Use two queries and bracket them into a transaction. That makes them from a logical and database point of view only one query in two chunks.
If you don't like that, use this inefficient solution:
UPDATE runquery.table1, runquery.table2 SET
runquery.table1.`Column1` = if(itemid=3,(runquery.table2.`Col1`/runquery.table2.`Col2`*100),Column1),
runquery.table1.`Column2` = if(itemid=5,(runquery.table2.`Col1`/runquery.table2.`Col2`*100),Column2)
where runquery.table1.`Userids` = runquery.table2.`userid`;