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July 7, 2019

Structure of Type IIL restriction-modification enzyme MmeI in complex with DNA has implications for engineering new specificities.

Authors: Callahan, Scott J and Luyten, Yvette A and Gupta, Yogesh K and Wilson, Geoffrey G and Roberts, Richard J and Morgan, Richard D and Aggarwal, Aneel K

The creation of restriction enzymes with programmable DNA-binding and -cleavage specificities has long been a goal of modern biology. The recently discovered Type IIL MmeI family of restriction-and-modification (RM) enzymes that possess a shared target recognition domain provides a framework for engineering such new specificities. However, a lack of structural information on Type IIL enzymes has limited the repertoire that can be rationally engineered. We report here a crystal structure of MmeI in complex with its DNA substrate and an S-adenosylmethionine analog (Sinefungin). The structure uncovers for the first time the interactions that underlie MmeI-DNA recognition and methylation (5'-TCCRAC-3'; R = purine) and provides a molecular basis for changing specificity at four of the six base pairs of the recognition sequence (5'-TCCRAC-3'). Surprisingly, the enzyme is resilient to specificity changes at the first position of the recognition sequence (5'-TCCRAC-3'). Collectively, the structure provides a basis for engineering further derivatives of MmeI and delineates which base pairs of the recognition sequence are more amenable to alterations than others.

Journal: PLoS biology
DOI: 10.1371/journal.pbio.1002442
Year: 2016

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