66 BIOCHEMISTRY FUNDAMENTALS
The criteria described have broadened as more zinc - fi nger proteins have
become known, so that the “ zincfi nger ” designation now serves to describe
any relatively short protein sequence that contains four or more cys and/or
his residues and which is believed to interact with a nucleic acid binding
domain.^28 Small differences in the primary, secondary, and tertiary structure
of the proteins are common; for instance, the α - helical region of the peptide
for TFIIIA extends through both histidine ligands; however, the α - helical
region for the ADR1 peptide extends only to the fi rst histidine ligand. In
individual zinc fi ngers, the helical region varies from 5 to 11 amino acids long.
Other zinc fi ngers exhibit 3 – 10 helices rather than the more common α - helix.
In all cases, the helical region is intimately involved in DNA interaction.
Other zinc - containing structural motifs are known, including the protein
GAL4, a transcription factor required for galactose utilization in S cerevisiae.^29
The crystal structure of this protein bound to an oligonucleotide indicates that
GAL4 is a protein dimer. Each monomer unit contains a binuclear zinc cluster
with two zinc ions tetrahedrally coordinated by six cysteines. Two of the cys-
teines are bridging. Zinc - fi nger proteins have been found in many species
includingXenopus TFIIIA as mentioned above, the yeast alcohol dehydroge-
nase regulatory gene ADR1,^30 the mouse protein ZIF268 extensively studied
by many techniques including X - ray crystallography,^31 and the human onco-
gene GLI protein,^32 one of more than 700 zinc - fi nger proteins now known to
be encoded within the human genome.
In summary, the zinc ions in zinc - fi nger proteins provide a structural
center to direct folding of the protein. The metal ions infl uence the protein ’ s
three - dimensional shape and defi ne the shape or folding pattern of the peptide
domain that interacts specifi cally with DNA. The proteins target specifi c
sites on DNA, meaning that at least one element of the site recognition by
DNA regulatory proteins appears to be recognition of complementary shapes.
Zinc fi ngers change the three - dimensional structure of the B DNA to which
they are bound, opening up the major groove. It is now believed that the
zinc - fi nger domain represents a ubiquitous structural motif for eukaryotic
DNA - binding proteins.^33 Zinc may be chosen for this purpose for at least
two reasons: (1) its natural abundance and (2) the absence of redox activity
associated with Zn(II) ions avoiding DNA damage, as might be the case
with redox active metal centers such as Fe(II)/(III) or Cu(I)/(II). The number
of zinc - fi nger domains in a single protein ranges from one to as many as
- A minimum of three fi ngers seems to be needed for optimal DNA
recognition and binding. Several representative zinc - fi nger domains are
shown in Figure 7.4 of reference 2. Some discussion of structural characteriza-
tion by NMR and X - ray crystallography of individual zinc - fi nger proteins
and attempts to design zinc - fi nger proteins for binding to specifi c DNA
sequences are discussed in the following section. References 34a and 34b refer
readers to two recent reviews on this active research topic, while 34c and 34d
refer to advances specifi c to therapeutic applications of zinc - fi nger – DNA
interactions.^34