Structural Biology of the HEAT‐Like Repeat Family of DNA Glycosylases

Abstract

DNA glycosylases remove aberrant DNA nucleobases as the first enzymatic step of the base excision repair (BER) pathway. The alkyl‐DNA glycosylases AlkC and AlkD adopt a unique structure based on α‐helical HEAT repeats. Both enzymes identify and excise their substrates without a base‐flipping mechanism used by other glycosylases and nucleic acid processing proteins to access nucleobases that are otherwise stacked inside the double‐helix. Consequently, these glycosylases act on a variety of cationic nucleobase modifications, including bulky adducts, not previously associated with BER. The related non‐enzymatic HEAT‐like repeat (HLR) proteins, AlkD2, and AlkF, have unique nucleic acid binding properties that expand the functions of this relatively new protein superfamily beyond DNA repair. Here, we review the phylogeny, biochemistry, and structures of the HLR proteins, which have helped broaden our understanding of the mechanisms by which DNA glycosylases locate and excise chemically modified DNA nucleobases.

Base Excision DNA Repair in Plants: Arabidopsis and Beyond

“…In human cells, MPG protein (also known as AAG or APNG) removes 3-methylpurines, hypoxanthine, and εA and belongs to a completely different structural family, resembling the C-terminal domain of methionyl-tRNA fMet formyltransferase [171,172]. Moreover, some bacteria (but not E. coli) possess DNA glycosylases belonging to the HEAT repeat domain and winged-helix domain superfamilies and specific for alkylated purines or purine adducts with some natural genotoxic antibiotics [173,174].…”

Non-flipping DNA glycosylase AlkD scans DNA without formation of a stable interrogation complex

“…DNA glycosylases can be classified into the structural superfamilies helix-hairpin-helix (HhH), helix-two-turn-helix (H2TH), and HEAT-like repeat (HLR), as well as the uracil-DNA glycosylase (UNG) and alkyladenine-DNA glycosylase (AAG) families 1,2 . Four of these are present in human cells, while the HEAT-like repeat family has only been detected in bacteria, archaea, and some simple uni-and multicellular eukaryotes [3][4][5][6] . Atomic-resolution structures of representative members of each family have been determined, both with and without DNA.…”

“…The discovery of the DNA-bound complex of the HLR DNA glycosylase AlkD revealed the first example of a DNA glycosylase whose activity does not depend on base-flipping or base-probing using a wedge residue as an essential part of DNA base interrogation, damage recognition, and excision 4,6,7 . AlkD removes the lesions N3-yatakemycinyl-2'-deoxyadenosine (d3yA), N3methyl-2'-deoxyadenosine (d3mA), and N7-methyl-2'-deoxyguanosine (d7mG) from DNA [5][6][7] , and in the case of the bulky d3yA adduct, damage recognition takes place by interaction with both the phosphoribose backbone and the d3yA compound 7,8 . The smaller and intrinsically labile d3mA and d7mG bases are conversely believed to be removed by hydrolysis due to stabilization of the increased positive charge on the deoxyribose backbone through electrostatic and CH-π interactions 7,9 .…”