258 GROUP I AND II METALS IN BIOLOGICAL SYSTEMS: GROUP II
A more detailed crystal structure for the Azoarcus sp. ribozyme was pub-
lished by Stahley and Strobel inScience magazine in 2005 (PDB:1ZZN).^31
This structure visualized a catalytically active group I intron splicing interme-
diate. The construct crystallized retained the ability to catalyze exon ligation
at a slow rate and displayed a structure attained just before the second chemi-
cal step (pre - 2S, Figure 6.1 , part iv). It contained the complete intron, both
exons, and the scissile phosphate, all the functional groups previously associ-
ated with catalytical metal ion coordination and the 2 ′ - OH of the terminal
guanosine ( ω G, PDB: 1ZZN residue G206). Inclusion of the ω G 2 ′ - OH nor-
mally would increase the rate of splicing 10^6 - fold; however, the rate is slowed
(to encourage crystallization) by a 2 ′ - deoxy substitution at the 5 ′ - exon ’ s last
nucleotide, U − 1 (5MU1 in the terminology of PDB: 1ZZN). Two metal ions
visualized in the structure serve to position the substrates (the 3 ′ - and 5 ′ -
exons), activate the nucleophile (O3 ′ of 1ZZN residue variously identifi ed as
5MU1, U − 1 , dt − 1 (in PDB: 1U6B)), and stabilize the charge on the leaving group
(O3′ of 1ZZN residue ω G) and the scissile phosphate. The two visualized
magnesium ions in the active site, placed 3.9 Å apart, coordinate 10 oxygen
ligands including those of the 5 ′ - exon attacking nucleophile (O3 ′ of
UMg− 11 −=^2 + 21.Å) and the intron leaving group (O3 ′ of ωGMg−= 22 + 21. Å).
See Figure 3C of reference 31. Other bond distances and angles are collected
in Table 6.2.
The pro - S p oxygen ’ s of nucleotides U 173 for Mg 12 + and A 87 for Mg 22 + make
coordination sphere contacts to complete the magnesium ion octahedral coor-
dination sphere in this structure. The two magnesium ions appear to be well -
placed to catalyze the exon ligation reaction with Mg 12 + coordinated to the
nucleophile (O3 ′ of U − 1 ) and the A +1 scissile phosphate pro - R p oxygen. Mg 22 +
also coordinates the A +1 scissile phosphate pro - R p oxygen, the O2 ′ oxygen, and
the O3 ′ leaving group of ω G (G206 in PDB: 1ZZN). In addition, the metal
ions coordinate all biochemically predicted metal ion ligands. In the PDB:
1ZZN structure the O3 ′ U − 1 nucleophile and A +1 scissile phosphate group are
ideally aligned for the predicted nucleophilic attack by a S N 2 mechanism with
the O3 ′ (U − 1 ) – P (A +1 ) distance equal to 3.2 Å and the O3 ′ (U − 1 ) – P (A +1 ) – O3 ′
(ω G) angle equal to 175 °. The catalytic site is illustrated in Figure 6.8 , with
nucleophile O3 ′ , phosphorus of scissile phosphate group, and leaving group
O3′ in yellow. Other magnesium ion ligand atoms are shown in orange. Exon –
exon bond formation is indicated.
The authors Stahley and Strobel^31 believe that this two - metal ion intermedi-
ate describes the catalytic site bonding characteristics better than that of the
three - metal ion described by Herschlag and Piccirilli.^27 Although Stahley and
Strobel ’ s results for PDB: 1ZZN do not rule out a disordered third metal ion
in their crystal structure, they believe that the great majority of the biochemi-
cal data is explained by their two - metal model. Consequently, they would
equate their Mg 12 + (M 1 ) with reference 27 ’ s M A and their Mg 22 + (M 2 ) with
reference 27 ’ s M B plus M C. These authors also refer to other group I intron
structures published in 2004 and 2005. In the PDB: 1X8W structure published