Creating an x509 v3 user certificate by signing CSR

You need to specify an extensions file.

For example:

openssl x509 -days 365 -in myCSR.csr -extfile v3.ext -CA myCA.crt -CAkey myCA.key -CAcreateserial -out userCertificate.crt

The extensions file (v3.ext) can look like this:

authorityKeyIdentifier=keyid,issuer
basicConstraints=CA:FALSE
keyUsage = digitalSignature, nonRepudiation, keyEncipherment, dataEncipherment