BIOINORGANIC CHEMISTRY A Short Course Second Edition

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

consisting of single - stranded RNA. They are smaller and simpler than viruses
and lack the typical viral protein cover. Hammerhead ribozymes also occur in
viroid - like satellite RNA (associated mostly with plant viruses) and in a few
eukaryotic species.^33 The hammerhead ribozyme motif effi ciently and site -
specifi cally cleaves RNA through a transesterifi cation reaction. The reaction
is initiated by a nucleophilic attack by the 2 ′ - oxygen of the nucleotide 5 ′ to
the cleavage site (in the hammerhead case, this is residue C17) on the cleavage
site phosphorus, yielding a 2 ′ ,3 ′ - cyclic phosphate and 5 ′ - hydroxyl product. (See
Figure 6.9 .)
The nucleophilic S N 2 mechanism requires that reactants be in line with each
other; that is, attack takes place along an approximate 180 ° axis. As will be
seen in descriptions of X - ray crystallographic structures below, this arrange-
ment does not appear to be the case in the solid - state structures, perhaps
because additional conformation changes are needed from the state visualized
by X - ray techniques. One or more cations may be required as catalysts for
ribozyme cleavage reactions. One cation may ionize the 2 ′ - hydroxyl group,
while another (or the same) cation may stabilize the pentacoordinate transi-
tion state by coordinating to the pro - R phosphate oxygen. During the trans-
esterifi cation the chirality of the phosphate group is inverted in an S N 2(P)
mechanistic process. The phosphorus atom in the phosphate connector is pro -
chiral since changing one of two oxygen atoms (substituting a sulfur for
instance as in the P - S rescue experiment) gives rise to a chiral center. Changing
one particular oxygen will give rise to an S confi guration (pro - S p oxygen),
while changing the other one would yield an R confi guration (pro - R p oxygen)
according to Cahn – Ingold – Prelog rules. (See Figure 6.2 .)
The hammerhead motif has a conserved secondary structure consisting of
a three - way helical junction. The helical elements may vary in base sequence
among species but thirteen bases at the three - way helical junction are con-
served and essential for ribozyme activity. X - ray structures to be discussed
below defi ne a domain organization based on the tertiary folding observed in

Figure 6.9 Hammerhead mechanism producing a 2 ′ ,3 ′ - cyclic phosphate.

C17

HO O

O

O

O

• O PO
  O

B

B

O

H:A A:

B:H B:H

C17

5'

2' 3'

A1.1

HO O

O

O

O

• O P
  O

B

B

O

Oδ

• B:H

C17

5'

2' 3'

A1.1

O

P

• O
  O

B

O

O

HO O

O

B OH

2' 3'

5'

A1.1

δ-

5' O

leaving group

2' O

nucleophile