SQL and LDAP

I have what I think is a complicated question. I don't need to know details on how to do this but if it would be feasible to do this. We have 2 different My SQL databases tied to 2 different IBM AS/400 systems we use for billing, trouble tickets,etc. We use the 2 databases to create new accounts, add/change information test username/passwords and perform LDAP searches and many other tasks. When we add or make a change in the databases it updates the info to the as/400. The 2 as/400's aren't merged (yet) because we were 2 separate companies at one time there are billing issues involved. The way we must perform LDAP searches now is this, if we are searching for a particular email address, user, or domain, we must use one database. If we are searching for a user, email address, etc on one of the many other domains that we have, we must use the the other database.
Now, the question. Is there a way to have the 2 databases perform LDAP searches on all the domains that we have. Making no difference which database you are using?