SELECT 
  c.company_id 
FROM 
  cscart_products_categories pc 
  LEFT JOIN cscart_categories c ON c.category_id = pc.category_id 
WHERE 
  pc.product_id = 559 
GROUP BY 
  c.company_id

Query time 0.00033

Explain
id select_type table type possible_keys key key_len ref rows Extra
1 SIMPLE pc ref pt,product_id_idx,product_category_idx product_category_idx 3 const 3 Using index; Using temporary; Using filesort
1 SIMPLE c eq_ref PRIMARY,p_category_id,idx_category_id PRIMARY 3 mahm3t_cs443.pc.category_id 1

Result

company_id
1
2
3