You just have to add index name while query, but in your global index email should be hash here all the attribute will be projected.
$response = $this->dbClient->query(
array(
"TableName" => "user",
"IndexName" => "index name",
"KeyConditions" => array(
"email" => array(
"ComparisonOperator" => ComparisonOperator::EQ,
"AttributeValueList" => array(
array(Type::STRING => "email@abc.com"))))));
then you can fetch userId