Upgrading MySQL versions is a quick and easy process, not much work involved. Always be sure to make a backup before you start though, just in case the upgrade fails or some other unforeseen issue arises.
cp -Rpf /var/lib/mysql /var/lib/mysql.BAK
Login to WHM –> Tweak Settings –> MySQL -> 5.0 and Save settings
/scripts/mysqlup –force
/scripts/perlinstaller –force Bundle::DBD::mysql
/scripts/realperlinstaller –force DBD::mysql
Recompile PHP
You’re done 
