Running yum search, there was an error:
[root@localhost~]# yum search system-config
rpmdb: Thread/process 1528/47869554445088 failed: Thread died in Berkeley DB library
error: db3 error(-30974) from dbenv->failchk: DB_RUNRECOVERY: Fatal error, run database recovery
error: cannot open Packages index using db3 – (-30974)
error: cannot open Packages database in /var/lib/rpm
Error: rpmdb open failed
To fix this, delete the rpm database.
[root@localhost~]# rm /var/lib/rpm/__db* -f
You can now try a yum update again and it will work correctly.