Table 3. Known base-flipping systems.

Specific protein	Catalytic reaction	PDB	Reference
DNA MTases
M.HhaI	Forms 5-methylcytosine in DNA	9mht	24,47
M.HaeIII	Forms 5-methylcytosine in DNA	1dct	64
M.TaqI	Forms N6-methyladenine in DNA	1G38	65
DNA glycosylases
T4 endonuclease V	Removes pyrimidine dimers from DNA	1vas	78
Human UDG	Removes uracil from DNA	2ssp	48,71,135
E.coli MUG	Removes uracil or thymine from DNA containing G:T or G:U	a	49,50
Human AAG	Removes 3-methyladenine from DNA	1bnk	51
E.coli AlkA	Removes 3-methyladenine from DNA	1diz	52
hOGG1	Remove 8-oxoguanine from DNA	1ebm	74
AP endonucleases
E.coli endonuclease IV	Cleaves the DNA backbone 5′ of AP sites	1qum	79
Human AP endonuclease (HAP1 or APE1)	Cleaves 5′ to AP sites	1dew	80

^aThe coordinates of MUG–DNA complexes are currently not available in PDB.