3BO2

A relaxed active site following exon ligation by a group I intron

Summary for 3BO2

• Entry DOI: 10.2210/pdb3bo2/pdb
• Related: 3BO3 3BO4
• Descriptor: Group I intron P9, RNA (5'-R(*AP*AP*GP*CP*CP*AP*CP*AP*CP*AP*AP*AP*CP*CP*AP*G)-3'), RNA (5'-R(*AP*CP*GP*GP*CP*C)-3'), ... (7 entities in total)
• Functional Keywords: group i intron, azoarcus, ribozyme, ligation, acetylation, mrna processing, mrna splicing, nucleus, ribonucleoprotein, rna-binding, spliceosome, nuclear protein-rna complex, nuclear protein/rna
• Biological source: Homo sapiens (human); More
• Cellular location: Nucleus: P09012
• Total number of polymer chains: 5
• Total formula weight: 83234.98

Authors

Lipchock, S.V.,Strobel, S.A. (deposition date: 2007-12-17, release date: 2008-04-01, Last modification date: 2024-02-21)

Primary citation

Lipchock, S.V.,Strobel, S.A.
A relaxed active site after exon ligation by the group I intron
Proc.Natl.Acad.Sci.Usa, 105:5699-5704, 2008

PubMed Abstract: During RNA maturation, the group I intron promotes two sequential phosphorotransfer reactions resulting in exon ligation and intron release. Here, we report the crystal structure of the intron in complex with spliced exons and two additional structures that examine the role of active-site metal ions during the second step of RNA splicing. These structures reveal a relaxed active site, in which direct metal coordination by the exons is lost after ligation, while other tertiary interactions are retained between the exon and the intron. Consistent with these structural observations, kinetic and thermodynamic measurements show that the scissile phosphate makes direct contact with metals in the ground state before exon ligation and in the transition state, but not after exon ligation. Despite no direct exonic interactions and even in the absence of the scissile phosphate, two metal ions remain bound within the active site. Together, these data suggest that release of the ligated exons from the intron is preceded by a change in substrate-metal coordination before tertiary hydrogen bonding contacts to the exons are broken.

PubMed: 18408159
DOI: 10.1073/pnas.0712016105

Experimental method

X-RAY DIFFRACTION (3.31 Å)