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2. A METAL ION STORY WITH A HAPPY ENDING
2.1. Discrepancies between biochemical and
crystallographic data
It is well known that mHHR sequences of only 43 residues retain almost full
catalytic activity, compared to the naturally found eHHR sequences with
63 residues, if the conserved core region is kept. The mHHR sequence
consists of three base-paired stems (stems I, II, and III) flanking a central core
of around 15 highly conserved nucleotide residues,
81-83
as shown in
Fig. 2.1
.
The conserved central bases, with few exceptions, are essential for the ribo-
zyme catalytic activity. The mHHR exhibits a turnover rate (
k
cat
) of about 1
molecule/min and a
k
m
in the order of 10 nM. The rate for cleavage and
ligation for the naturally occurring eHHR motifs are around 1000 and
2000 times
faster,
respectively,
than the
corresponding rates
for
mHHR.
84-86
Due to its size, the mHHR had originally been the main target to study
HHR and has been exhaustively studied by biochemists and enzymologists
as well as by X-ray crystallographers, NMR spectroscopists, and other
experimentalists using various biophysical techniques. The first detailed
Figure 2.1 The minimal functional HHR sequence (mHHR) with conserved core region
labeled with bold and italic letters. The letter N represents any RNA nucleotide (under
the complimentary sequence constraint).
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