Is it obligatory to pay the shop's Zakat for the past five years, or is it to be paid only for the current year, given that paying it for previous years will reduce the capital? And is Zakat paid only from the profit or from the entire capital?

Zakat (definition) must be paid for previous years, as its obligation does not lapse with time. The fact that the amount is large does not prevent one from fulfilling the right of Allah and the poor, for it is a fixed debt that must be paid. Zakat on trade goods is obligatory on the capital used for trade along with its profits upon the completion of a full lunar year.