PDBsum entry 1afx

RNA

PDB id: 1afx

Contents

DNA/RNA

PDB id:

1afx

Name:

RNA

Title:

Ugaa eukaryotic ribosomal RNA tetraloop, nmr, 13 structures

Structure:

RNA (5'-r( Gp Gp Up Gp Up Gp Ap Ap Cp Ap Cp C)-3'). Chain: a. Synonym: uga. Engineered: yes. Other_details: conserved ugaa tetraloop from eukaryotic 16s-like ribosomal RNA (5'-r(ggugugaacacc)-3')

Source:

Synthetic: yes

NMR struc:

13 models

Authors:

S.E.Butcher,T.Dieckmann,J.Feigon

Key ref:

S.E.Butcher et al. (1999). Solution structure of the loop B domain from the hairpin ribozyme. Nat Struct Biol, 6, 212-216. PubMed id: 10074938 DOI: 10.1038/6651

Date:

15-Mar-97 Release date: 15-May-97

DNA/RNA chain

G-G-U-G-U-G-A-A-C-A-C-C 12 bases

DOI no: 10.1038/6651

Nat Struct Biol 6:212-216 (1999)

PubMed id: 10074938

Solution structure of the loop B domain from the hairpin ribozyme.

S.E.Butcher, F.H.Allain, J.Feigon.

ABSTRACT

The hairpin ribozyme is a small catalytic RNA with a unique two-domain structure. Here we present the solution structure of the loop B domain of the hairpin ribozyme, which contains most of the catalytically essential nucleotides. The 38-nucleotide domain contains a 16-nucleotide internal loop that forms one of the largest non-Watson-Crick segments of base pairing thus far determined by either NMR or crystallography. Since the solution structure of the smaller loop A domain has been previously solved, an NMR structure-based model of the 22,000 Mr hairpin ribozyme-substrate open complex emerges by joining the two domain structures. Strikingly, catalytically essential functional groups for the loop B domain are concentrated within an expanded minor groove, presenting a clear docking surface for the loop A domain.

Selected figure(s)

Figure 2.
Figure 2. The 10 lowest energy structures (of 28 converged structures; Table 1). a, Structures superimposed on the internal loop B (residues 20−26, 36−40, 42−44). View is into the minor groove of the internal loop B. Stem 1 and stem 2 and UUCG tetraloop from the lowest energy structure are shown. b, Superimposition on the residues forming the UV-photosensitive module (residues 20−23, 40−44). c, Superimposition on the 12 residues forming the lower stem and the UUCG tetraloop. Adenine nucleotides are shown in red, guanines in green, cytosines in yellow and uracils in cyan. For clarity, only 10 structures are shown superimposed.

Figure 3.
Figure 3. a, Stereo view of the lowest energy structure of the internal loop B. b, The seven non-Watson−Crick base pairs of the lowest energy structure. These base orientations were found for the majority of the 28 converged structures of loop B. Color scheme is the same as Fig. 2.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1999, 6, 212-216) copyright 1999.

Figures were selected by an automated process.