Group I Intron Domain 4-6


1. Golden BL, Gooding AR, Podell ER, Cech TR. 1998. A preorganized active site in the crystal structure of the Tetrahymena ribozyme. Science 282:259-264 [Medline abstract]. Full-text HTML version

2. Cate, et al., 1996. Crystal Structure of a Group I Ribozyme Domain: Principles of RNA Packing. Science 273:1678. [Medline abstract] Full-text HTML version

I. Introduction
The group I intron from Tetrahymena was the first RNA for which a catalytic activity was described (ribozyme). It consists of ~400 nts of RNA, shown below, which can self-splice itself from a ribosomal RNA transcript.

The crystal structure of most of the ribozyme has been determined. (ref. 1) A domain of the intron, which has been shown to fold autonomously, called P4-P5-P6, has also been crystallized (ref. 2). This tutorial covers part of both papers. The P4-P6 domain is shown in purple, and the P3-P9 domain is shown in green. The P3-P9 domain wraps around the P4-P6 domain.

Click here <> to color the structure according to the secondary structure above and fig1 of ref1. The molecule rotated about 90 degrees from the begining of the tutorial. The active site, to which the substrate helix P1 (not shown) binds occurs near the interface of these domains, at the red J8/7 region and P7.

The crystal structure of the P4-P5-P6 domain of the group I intron provided several novel discoveries. Besides being the largest nucleic acid crystal structure solved to date, the structural model provided information on the tetraloop receptor, the tight turn, and the adenosine platform. You can compare structures of these motifs in the crystal of the whole ribozyme (this tutorial) with that for the P4-P6 domain alone. In general, the structure of the P4-P6 domain is very similar in both structures.
Click here <> to color the intron according to the secondary structure from ref. 2 below. It serves as a guide for the motifs described below. The tetraloop receptor is shown in green, the tetraloop is orange, and the tight turn is red.

I. The tetraloop receptor
The GNRA tetraloop is a conserved 4 nucleotide loop which is commonly found on RNA helices. In a previous theoretical model of the groupI intron structure, Michel and Westoff noticed that the sequence of some GNRA tetraloops influenced the sequence of base pairs in other helices, suggesting that they might form a tertiary interaction. Costa and Michel further noticed that the GAAA tetraloop seemed to interact with a particular sequence motif, termed the tetraloop receptor. Click here to see the structure of the tetraloop and receptor <>. The tetraloop is orange and the receptor is green. The A residues of the tetraloop H-bond and intercalate with the receptor. Click here to see a subset of these bases <>. A153 of the loop H-bonds to G150 within the loop, via N7 of A. N1 and N3 of A153 H-bond to the 2'-OH and exocyclic amine, respectively, of G250 of the receptor, resulting in a quadruple base interaction. The 2'-OH of A153 H-bonds to the O2 and 2'-OH of C223, which in turn forms a W-C pair with G250. This button < > shows the rest of the tetraloop receptor. A248 and U224 within the receptor form a reverse Hoogsteen A-U pair. A248 in turn forms a symmetric A-A pair with A151 of the tetraloop. The 2'-OH of U224 H-bonds to both N3 and the 2'-OH of A152.

II. The adenosine platform
Residues A225 and A226 within the tetraloop receptor form a structure termed the adenosine platform. These consecutive residues H-bond with each other (from N3 of A225 to N6 of A226) to form a motif which presents the adenosine residues for H-bonding or stacking with other residues. To zoom in on the adenosine platform of the tetraloop receptor, click here < >. In this case the adenosine platform stacks onto A151 of the tetraloop, shown in orange. Other adenosine platforms are found at residues 171-172 and at 218-219 of the P4-6 domain.

III. The tight turn
Residues 183 through 188 of the P4-6 domain form a tight turn of the RNA backbone. The phosphate oxygens of the backbone residues come within 3 angstroms in places. This is made possible by two Mg++ cations which coordinate with the phosphate oxygens of residues 183, 184, 186 and 187. Click here to zoom in on the tight turn <>. The Mg ions are not shown here, but can be seen in the P4-P6 tutorial. The backbone of the residues of the tight turn is shown in standard CPK colors and the bases are colored red. Residues flanking the tight turn are shown as a blue ribbon, and their base pairing partners are shown as a cyan ribbon.

IV. The ribose zipper
This region also includes another motif known as the ribose zipper, shown here <>. This interaction stabilizes the docking of antiparallel backbones through a series of H-bonds. In this case, the 2'OH of G110 H-bonds with the N3 and 2'OH of residue 183. Likewise, the 2'OH of A184 H-bonds with the 2'OH and O2 of C109. This interaction is not base specific, since the H-bonds are between a pair of 2'OH groups or between a 2'OH and purine N3 or pyrimidine O2.

This section Still Under Construction
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Comments or Suggestions to: Jim Nolan at