What an interesting spot!
I think this is one of those pivotal moments you get in tournaments where you have to go with your read. The Villain has rased pre, c bet the flop and raised the turn. This could be an overpair and if he has two black kings, queens or jacks you are only 38% so you need to ask yourself if raising this particular player is going to push him off such a strong hand (would he fold one pair to a hefty raise?).
I don"t like flatting although others may disagree - if you miss on the river are you calling a 20k bet?
If he has a set, also possible, your in even worse shape at 25%.
A flush draw is unlikely and
is one of the few hands you are beating, apart from an outright bluff wich looks doubtful.
In addition we also have to think about seat 2 who hasn"t gone away yet and could be sat on a set himself.
At first glance my instinct was to say I"m not folding. I"ve got top pair, nut flush draw and a gutshot straight. The maths seems to say a fold is not terrible, and is probably the optimal play. I"m pretty sure I wouldn"t have folded though and would have been prepared to get it all in. But I think that would be a leak in the long term.
Look forward to hearing how this developed.