misincorporation or deamination of cytosine. The structure of the human uracil DNA glycoslyase shows
that the glycosylase completely encompasses the substrate. Another example is the enzyme 3-methyl-
adenine DNA glycosylase, which excises that base from damaged DNA by intercalation into the minor groove
using two -strands, and by flipping the damaged base into the active site for base excision.^37
10.5.4 Photolyases
Light is the primary source of energy for most life on earth, but ultraviolet light induces spontaneous dam-
age to DNA in the way of covalent photo-adducts. One such example is the dimer formed from pyrimidines,
cyclobutadipyrimidine. Organisms in all three domains of life have evolved enzymes that repair the light-
induced damage by using the energy of light itself. These enzymes are carbon–carbon photolyases.
Photolyases share a common fold and use a catalytic mechanism that involves conjugated co-factors for
photo-induced electron transfer. One co-factor that is used directly in the catalytic process is the reduced
form of flavin-adenine dinucleotide (FAD-H 2 ). The second chromophore acts as an antenna to transfer
light energy to the FAD-H 2 , which in turn supplies the electron to rupture the carbon–carbon bond. In most
enzymes the antenna co-factor is 5,10-methenyl-tetrahydrofolate, but certain photolyases instead use
5-deazariboflavin. The active site engulfs the pyrimidine substrate, which is in van der Waals contact with
the FAD. The FAD is sandwiched by aromatic stacking with side chains of two conserved tryptophan
residues, which are thought to become radicals transiently in the transfer process.^38 There is little room
to accommodate a duplex DNA. So these enzymes probably flip out the pyrimidine dimer from the duplex,
in loose analogy with the flipping mechanism used by other DNA-repair enzymes (Sections 10.5.2
and 10.5.3).
10.5.5 Structure-Selective Nucleases
In DNA recombination, an intermediate is formed in which four strands join together (Figure 10.14a and
Section 2.3.7) These structures are resolved back into two duplex DNA molecules by the activity of structure-
specific endonucleases, which are found in all three domains of life. Site-specific recombinases (e.g. FLP
protein, Figure 10.14b) use the hydroxyl group of either serine or tyrosine as the nucleophile for cutting and
rejoining DNA. Topoisomerases also use a tyrosine hydroxyl group for a similar purpose (Section 10.8.3).
Protein–Nucleic Acid Interactions 407
Figure 10.14 (a) The structure of a four-way DNA junction. (b) Its complex with the recombinase FLP protein
(PDB: 1P4E)