The Mre11/Rad50 complex plays an essential role in the repair of DNA double-strand breaks by initiating the processing of the DNA ends. The MR complex is made up of two subunits of the Mre11 nuclease and two subunits of the Rad50 ATPase. The precise role of Rad50’s ATPase activity is unclear. Some reports suggest that the ATP acts as an allosteric switch that turns on the activity of Mre11, while others suggest ATP is used to power translocation or unwinding of DNA. To test this hypothesis in Rad50, we developed a method to create heterodimeric Rad50 so that that ATP sites can be individually controlled. Using two active site mutations (E505Q and D512A), a heterodimeric Rad50 containing a single functioning ATP active site was generated and purified. Characterization of the single ATP site heterodimer indicates that in the absence of Mre11 and DNA, the two active sites act in an independent fashion. Upon complex formation with Mre11 and DNA, the active sites now display strong coupling, such that DNA no longer acts as an allosteric activator of Rad50 ATP hydrolysis. Additionally, it was found that the MR complex with a single ATP site is no longer able to perform multiple nucleotide excisions during a single binding event. Overall, these results support the hypothesis that the MR complex acts as a motor protein that requires coordination between ATP sites for processive nuclease activity.