MAGNESIUM AND CATALYTIC RNA 255
the Scott Strobel research group (PDB: 1U6B).^22 This 222 nucleotide structure
included theAzoarcus intron in complex with both of its exons in a confor-
mational state preceding the second step of splicing. This is called the pre - 2S
state, in Figure 6.1 represented as the part iv structure, preceding the chem.2
step. The crystallized pre - 2S state involved the introduction of 2 ′ - deoxy sub-
stitutions at U − 1 (dt − 1 ), A +1 (da +1 ), A205 (da 205 ), and Ω G ( Ω dg, the 3 ′ - OH ter-
minus, PDB: 1U6B residue G206). These substitutions reduce the intron ’ s
splicing activity 10^6 - fold so that the structure may be visualized using X - ray
crystallography. The intron – exon complex was prepared by annealing the
RNA transcript — residues α G1 – A190 — with two RNA – DNA chimerical oli-
gonucleotides (CAT, 3 nt, PDB: 1U6B chain D and dCIRC, 22 nt, PDB: 1U6B
chain C containing theΩ G, G206 residue). The chimerical oligonucleotides are
represented by lowercase letters — that is, cadt − 1 for the CAT nucleotide and
da+1 through Ω dg for the dCIRC nucleotide. The all - ribose version of this
complex produced ligated exons, whereas the crystallized, deoxy - substituted
complex showed no splicing activity after several days. The pre - 2S intron
appears as three coaxially stacked helical elements. The fi rst of these includes
P10 (PDB: 1U6B residues α G1, 5 – 9), P1 PDB: 1U6B residues 10 – 12), and P2
(PDB: 1U6B residues 13 – 37, including a GAAA tetraloop). In Figure 6.7 ,
these are colored orange. The second element includes P5 (PDB: 1U6B resi-
dues 60 – 84, including a GCCC tetraloop), P4 (PDB: 1U6B residues 51 – 56 and
88 – 93), P6 (PDB: 1U6B residues 94 – 96 and 122 – 124), and P6a (PDB: 1U6B
residues 100 – 119, including a large loop that interfaces with the co - crystallized
RNA binding protein U1A). These elements are colored green in Figure 6.7.
The third element includes P9.0 and P9 (PDB: 1U6B residues 180 – 205, includ-
ing a GAaa tetraloop), P7 (PDB: 1U6B residues 173 – 178 and 128 – 135), P3
(PDB: 1U6B residues 41 – 47 and 136 – 143 and P8 (PDB: 1U6B residues 144 –
166, including a CAAA tetraloop). These elements are colored blue in Figure
6.7. Additionally, a number of connectors join helical segments. These include:
J2/3 (residues 38 – 40); J3/4 (residues 47 – 50); J4/5 (57 – 59); J5/4 (85 – 87); J6/7
(126 – 128); and J8/7 (residues 167 – 172). This last important joint is colored
violet in Figure 6.7. Chimerical internal guide sequence (IGS) deoxy residues
a+1 – c +6 and dt − 1 – c − 3 are colored yellow except for a +1 and dt − 1 , which are colored
red and displayed in ball - and - stick format. This pair is in close proximity to
theΩ G (PDB: 1U6B G206) residue, visualized in space fi ll format in Figure
6.7. The structure also visualizes 18 metal ions, some of which are shown in
Figure 6.7. Note that a potassium ion as well as a magnesium ion are positioned
to bond to atoms inΩ G, a +1 , and dt − 1. The P2 GAAA tetraloop forms contacts
with tetraloop receptors in helix P8 (GAAA tetraloop residues in orange stick
format in Figure 6.7 ), while the P9 tetraloop (GAaa) forms interactions with
residues in helix P5. The relative placement of helices P4 – P6 and P3 – P9.0
approximates that observed in theTetrahymena structures discussed previ-
ously in this section. In the PDB: 1U6B structure, the 5 ′ - exon ’ s 3 ′ - OH group
(residue dt − 1 ) is positioned for inline nucleophilic attack on the scissile phos-
phate at position da +1 of the intron - 3 ′ – exon junction (see below).