Virtuelle (Nano) Welten PDB Molecule of the Month 91: Thymine Dimers

Error Control

We spend a lot of time in the sun, so it will come as no surprise that we have a powerful mechanism for correcting these problems. Our cells use a process called nucleotide excision repair, which requires the concerted effort of a large collection of proteins that recognize the corrupted bases, clip out the section of DNA with the error, and then build a new copy of the damaged area. Other organisms have additional correction mechanisms. For instance, the enzyme on the left (PDB entry 1vas) is an endonuclease that clips out the damaged bases, making the site available for repair. Surprisingly, this endonuclease doesn't recognize the thymine dimer directly. You can see in this picture that the thymine dimer (colored magenta) doesn't touch the enzyme at all. Instead, the enzyme recognizes one of the adenines that is paired with the dimer. Since the base pair is weakened by the contorted shape of the dimer, the adenine is easily flipped out and bound to a pocket in the enzyme. The enzyme on the right (PDB entry 1tez) is a photolyase that directly breaks the bonds connecting the dimer, correcting the error in place. Ironically, photolyases use visible light to power this process. This structure captures the DNA after the thymine dimer has been fixed. Notice that the two thymine bases (colored magenta) are flipped out of the normal DNA helix and are bound in a pocket on the enzyme surface.

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