[Dave]

Check the access.log to be entirely sure it's a DoS attack.
Also it's odd that your web-server doesn't crash, but your MySQL server does. It's usually the other way around.

If you're entirely sure it's a DoS attack, you can do several things:
1) Find which IP is doing it and block the IP. A DoS attack is 1 IP, a DDoS attack is sent from a bunch of infected hosts.
2) Go to a host which offers DDoS protection. (Expensive)
3) Use Cloudflare and enable "I'm under attack mode" at the security settings. This should eliminate most attacks. Be sure that you only allow connections to your webs-server from Cloudflare its IP's if you do this.