If a picture is worth 1,000 words, then X-ray crystallography is more like a Game of Thrones novel. The same technology that gave us the double helix structure of DNA way back in the groovy days of genetics has now captured images of Tet doing its demethylation dance with DNA in Naegleria. Xiaodong Cheng and his team at Emory University (Georgia) teamed up with New England Biolabs to snap the shots and provide new insights about the structure and mechanisms underlying the novel bases of active DNA demethylation and the Tet family of proteins. Here’s what they saw:
- Just like its mammalian buddies, NgTet1 has an affinity for 5mC and leaves behind its 5hmC, 5fC, and 5caC ‘offspring’.
- Tet forms a complex with DNA containing a “5mCpG site”.
- Tet employs a base-flipping mechanism to gets its hands on some fresh 5mC.
- It turns out that the DNA is grabbed from the minor groove and bent towards the major groove, with this flipped 5mC position being perfect for the chemistry of Tet’s active site.
Cheng shares that “This base flipping mechanism is also used by other enzymes that modify and repair DNA, but we can see from the structure that the Tet family enzymes interact with the DNA in a distinct way.” Cheng adds that since the group “chose to study the enzyme from Naegleria because it was smaller and simpler and thus easier to crystallize than mammalian forms of the enzyme, yet still resembles mammalian forms in protein sequence”, that the results should be interpreted with caution. This is because the “mammalian Tet enzymes appear to have an additional regulatory domain that the Naegleria forms do not.” But he optimistically concludes that “working out how that domain functions will be a new puzzle opened up by having the Naegleria structure.”
Sneak a peek over at Nature, January 2014