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Non-Enzymatic Biological Catalysis 257
The rate of reaction is in fact limited by formation of the starting complex
rather than the phosphotransfer step, so the Tetrahymena ribozyme is highly
eYcient at catalysing its own self-splicing. However, it is debatable whether the
Tetrahymena ribozyme can be classiWed as a true catalyst, since it is modiWed in
structure by the reaction.
There are now a number of examples of such catalytic RNA species, whose
mechanisms of catalysis can be studied. The hairpin ribozyme is a 92-nucleotide
catalytic RNA which catalyses the reversible, site-speciWc cleavage of the
phosphodiester backbone of RNA through transesteriWcation. Although this
catalytic RNA requires Mg 2þ for activity (a common feature of catalytic
RNA), replacement with [Co(NH 3 ) 6 ] 3þ retains activity, implying that Mg 2þ
ions are not directly involved in catalysis. Determination of the X-ray crystal
structure of the hairpin ribozyme in complex with a pentavalent vanadate
transition state analogue (shown in Figure 12.2) has shown that a rigid active
site makes additional hydrogen bonds to the transition state. These hydrogen
bonds are formed by nitrogen atoms of active site RNA bases, as shown in
Figure 12.3. These observations suggest that RNA catalysis can employ transition
state stabilisation by RNA bases, in a similar fashion to protein-based
enzymes.
It has long been established that the ribosome, the cellular machinery
responsible for protein biosynthesis, contains RNA. Biochemical studies of
the peptidyl transferase activity of the ribosome have indicated that RNA is
responsible for catalysis, which was proved in dramatic fashion in 2000 by the
determination of the X-ray crystal structure of the large ribosomal sub-unit of
the Haloarcula marismortui ribosome. Co-crystallisation with substrate analogues
has shown that the catalytic site is composed entirely of RNA, with N-3
of A2486 apparently involved in acid–base catalysis during peptide bond formation,
as shown in Figure 12.4.
The fact that RNA can catalyse chemical reactions and carry genetic information
oVers the possibility that it might have been the information storage
system of primitive pre-cellular life. This would solve a paradox, that whilst
DNA is a superb carrier of genetic information, it requires protein in order for
the information to be expressed; whereas protein is highly proWcient in catalysis,
but it requires DNA to encode its sequence. There is, therefore, considerable
interest in the study of catalytic RNA as an evolutionary forerunner of DNAbased
information storage and protein catalysis. In this respect it is interesting
to note that many of the coenzymes that are used today in enzymatic reactions
contain ribonucleotides: adenosine triphosphate (ATP), nicotinamide adenine
dinucleotide (NAD), Xavin adenine dinucleotide (FAD), S-adenosyl methionine
(SAM) and vitamin B 12 . Maybe these molecules (or their ancestors) were
key players in pre-biotic chemistry.