can I install an SMG gearbox to a BMW E39? this gearbox comes with a 2000+ mod BMW M3 or BMW M5 mod 2005.

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No. It was never available in europe, so you can't even get the engine computer to talk to the transmission computer. The SMG transmission can't handle the additional torque of the 5.0L V8 on the E39 M5. The E46 M3 has less power and MUCH less torque, so it works. The 2005 M5 has a V10 engine and totally different electronics from the E39 chassis. Also the SMG III in the new M5 is a seven speed unit which is dimensionally different from your transmission.