Sure thing...
You'll need to install the proper ODBC drivers on your AE machine:
Installing ODBC and JDBC for FileMaker 11 | FileMaker
In the Data Sources (ODBC) program (under Admin tools on your Windows server), you'll create a System DSN. This sets up the connection to the database (server url, login credentials, etc...). Once that is done, you can set up SmartNames that do a Database Query. Just use the named ODBC connection, then use an SQL Select command to pull your data. There should be some Esko documentation on this.
W3Schools has some great tutorials on that:
SQL SELECT Statement
You're somewhat limited in the SQL calls you can make anyway, but you'll be looking to do something like: "SELECT dataA, dataB FROM datatable_name WHERE job_id=jobnumber"
It's important to remember that in the SmartMarks database query, it will return ONE and only ONE result, so you must be specific in the table row you want. If you do a SELECT that returns multiple rows, you only get one (can't recall if it's first or last).
The other option is as Simon mentioned above, adding triggers to the database to refresh the information in Automation Engine. So, if field X changes, push new XML to AE. That would be dependent on those "powers that be", however.