July 2011 Molecule of the Month by David Goodsell
Keywords: epigenetics, DNA methylation, DNMT1, DNMT3, restriction modification system
Your body is built of skin cells, nerve cells, bone cells, and many other different types of cells. These cells are different shapes and sizes, and each type of cell builds a characteristic collection of proteins that are needed for its function. However, every cell in your body contains the same genetic information, encoded in strands of DNA. How does each cell decide which genes to use and which ones to ignore?
Genetics and Epigenetics
Scientists have discovered that the information in DNA does not end at the simple genetic sequence of bases. Cells layer additional forms of control on top of the genetic code, creating "epigenetic" information that modifies the use of particular genes. In some cases, this control is performed by the positioning of nucleosomes. In other cases, bases in the DNA are methylated, modifying how they are read during protein synthesis.
In the first minutes of life, when we are composed of a single cell, this epigenetic information has been wiped clean. In the fertilized egg, the methyl groups have been removed and every gene is like all the others. Then, as cells divide in the embryo, they have to make choices about what they are going to do--becoming skin cells or nerve cells or their particular fate. At this point, DNA methyltransferases come into play, and they add methyl groups to genes, shutting off some and activating others. The DNA methyltransferase DNMT3, shown here from PDB entry 2qrv, performs this important job, creating the proper epigenetic coding of methyl groups throughout the genome.
Once each cell has decided its fate, this epigenetic code must be maintained for the rest of
the life of the organism. When a cell divides, the information must be transmitted to each
of the new cells. The DNA methyltransferase DNMT1, shown here from PDB entry
performs this job. As DNA is being replicated, it adds the proper methyl groups to the
new DNA strands. The information is propagated in a tricky way. Methyl groups are
almost always added to cytosine bases with the sequence:
Bacteria also use DNA methylation, but they use it to protect themselves from viruses. They build restriction enzymes that cut DNA at specific sequences. Then, they build specific DNA methyltransferases, such as the one shown here from PDB entry 1mht, that add methyl groups to these sequences. The methyl groups block the restriction enzyme, but still allow proper reading of the bases during transcription and replication. So, the restriction enzyme floats around the cell with nothing to do, until a virus infects the cell. The DNA from the virus typically does not contain any methyl groups, so the restriction enzyme quickly chops it into pieces.
click on the above Jmol tab for an interactive visualization
Exploring the Structure
Several structures have helped to explain how DNA methyltransferases perform their jobs. PDB entry 3pt6 includes DMNT1 and a small piece of DNA. The enzyme wraps around the DNA and probes the edges of the bases in the DNA. This structure was solved using DNA with no methyl groups, which would normally not be a substrate of the enzyme. Sure enough, the structure shows that the enzyme recognizes the unmethylated bases on both sides, and holds the DNA away from the active site. There is currently no structure of DNMT1 with a half-methylated DNA, but we can get an idea of how it might act by looking at a bacterial methyltransferase, pdb entry 1mht. The DNA binds deeper in the active site, and flips out the cytosine base that will be methylated. To take a closer look at these structures, click on the images for an interactive Jmol.
- R. Z. Jurkowska, T. P. Jurkowski and A. Jeltsch (2011) Structure and Function of Mammalian
- DNA Methyltransferases. ChemBioChem 12, 206-222. X. Cheng and R. M. Blumenthal (2008) Mammalian DNA Methyltransferases: A Structural Perspective. Structure 16, 341-350.
© 2015 David Goodsell & RCSB Protein Data Bank