar puckers in group II intron splicing.

Plangger Raphael R   Juen Michael Andreas MA   Hoernes Thomas Philipp TP   Nußbaumer Felix F   Kremser Johannes J   Strebitzer Elisabeth E   Klingler David D   Erharter Kevin K   Tollinger Martin M   Erlacher Matthias David MD   Kreutz Christoph C  

Nucleic acids research 20191201 21


Although group II intron ribozymes are intensively studied the question how structural dynamics affects splicing catalysis has remained elusive. We report for the first time that the group II intron domain 6 exists in a secondary structure equilibrium between a single- and a two-nucleotide bulge conformation, which is directly linked to a switch between sugar puckers of the branch site adenosine. Our study determined a functional sugar pucker equilibrium between the transesterification active C2  ...[more]

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