When you
digitalWrite(ShutdownPin, LOW);
The ATmega2560 will connect that port to ground. If the current draw on this port would exceed the Absolute Maximum Ratings, specified on page 355 of the datasheet, you can use an NPN transistor, connecting the Power Boost enable pin to the collector, the MCU port to the base and the emitter to ground. Depending on which transistor you select, or trasistor IC, you may need additional biasing resistors etc. In this case you would:
digitalWrite(ShutdownPin, HIGH);
I don't believe the current draw will exceed the Absolute Maximum Ratings, but you can test this by setting your multimeter to measure current and connecting the positive lead to the enable pin and the negative lead to ground. The meter should not read more than 20 mA, assuming you are running the Mega2560 on 5.2 Volts DC.