PDBsum entry 4faq

RNA

PDB id: 4faq

Contents

DNA/RNA

Ligands

SPM ×2

EPE ×6

Metals

_CA ×24

__K ×20

Waters ×45

PDB id:

4faq

Name:

RNA

Title:

Structure of oceanobacillus iheyensis group ii intron in the presence of k+, ca2+ and 5'-exon

Structure:

Group iic intron. Chain: a. Fragment: domains 1-5. Engineered: yes

Source:

Synthetic: yes. Oceanobacillus iheyensis. Organism_taxid: 182710. Other_details: in vitro transcription

Resolution:

3.11Å R-factor: 0.204 R-free: 0.258

Authors:

M.Marcia,A.M.Pyle

Key ref:

M.Marcia and A.M.Pyle (2012). Visualizing group II intron catalysis through the stages of splicing. Cell, 151, 497-507. PubMed id: 23101623

Date:

22-May-12 Release date: 14-Nov-12

DNA/RNA chain

G-U-U-A-U-G-U-G-U-G-C-C-C-G-G-C-A-U-G-G-G-U-G-C-A-G-U-C-U-A-U-A-G-G-G-U-G-A-G- ... 396 bases

Cell 151:497-507 (2012)

PubMed id: 23101623

Visualizing group II intron catalysis through the stages of splicing.

M.Marcia, A.M.Pyle.

ABSTRACT

Group II introns are self-splicing ribozymes that share a reaction mechanism and a common ancestor with the eukaryotic spliceosome, thereby providing a model system for understanding the chemistry of pre-mRNA splicing. Here we report 14 crystal structures of a group II intron at different stages of catalysis. We provide a detailed mechanism for the first step of splicing, we describe a reversible conformational change between the first and the second steps of splicing, and we present the ligand-free intron structure after splicing in an active state that corresponds to the retrotransposable form of the intron. During each reaction, the reactants are aligned and activated by a heteronuclear four-metal-ion center that contains a metal cluster and obligate monovalent cations, and they adopt a structural arrangement similar to that of protein endonucleases. Based on our data, we propose a model for the splicing cycle and show that it is applicable to the eukaryotic spliceosome.