I got the same problem!
Updated to PHP 5 all my sites on MT, but MySQL is: Server version: 4.1.25-Debian_mt1
I found this article from MT to update MySQL to version 5:
https://wiki.mediatemple.net/w/(gs):Upgrading_from_MySQL_4.x_to_5.x
But it’s ridiculous how you they mention an “upgrade tool” without telling you where to find it: “The upgrade from MySQL 4.x to 5.x is very easy with the (mt) provided tools, but that doesn’t mean you should just run the tool.”
Also, they say it’s safer to “Open a new (gs) Grid-Service; all new sites include MySQL 5.” but should we BUY a new service and than transfer all our sites? What kind of info is that? You don’t understand a thing!
Or should we wait for this to happen?
https://status.mediatemple.net/maintenances/2185-mysql-5-upgrades-for-select-cluster-03-users-72111/
Maybe it’s just me, but this is awful management from MediaTemple, really!