2M57

NMR solution structure of domain 5 from Azotobacter vinelandii Intron 5 at pH 7.8

Summary for 2M57

• Entry DOI: 10.2210/pdb2m57/pdb
• NMR Information: BMRB: 19039
• Descriptor: RNA_(35-MER) (1 entity in total)
• Functional Keywords: rna, ribozyme, group ii intron, hairpin
• Biological source: Azotobacter vinelandii
• Total number of polymer chains: 1
• Total formula weight: 11268.71

Authors

Pechlaner, M.,Donghi, D.,Zelenay, V.,Sigel, R.K.O. (deposition date: 2013-02-15, release date: 2014-02-26, Last modification date: 2025-03-12)

Primary citation

Pechlaner, M.,Donghi, D.,Zelenay, V.,Sigel, R.K.
Protonation-Dependent Base Flipping at Neutral pH in the Catalytic Triad of a Self-Splicing Bacterial Group II Intron.
Angew.Chem.Int.Ed.Engl., 54:9687-9690, 2015

PubMed Abstract: NMR spectroscopy has revealed pH-dependent structural changes in the highly conserved catalytic domain 5 of a bacterial group II intron. Two adenines with pK(a) values close to neutral pH were identified in the catalytic triad and the bulge. Protonation of the adenine opposite to the catalytic triad is stabilized within a G(syn)-AH(+) (anti) base pair. The pH-dependent anti-to-syn flipping of this G in the catalytic triad modulates the known interaction with the linker region between domains 2 and 3 (J23) and simultaneously the binding of the catalytic Mg(2+) ion to its backbone. Hence, this here identified shifted pK(a) value controls the conformational change between the two steps of splicing.

PubMed: 26119804
DOI: 10.1002/anie.201504014

Experimental method

SOLUTION NMR