If my accountant filed an extension for me for 2016 taxes, can I still file through Turbo even through the extension was put in by an accountant?

Yes.  Just file as normal.  Did you make a payment with the extension?

You can type estimates paid in the search box at the top of your return and click Find and it will give you a link to Jump To the screen where you enter Extension Payments.

To enter the amount you paid with an extension (including state extension)  go to
Federal Taxes (or Personal for H&B/Self Employed version)
Deductions and Credits
Choose Jump to Full List -or  I'll choose what I work on
Then scroll way down to Estimates and Other Taxes Paid
Other Income Taxes - Click the Start or Update button

Next page second section Payments with Extension
Either Visit All or Click Start or Update by the extension you paid