GDDR -- common to Graphics cards -- is not the same thing as DDR memory installed in PCs & shouldn't be confused for one another. And a GDDR3 card will work just fine in a machine equipped with DDR system memory, insofar as the expansion slot (AGP/PCIe) on the machine will support the type of card.
The memory on the video card does not need to match the ram on the motherboard. You could have DDR3 memory on a geforce 6600gt card even if your motherboard has DDR1 memory. It definitely does not matter.
BUT just make sure your Power Supply Unit gives enough power for the card you use