That is not Apple supported format it is easy to get around since you would require no conversion to get it in .mp4 format/container since it will most likely have h.264 video in there. You can use a command line tool like ffmpeg to simply copy the video and audio to a .mp4 file something like this for a command line.
ffmpeg -i file.mkv -vcodec copy -acodec copy file.mp4
the MKV bit is the lesser of the problems, you can't play ANYTHING from a USB drive, AppleTV has never supported USB connected media for anything.
Plenty of apps out there to convert and then add to your iTunes library though and home share across to AppleTV. Or the upcoming tvOS apps such as Plex and a networked media server.