5,000,000 isn't that large a database, MySQL should be able to handle it. I'm not to sure where the management tools are on MySQL. It doesn't come with equivalents to SQL Server Tools, but I have a suspiscion its self maitaining. Ie recovers space dynamically, self optimises. If you have bulk updates / deletes then it may be prudent to reindex the database - not too sure what the correct command for that is though.
Have you considered approach mySQL directly? I've always found them to be very approachable and helpful