Crystal Structure of a Group I Ribozyme Domain: Principles of RNA Packing

  title={Crystal Structure of a Group I Ribozyme Domain: Principles of RNA Packing},
  author={Jamie H. D. Cate and Anne R Gooding and Elaine R. Podell and Kaihong Zhou and Barbara L Golden and Craig E Kundrot and Thomas R. Cech and Jennifer A. Doudna},
  pages={1678 - 1685}
Group I self-splicing introns catalyze their own excision from precursor RNAs by way of a two-step transesterification reaction. The catalytic core of these ribozymes is formed by two structural domains. The 2.8-angstrom crystal structure of one of these, the P4-P6 domain of the Tetrahymena thermophila intron, is described. In the 160-nucleotide domain, a sharp bend allows stacked helices of the conserved core to pack alongside helices of an adjacent region. Two specific long-range interactions… 
Joining the Two Domains of a Group I Ribozyme to Form the Catalytic Core
Site-directed mutagenesis and kinetic analysis of RNA splicing were used to identify a base triple in the conserved core of both a cyanobacterial and a eukaryotic (Tetrahymena) group I intron, revealing exceptionally dense packing of RNA.
Metal-binding sites in the major groove of a large ribozyme domain.
Crystal structure of a phage Twort group I ribozyme–product complex
The structure of the active site of an active ribozyme derived from the orf142-I2 intron from phage Twort bound to a four-nucleotide product RNA is solved and reveals three potential binding sites for catalytic metals.
Crystal structure of a group I intron splicing intermediate.
Models of the pre-first and pre-second steps of intron splicing are proposed with full-sized tRNA exons, suggesting that the tRNA undergoes substantial angular motion relative to the intron between the two steps of splicing.
Crystal structure of the ribosomal RNA domain essential for binding elongation factors.
The structure of a 29-nucleotide RNA containing the sarcin/ricin loop (SRL) of rat 28 S rRNA has been determined and comparisons with other RNA crystal structures establish the cross-strand A stack and the GNRA tetraloop as defined and modular RNA structural elements.
Contributions to the study of the architecture and evolution of ribozymes
The pk-turn, a new RNA motif related to k-turns that allow for the formation of a bend of 60° between stems P16 and P17 from the bacterial RNaseP, is identified.
A minor groove RNA triple helix within the catalytic core of a group I intron
Using nucleotide analog interference suppression (NAIS), it is demonstrated that the P1 substrate helix and J8/7 single stranded segment form an extended minor groove triple helix within the catalytic core of the ribozyme.
Structure and thermodynamics of metal binding in the P5 helix of a group I intron ribozyme.
Structural and thermodynamic results provide systematic new information about major groove metal ion binding in RNA and can be understood in terms of the different structures of the corresponding metal ion-RNA complexes.


An independently folding domain of RNA tertiary structure within the Tetrahymena ribozyme.
The Tetrahymena thermophila pre-rRNA contains a 413-nucleotide self-splicing group I intron, which is modular, containing a separable domain and subdomain of tertiary structure and a subdomain-stabilized structure involving long-range interactions.
Self-assembly of a group I intron active site from its component tertiary structural domains.
The proposed tertiary structure domains of the Tetrahymena intron were synthesized separately and shown to self-assemble into a catalytically active complex, revealing that the domains interact with nanomolar apparent dissociation constants, even though there is no known base pairing between P4-P6 and P3-P9.
Two major tertiary folding transitions of the Tetrahymena catalytic RNA.
It is concluded that the role of the extended P4‐P6 domain and of the 3′‐terminal peripheral elements is at least in part to stabilize the catalytic core.
RNA Tertiary Structure Mediation by Adenosine Platforms
The crystal structure of a group I intron domain reveals an unexpected motif that mediates both intra- and intermolecular interactions and provides explanation for the abundance of adenosine residues in internal loops of many RNAs.
Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix
The crystal structure of an intermolecular complex between a GAAA tetraloop and an RNA helix is described, suggesting that this complex is a legitimate model for intramolecular tertiary interactions mediated by GNRA tetraloops in large structured RNAs.
Three-Dimensional Structure of Yeast Phenylalanine Transfer RNA: Folding of the Polynucleotide Chain
At 4 � resolution the polynucleotides in yeast phenylalanine transfer RNA are seen in a series of electron dense masses about 5.8 � apart, and it is possible to trace the entire polyn DNA chain with only two minor regions of ambiguity.
RNA folding causes secondary structure rearrangement.
  • M. Wu, I. Tinoco
  • Chemistry, Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1998
The secondary structure of the P5abc subdomain (a 56-nt RNA) of the Tetrahymena thermophila group I intron ribozyme has been determined by NMR and its base pairing in aqueous solution is significantly different from the RNA in a crystal but is consistent with thermodynamic predictions.
Solution structure of a GAAA tetraloop receptor RNA
The solution structure of the isolated tetraloop receptor is reported as solved by multidimensional, heteronuclear magnetic resonance spectroscopy and a model for an alternative binding site within the receptor is proposed based on the NMR structure, phylogenetic data and previous crystallographic structures of tetraloops interactions.
A conserved base pair within helix P4 of the Tetrahymena ribozyme helps to form the tertiary structure required for self‐splicing.
It is proposed that, in addition to its pairing in P4, G212 is involved in a base triplet or an alternate base pair that contributes to the catalytically active tertiary structure of the ribozyme.