Crystal structure of NaeI--an evolutionary bridge between DNA endonuclease and topoisomerase

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Abstract
NaeI is transformed from DNA endonuclease to DNA topoisomerase and recombinase by a single amino acid substitution. The crystal structure of NaeI was solved at 2.3 Å resolution and shows that NaeI is a dimeric molecule with two domains per monomer. Each domain contains one potential DNA recognition motif corresponding to either endonuclease or topoisomerase activity. The N‐terminal domain core folds like the other type II restriction endonucleases as well as λ‐exonuclease and the DNA repair enzymes MutH and Vsr, implying a common evolutionary origin and catalytic mechanism. The C‐terminal domain contains a catabolite activator protein (CAP) motif present in many DNA‐binding proteins, including the type IA and type II topoisomerases. Thus, the NaeI structure implies that DNA processing enzymes evolved from a few common ancestors. NaeI may be an evolutionary bridge between endonuclease and DNA processing enzymes.