Abstract
The primary role of apurinic/apyrimidinic (AP) endonuclease APE1 in human cells is the cleavage of the sugar phosphate backbone 5′ to an AP site in DNA to produce a single-strand break with a 5′-deoxyribose phosphate and 3′-hydroxyl end groups. APE1 can also recognize and incise some damaged or modified nucleotides and possesses some minor activities: 3′–5′ exonuclease, 3′-phosphodiesterase, 3′-phosphatase, and RNase H. A molecular explanation for the discrimination of structurally different substrates by the single active site of the enzyme remains elusive. Here, we report a mechanism of target nucleotide recognition by APE1 as revealed by the results of an analysis of the APE1 process involving damaged DNA and native RNA substrates with non-canonical structures. The mechanism responsible for substrate specificity proved to be directly related to the ability of a target nucleotide to get into the active site of APE1 in response to an enzyme-induced DNA distortion.
Highlights
Human apurinic/apyrimidinic (AP) endonuclease APE1 is the key enzyme of the base excision repair pathway, which is responsible for processing AP sites in DNA (Wilson and Barsky, 2001; Demple and Sung, 2005)
According to our previous findings (Kuznetsova et al, 2018b), the substrate specificity of APE1 to damaged nucleotides in the duplexes is controlled by the ability of a given damaged nucleotide to be everted from the DNA double chain in response to an enzyme-induced DNA distortion
A series of damaged DNA substrates and undamaged RNA substrates of a non–B-form structure was tested to evaluate the structural aberrations facilitating the process of target nucleotide recognition by APE1 and the formation of a catalytically competent complex
Summary
Human apurinic/apyrimidinic (AP) endonuclease APE1 is the key enzyme of the base excision repair pathway, which is responsible for processing AP sites in DNA (Wilson and Barsky, 2001; Demple and Sung, 2005). As illustrated recently (Whitaker et al, 2018) in an elegant series of highresolution APE1–DNA structural snapshots, APE1 removes 3 nucleotides in the course of the 3 –5 -exonuclease reaction by placing the 3 group within the intra-helical DNA cavity via a non–base-flipping mechanism. This process is facilitated by DNA structural disturbances caused by the presence of a mismatched or damaged base or nick formation as well as DNA bending. The reality of this mechanism in endonuclease reactions is questionable due to significant restrictions on the nucleotide mobility in an unbroken DNA chain
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