MAGNESIUM AND CATALYTIC RNA 261
conserved features in other RNA – RNA or RNA – protein structures. For
instance, the Twort guanosine - binding site for the ω G nucleotide adopts a
tertiary structure very similar to that found in other group I introns only
changing the specifi c nucleotide found at a given position. Reference 32 lists
these homologous positions for the Twort, Tetrahymena thermophila and Azo-
arcus introns in its Table 1. These researchers describe the guanosine - binding
site as located in the six - base - pair P7 helix with a single - base bulge at residue
C121. Contributions from nucleotides in the J6/7 and J8/7 junctions are also
found in the P7 major groove. Notably in the PDB: 1Y0Q structure, ω G (G252)
forms a base triple interaction with the G122 – C192 base pair within helix P7.
The G122 – C192 base pair also interacts with the C121 bulge base. A second
base triple composed of A120 – U193 ∼ C121 stacks with the ω G ∼ G122 – C192
triple. Similar base triple interactions for PDB: 1X8W are shown in Figure 6.6.
The ω G (G206) base triple is formed by ω G ∼ G128 – C178 (PDB: 1Y0Q num-
bering) with a continuing interaction to A129.
Next, the Golden research group co - crystallized the Twort ribozyme with
manganese ions (as better diffracting magnesium ion analogs) to show interac-
tions of metal ions within the PDB: 1Y0Q structure. A manganese - binding site
(Mn1) was positioned well to be M A of the three - metal - ion mechanism based
on biochemical experiments, especially those of Herschlag and co - workers as
discussed for the other group I introns.^27 In the PDB: 1Y0Q structure, Mn1
was placed within 4 Å of the O3 ′ of ω G and the O3 ′ of U − 1 (U4, chainB in
PDB: 1Y0Q) at the 5 ′ splice site and exhibited innersphere coordination to
other nonbridging phosphates as predicted by the biochemical experiments.
The same metal ion showed coordination to a scissile phosphate oxygen when
this group was modeled into the structure. The biochemically predicted M B
and M C metal ions were not observed in the electron density maps for PDB:
1Y0Q. Modeling of M C into the structure placed it in a position for interaction
with the scissile phosphate and other biochemically predicted phosphate
oxygens (as discussed above forTetrahymena and Azoarcus introns). In com-
parison to the Azoarcus structures PDB: 1U6B and 1ZZN, the PDB: 1Y0Q
structure is similar with respect to the placement of M A (M 1 in PDB: 1U6B
and 1ZZN) and the PDB: 1Y0Q modeled M C (M 2 in PDB: 1U6B and 1ZZN).
However, none of these crystal structures visualize a metal ion at the bio-
chemically predicted position M B. The reference 32 authors agree with the
statements of other researchers in this area that more work will be necessary
to determine the position of metal ions in the ground and/or transition states
of group I introns. It should be said before beginning discussion of the ham-
merhead ribozyme that there is much more agreement on structure – function
details for the group I introns than will be found for the hammerhead
ribozyme.
6.2.4 The Hammerhead Ribozyme
The hammerhead ribozyme, so named because of its claw hammer shape, is a
small catalytic motif conserved in plant viroids. Viroids are infectious agents