Duplex interrogation by a direct DNA repair protein in search of base damage.
ALKBH2 is a direct DNA repair dioxygenase guarding the mammalian genome against N(1)-methyladenine, N(3)-methylcytosine and 1,N(6)-ethenoadenine damage. A prerequisite for repair is to identify these lesions in the genome. Here we present crystal structures of human ALKBH2 bound to different duplex DNAs. Together with computational and biochemical analyses, our results suggest that DNA interrogation by ALKBH2 has two previously unknown features: (i) ALKBH2 probes base-pair stability and detects base pairs with reduced stability, and (ii) ALKBH2 does not have nor need a damage-checking site, which is critical for preventing spurious base cleavage for several glycosylases. The demethylation mechanism of ALKBH2 insures that only cognate lesions are oxidized and reversed to normal bases, and that a flipped, non-substrate base remains intact in the active site. Overall, the combination of duplex interrogation and oxidation chemistry allows ALKBH2 to detect and process diverse lesions efficiently and correctly.
State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
Chengqi
C
Yi
Baoen
B
Chen
Bo
B
Qi
Wen
W
Zhang
Guifang
G
Jia
Liang
L
Zhang
Charles J
CJ
Li
Aaron R
AR
Dinner
Cai-Guang
CG
Yang
Chuan
C
He
D000071499:AlkB Homolog 2, Alpha-Ketoglutarate-Dependent Dioxygenase; D004249:DNA Damage; D004260:DNA Repair; D045643:DNA Repair Enzymes / Q000737:chemistry / Q000378:metabolism*; D049308:Dioxygenases / Q000737:chemistry / Q000378:metabolism*; D008958:Models, Molecular
D049308:Dioxygenases; C486440:ALKBH2 protein, human; D000071499:AlkB Homolog 2, Alpha-Ketoglutarate-Dependent Dioxygenase; D045643:DNA Repair Enzymes