According to which MacPro you have, there is probably a 3.6 volt AA Lithium battery. It looks like this: http://www.frys.com/product/2977135
I would replace that first. This is most likely a power supply issue and not a logic board issue. Here is a discussion on your problem: http://www.blograndom.com/blog/2007/11/changing-the-power-supply-unit-on-a-powermac-g5-after-it-blows-up/
Do not replace the power supply unless you have the original system installation disks as they contain a program for syncing the fans. If the sync is not done the fans will run wild. If you can let us know about the battery and any symptoms at all it would help. There are specific tests for the lead out on the power supply and how much voltage each lead should have. If you want or need to go that far let me know.