The USN has always claimed this, but other accounts do have the PBY 'attacking'.
The first shot of the Pacific War, fired by the destroyer USS Ward before dawn on 7 December 1941. Ward was patrolling in an restricted zone off the entrance to Pearl Harbor when the minesweeper Condor reported that she had spotted a submarine periscope at 3:42AM. Nearly three hours later, a PBY patrol plane also sighted a periscope and marked the spot with a smoke pot. Ward came over, fired her guns at the sub and dropped depth charges, reportedly sinking it.
Don't think this particular sub is one of the ones found so far.