Interdomain communication in the endonuclease/motor subunit of Type I restriction-modification enzyme EcoR124I

 

Katsiatyna Shamayeva1,2, Dhiraj Sinha1,2Vyas Ramasubramani3, David Reha1,2, Vitali Bialevich1,2, Morteza Khabiri1Alena Guzanova4, Marie Weiserova4, Eva Csevalvay1, Jannette Carey3, Rudiger Ettrich1,2

 

1Institute of Nanobiology and Structural Biology, Global Change Research Center, Academy of Sciences of the Czech Republic, Zamek 136, CZ-373 33 Nove Hrady, Czech Republic

2Faculty of Sciences, University of South Bohemia in Ceske Budejovice, Zamek 136, CZ-373 33 Nove Hrady, Czech Republic

 3Chemistry Department, Princeton University, Princeton, New Jersey 08544-1009, USA

4Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083,

142 20 Praha 4, Czech Republic

 

Restriction-modification systems protect bacteria from foreign DNA. Type I restriction-modification enzymes are multifunctional heteromeric complexes with DNA cleavage and ATP-dependent DNA translocation activities located on endonuclease/motor subunit HsdR. The recent structure of the first intact motor subunit of the Type I restriction enzyme from plasmid EcoR124I suggested a mechanism by which stalled translocation triggers DNA cleavage via a lysine residue on the endonuclease domain that contacts ATP bound between the two helicase domains. In the present work molecular dynamics simulations are used to explore this proposal as the protein samples conformational space. MD suggests that the Lys-ATP contact alternates with a contact to a nearby loop housing the conserved QxxxY motif that had been implicated in DNA cleavage. This model is tested here by using in vivo and in vitro experiments. The results indicate how local interactions are transduced to domain motions within the endonuclease/motor subunit.