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PDB:1TEZ

Protein Name

Deoxyribodipyrimidine photolyase/DNA complex

Species

Synechococcus sp. PCC 6301 (cyanobacteria)

Biological Context

Most people would agree that a couple of weeks on a tropical beach is a great way to spend one's holidays. The lazy days by the emerald sea waters might be wonderful, but there are also dangers even in this paradise. Exposure of unprotected skin to sunlight brings potential dangers. Ultraviolet sun rays, whose intensity has increased due to the thinning ozone layer, damage the skin and cause mutations in the cells' DNA . Complications may lead to tumor formations and development of diseases such as melanoma. Fortunately, organisms, including humans, have developed a system for repair of damaged DNA. In 1962 Wulff and Rupert showed that cyclobutane pyrimidine dimers (CPDs), which form in UV-damaged DNA, can be repaired by an enzyme called photoreactivating enzyme or DNA photolyase.

Structure Description

1tez1tez_x1tez_y

This is a single-step process in which the dimer is converted back into two adjacent pyrimidines. The crystal structure of photolyase and damaged DNA shown here can explain exactly how this process is being accomplished. The photolyase bound DNA double helix is bent at 50 degrees and highly distorted at the CPD lesion site . It is partially unwound and a 10x10A hole is created between the complementary chains . Stabilization of this structure is achieved by numerous hydrogen bonds and salt bridges between the protein and the DNA strand . The dipole moments of the enzyme helices create an environment that additionally immobilizes the DNA . The erroneous thymine dimer sticks out of the double strand hole and into the active site of the enzyme . So how DNA is being repaired ? Blue light is absorbed by one of the photolyase's cofactors, methenyltetrahydrofolate, which donates an electron to the flavin adenine dinucleotide, reduced state ( FADH(-)) cofactor. The exposed thymines are an easy target for FADH(-), which transfers the electron to the CPD lesion . This causes the breakage of the cyclobutane ring . After that, the electron is returned back to the FADH cofactor , and it returns back to its reduced state . Now it is ready for another DNA molecule . That's how DNA photolyases work like a kind of molecular pliers to bind the DNA, stretch the strands apart and bare the mutated bases. It is not yet clear exactly how FADH(-) transfers the electron to the CPD lesion . One possible mechanism for this transfer would include FADH's adenine ring, because it connects the isoalloxazine ring, the actual electron donor , and the thymine dimer , the acceptor, via two hydrogen bonds. A direct transfer is also quite possible due to the proximity of the donor and the acceptor.

Protein Data Bank (PDB)

References

Source

Mees, A. Klar, T. Gnau, P. Hennecke, U. Eker, A.P.M. Carell, T. Essen, L.-O.; "Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair"; Science; (2004) 306:1789-1793 PubMed:15576622.

Others

UniProt:P05327

author: Rossen Apostolov


Japanese version:PDB:1TEZ