This affected me as well, after upgrading a digital ocean VM from 14.04
to 16.04.1.

I straced the call, as well as using inotify tools to capture the
temporary files created.  An interesting line in the strace is:

[pid  2608] execve("/usr/bin/apt-key", ["/usr/bin/apt-key", "--quiet", "
--readonly", "verify", "--status-fd", "3", "/tmp/apt.sig.CbTOUo",
"/tmp/apt.data.rwmcWB"], [/* 25 vars */]) = -1 EPERM (Operation not
permitted)


Can post the entire strace dump if people think it would be helpful.  The 
apt.sig file was empty, whereas the apt.data file was 13k.

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https://bugs.launchpad.net/bugs/1577926

Title:
  apt-key works fine, yet apt fails with "Could not execute 'apt-key'"

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