The AlkB Family of Fe(II)/α-Ketoglutarate-dependent Dioxygenases: Repairing Nucleic Acid Alkylation Damage and Beyond

Abstract

The AlkB family of Fe(II)- and α-ketoglutarate-dependent dioxygenases is a class of ubiquitous direct reversal DNA repair enzymes that remove alkyl adducts from nucleobases by oxidative dealkylation. The prototypical and homonymous family member is an Escherichia coli "adaptive response" protein that protects the bacterial genome against alkylation damage. AlkB has a wide variety of substrates, including monoalkyl and exocyclic bridged adducts. Nine mammalian AlkB homologs exist (ALKBH1-8, FTO), but only a subset functions as DNA/RNA repair enzymes. This minireview presents an overview of the AlkB proteins including recent data on homologs, structural features, substrate specificities, and experimental strategies for studying DNA repair by AlkB family proteins.

Keywords: DNA demethylation; DNA repair; RNA demethylation; RNA repair; alkB; alkylation damage; dioxygenase; direct reversal; metalloprotein; substrate specificity.

FIGURE 1.

Examples of oxidative dealkylation reactions (m3C, ϵA, and m6A) catalyzed by AlkB family dioxygenases and their proposed mechanisms. HO-m3C is 3-hydroxymethylcytosine, and HO-m6A is N⁶-hydroxymethyladenine.

FIGURE 2.

Structural aspects of E. coli AlkB protein. A, crystal structure (Protein Data Bank (PDB) 3O1P) of E. coli AlkB, featuring the jelly-roll fold, with the m1A substrate flipped out of the DNA duplex into the active site of the enzyme. The orange sphere denotes the position of the central metal ion (here Mn(II)). B, active site of E. coli AlkB showing the octahedral coordination around the central metal ion and the relative position of the substrates m1A and ϵA, shown overlaid. The red sphere denotes a water molecule crystalized at the molecular oxygen binding site. C and D, the ethenoguanine lesions 1,N²-ϵG and N²,3-ϵG modeled in the E. coli AlkB active site (PDB 3O1P) showing the distances between the iron-oxo moiety (red sphere of the left side of each central Fe(II)) and the exocyclic bridge carbons). (Reproduced with permission from Chang et al. (87).