Various certificates used for Network Security Services (NSS) are stored in their own database, which is not an LDAP database. Two utilities, certutil and crlutil, are provided with Messaging Server to store the certificates and associated CRLs in the database. You can also use these utilities to search the database.
See the Sun Java System Directory Server Administration Guide (http://download.oracle.com/817-7613) for more information about certutil. Use the help text that comes with crlutil for more information about that utility (view the online help of both utilities by executing them without arguments).