PDBsum entry 2a12

Ribonucleic acid

PDB id: 2a12

Contents

DNA/RNA

Theoretical model

PDB id:

2a12

Name:

Ribonucleic acid

Title:

Theoretical model of the ai5g group ii intron

Structure:

42-mer. Chain: a. Fragment: group ii intron - fragment 1. 220-mer. Chain: b. Fragment: group ii intron - fragment 2. 83-mer. Chain: c. Fragment: group ii intron - fragment 3.

Source:

Saccharomyces cerevisiae. Yeast. Yeast

Authors:

A.De Lencastre,S.Hamill,A.M.Pyle

Key ref:

A.de Lencastre et al. (2005). A single active-site region for a group II intron. Nat Struct Mol Biol, 12, 626-627. PubMed id: 15980867 DOI: 10.1038/nsmb957

Date:

17-Jun-05 Release date: 05-Jul-05

DNA/RNA chains

G-U-G-G-U-G-G-G-A-C-A-U-U-U-U-C-G-A-G-C-G-G-U-C-U-G-A-A-A-G-U-U-A-U-C-A-U-A ... 42 bases

U-A-U-A-U-U-U-U-U-A-U-C-A-A-U-A-U-A-A-G-U-C-U-A-A-U-U-A-C-A-A-G-U-G-U-A-U-U ... 220 bases

A-A-A-U-G-G-U-U-G-A-U-G-U-U-A-U-G-U-A-U-U-G-G-A-A-A-U-G-A-G-C-A-U-A-C-G-A-U ... 83 bases

U-A-U-U-U-A-U-G-A-U-A-A-A-A-C-A-G-A-A-U-A-A-C-U-C-C-U 27 bases

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

U-G-A-G-C-C-G-U-A-U-G-C-G-A-U-G-A-A-A-G-U-C-G-C-A-C-G-U-A-C-G-G-U-U-C-U-U-A ... 45 bases

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

DOI no: 10.1038/nsmb957

Nat Struct Mol Biol 12:626-627 (2005)

PubMed id: 15980867

A single active-site region for a group II intron.

A.de Lencastre, S.Hamill, A.M.Pyle.

ABSTRACT

Despite the biological importance of self-splicing group II introns, little is known about their structural organization. Synthetic incorporation of site-specific photo-cross-linkers within catalytic domains resulted in functional distance constraints that, when combined with known tertiary interactions, provide a three-dimensional view of the active intron architecture. All functionalities important for both steps of splicing are proximal before the first step, suggestive of a single active-site region for group II intron catalysis.

Selected figure(s)

Figure 1.
Figure 1. Photo-cross-links from the branch site and from the 3' exon. (a) Polyacrylamide gel for visualization and isolation of cross-linked [32P]D56 and [32P]D56(+1) species (bands A -C). Lanes 1 and 2, unmodified D56; lanes 3 and 4, D56 containing a s6dG at the branch site (A880); lanes 5 and 6, D56 ligated with s6dG at the 3' end (D56(+1)). Cross-linking efficiencies are 3.3%, 5.1% and 1.2%, respectively, for bands A -C. (b) Mapping of cross-links A and C by reverse transcriptase primer extension (lanes 4 and 5, respectively; lane 3, primer extension control on un-cross-linked material).

Figure 2.
Figure 2. A close-up view of the active-site region, derived from the ai5 gamma group II intron model (Supplementary Fig. 4 online). Regions of proximity are highlighted in green (G817, D5 bulge, first nucleotides of the 5' exon and 3' exon, and the branch site (A880)). The scissile phosphate (yellow ball), branch site 2'-OH (red ball) and first nucleotide of the 3' exon (gray line) are shown. Color scheme: IBS1, purple; 5'-end of domain 1, including , magenta; ', pink; coordination loop- , cyan; EBS1, brown; J2/3, blue; D5, red; bottom stem of D6, orange.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2005, 12, 626-627) copyright 2005.