Nmr solution structure of the d3'-stem closed by a gaaa tetraloop of the group ii intron sc.Ai5(gamma)
Structure:
5'-r( Gp Gp Ap Gp Up Ap Up Gp Up Gp Ap Ap Ap Gp Cp Ap Up Ap Cp Up Cp C)-3'. Chain: a. Engineered: yes
Source:
Synthetic: yes
NMR struc:
20 models
Authors:
D.Kruschel,R.K.O.Sigel
Key ref:
D.Kruschel
et al.
(2014).
NMR structure of the 5' splice site in the group IIB intron Sc.ai5γ--conformational requirements for exon-intron recognition.
Rna,
20,
295-307.
PubMed id: 24448450
DOI: 10.1261/rna.041137.113
NMR structure of the 5' splice site in the group IIB intron Sc.ai5γ--conformational requirements for exon-intron recognition.
D.Kruschel,
M.Skilandat,
R.K.Sigel.
ABSTRACT
A crucial step of the self-splicing reaction of group II intron ribozymes is the
recognition of the 5' exon by the intron. This recognition is achieved by two
regions in domain 1 of the intron, the exon-binding sites EBS1 and EBS2 forming
base pairs with the intron-binding sites IBS1 and IBS2 located at the end of the
5' exon. The complementarity of the EBS1•IBS1 contact is most important for
ensuring site-specific cleavage of the phosphodiester bond between the 5' exon
and the intron. Here, we present the NMR solution structures of the d3' hairpin
including EBS1 free in solution and bound to the IBS1 7-mer. In the unbound
state, EBS1 is part of a flexible 11-nucleotide (nt) loop. Binding of IBS1
restructures and freezes the entire loop region. Mg(2+) ions are bound near the
termini of the EBS1•IBS1 helix, stabilizing the interaction. Formation of the
7-bp EBS1•IBS1 helix within a loop of only 11 nt forces the loop backbone to
form a sharp turn opposite of the splice site, thereby presenting the scissile
phosphate in a position that is structurally unique.
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