If this is one 1 ticket, the UA check-in agents at origin will be able to check you in all the way to final destination. You may not be able to select seats yourself, but it doesn't mean that UA check-in agents can do it.

If you are on separate tickets (it is not clear from your post), you should try to check-in with TK (website or app) for the BRU-IST leg. If unsuccessful, you go to transfer desk at BRU. Def. no check-in at the gate as it will be too late/past the check-in deadline.