Yes. The GPU RAM and Motherboard RAM have no consolation to each other in that type of case. A Motherboard using DDR2 can use GDDR# (think it goes up to 5 now) just like DDR3 can use GDDR#. So no worries for that, just have to watch the PSU/Interface/CPU. 
I'm sure you didn't intend to say it like this, a motherboard that's designed for DDR2,3 or whatever can _not_ use GDDR of any kind.
The motherboard can not use it.
It can however support a graphics card plugged in agp/pci-e lane that uses any type of memory it happens to be built for.