BIOINORGANIC CHEMISTRY A Short Course Second Edition

240 GROUP I AND II METALS IN BIOLOGICAL SYSTEMS: GROUP II

nucleic acid – base interactions but also on interactions between ribose sugars
and phosphates as well. One author pointed out that protein enzymes and
ribozymes seem “ inside out ” with respect to each other. Ribozyme secondary
structure is dependent on hydrogen bonding between nucleic acid bases that
point inward with only the repetitive sugars and phosphates pointing outward,
whereas protein enzyme secondary structure involves the peptide backbone
with diverse amino acid side chains pointing outward for higher - order interac-
tions.^9 To show that sugar positions must be used in assembling a ribozyme ’ s
active site, researchers substituted 2 ′ - deoxy, 2 ′ - methoxy, or 2 ′ - fl uorine site -
specifi cally for RNA ’ s 2 ′ - OH group and measured the activity of the resulting
mutant. These experiments revealed specifi c sugar backbone contacts neces-
sary for catalysis.^10 Installation of a photocrosslinkable group on the 5 ′ phos-
phate of the so - called internal guide sequence (IGS) of Group I introns
showed that conformation changes at this site must accompany substrate
binding and reaction.^11 In these systems, a specifi c guanosine binding site (the
G site) is found on the intron RNA, an exogenous (from solution) guanosine
(GOH ) binds there, and the intron provides an “ internal guide sequence ” (IGS)
to bring the two exons (3 ′ exon region and 5 ′ exon region) close together. (See
Figure 6.1 .)
Important questions regarding the individual steps in the reaction mecha-
nism were studied during the 1990s by substituting DNA (deoxy at the 2 ′ - sugar

Figure 6.1 The group I intron exon - splicing mechanism. (Adapted with permission
from Figure 1 of reference 24. Copyright 2004, with permission from Elsevier.)

ωG ωG

OH

ωG

OH

ωG

G

iv

ωGOH

G

vi v

ωG

ωGOH

G

ωG

Watson-Crick pairs

key to figure

G-U wobble base pair

exon

intron

G

G site GOH

G-binding

GOH

3'

5'

3'

5' G

chem.1

i ii iii

conformational

changes

5'

5' 5'

3'

3'

3'

exon release chem.2

phosphotransesterification #1

phosphotransesterification #2

chem.3

RNA oligonucleotide

release

(like PDB: 1Y0Q)

vii

PDB: 1U6B

and 1ZZN