I'm only a fellow student, but I believe the answer is that in German sentences the verb is always in the second position.
So if the sentence were just "es ist geschlossen" the word order would be as you expect, however, when adding the "Ja, aber heute .. which occupies the "first position" the verb "ist" must come next.
Scan through the topic headings for the lessons on word order.
The curious thing though is that With "Ja, aber" it seems to me that the "heute" should be kicked to a later position like for example, "Ja, aber ist es heute Geschlossen."
My only guess is that Maybe Ja, doesn't count for some reason?
Let's hope an expert helps us out soon.