1R2P

Solution structure of domain 5 from the ai5(gamma) group II intron

Summary for 1R2P

• Entry DOI: 10.2210/pdb1r2p/pdb
• Related: 1kxk
• NMR Information: BMRB: 5962
• Descriptor: 34-MER (1 entity in total)
• Functional Keywords: rna hairpin, tetraloop, bulge, metal ion, magnesium, rna
• Total number of polymer chains: 1
• Total formula weight: 10970.57

Authors

Sigel, R.K.O.,Sashital, D.G.,Abramovitz, D.L.,Palmer III, A.G.,Butcher, S.E.,Pyle, A.M. (deposition date: 2003-09-29, release date: 2004-02-03, Last modification date: 2024-05-22)

Primary citation

Sigel, R.K.,Sashital, D.G.,Abramovitz, D.L.,Palmer, A.G.,Butcher, S.E.,Pyle, A.M.
Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif.
Nat.Struct.Mol.Biol., 11:187-192, 2004

PubMed Abstract: Domain 5 (D5) is the central core of group II intron ribozymes. Many base and backbone substituents of this highly conserved hairpin participate in catalysis and are crucial for binding to other intron domains. We report the solution structures of the 34-nucleotide D5 hairpin from the group II intron ai5 gamma in the absence and presence of divalent metal ions. The bulge region of D5 adopts a novel fold, where G26 adopts a syn conformation and flips down into the major groove of helix 1, close to the major groove face of the catalytic AGC triad. The backbone near G26 is kinked, exposing the base plane of the adjacent A-U pair to the solvent and causing bases of the bulge to stack intercalatively. Metal ion titrations reveal strong Mg(2+) binding to a minor groove shelf in the D5 bulge. Another distinct metal ion-binding site is observed along the minor groove side of the catalytic triad, in a manner consistent with metal ion binding in the ribozyme active site.

PubMed: 14745440
DOI: 10.1038/nsmb717

Experimental method

SOLUTION NMR