Alkyltransferase-like protein (Atl1) distinguishes alkylated guanines for DNA repair using cation–π interactions

Abstract

Alkyltransferase-like (ATL) proteins in Schizosaccharomyces pombe (Atl1) and Thermus thermophilus (TTHA1564) protect against the adverse effects of DNA alkylation damage by flagging O 6 -alkylguanine lesions for nucleotide excision repair (NER). We show that both ATL proteins bind with high affinity to oligodeoxyribonucleotides containing O 6 -alkylguanines differing in size, polarity, and charge of the alkyl group. However, Atl1 shows a greater ability than TTHA1564 to distinguish between O 6 -alkylguanine and guanine and in an unprecedented mechanism uses Arg69 to probe the electrostatic potential surface of O 6 -alkylguanine, as determined using molecular mechanics calculations. An unexpected consequence of this feature is the recognition of 2,6-diaminopurine and 2-aminopurine, as confirmed in crystal structures of respective Atl1-DNA complexes. O 6 -Alkylguanine and guanine discrimination is diminished for Atl1 R69A and R69F mutants, and S. pombe R69A and R69F mutants are more sensitive toward alkylating agent toxicity, revealing the key role of Arg69 in identifying O 6 -alkylguanines critical for NER recognition.

Biochemical and Structural Studies of the Mycobacterium tuberculosis O 6 -Methylguanine Methyltransferase and Mutated Variants

“…In principle, such a solvent-exposed conformation of the MtOGT active-site loop still allows the HTH motif to peculiarly bind the substrate DNA at its minor groove, as disclosed by structural studies of AGT and ATLs (25,44,48,49), and is fully compatible with the housing of the modified base inside the active site (Fig. 4C, left).…”

“…However, different from what was observed in all the crystal structures of OGTs, in both the MtOGT and MtOGT-R37L models the active-site loop is oriented toward the exterior of the protein body (Fig. 4A), adopting a conformation that closely resembles the one displayed by the equivalent region in the structures of alkyltransferase-like proteins (ATLs) (47) in complex with alkylated DNA (48,49) (Fig. 4B).…”

The bacterial alkyltransferase-like (eATL) protein protects mammalian cells against methylating agent-induced toxicity

“…In addition, in bacteria and yeast, there are proteins with some sequence homology to AGTs, collectively designated as alkyltransferase-like (ATL) proteins. Where examined, these proteins exhibit no alkyltransferase activity [13,14], but are able to bind to a wide variety of O 6 -alkylguanine lesions [13,15] and confer resistance to the toxic and mutagenic effects of alkylating agents [16,17].…”

Cations Form Sequence Selective Motifs within DNA Grooves via a Combination of Cation-Pi and Ion-Dipole/Hydrogen Bond Interactions

“…Cation-pi interactions have also been established as a stabilizing interaction between aromatic side chains and hydrogen bond donors [12] or anionic side chains [13], [14]. Cation-pi interactions are thought to contribute to a disparate and eclectic range of systems including the binding of a wide array of neurotransmitters to their receptors [15], [16], [17], [18], induction of kinking in a hinge region of RNA polymerase [19], apoA1/HDL structure and function reviewed in [20] and the detection of alkylated bases [21] and in DNA repair [22].…”