As a marketplace administrator, you can choose to charge a transaction fee for each paid transaction. This fee is charged automatically after each transaction.
When a buyer in your marketplace buys something, the entire amount is moved to the seller's PayPal account (minus PayPal's payment processing fees), after which your transaction fee is automatically charged from the seller's PayPal account in a separate transaction. This fee is deposited in your PayPal account.
PayPal will take a small cut from the second (commission) transaction. The standard PayPal fees apply. However, if your commission fees are small, it might be possible to reduce these fees by contacting PayPal support and enabling micropayment transaction fees for your PayPal account.
Can you show me an example fee?
You can see a few example transactions here.