Tokyo, strangely, is a city in Japan (5)
I believe the answer is:
'a city in japan' is the definition.
(I've seen this in another clue)
'tokyo strangely' is the wordplay.
'strangely' indicates an anagram.
'tokyo' with letters rearranged gives 'KYOTO'.
'is' is the link.
(Other definitions for kyoto that I've seen before include "Tokyo (anag) - former capital of Japan" , "Japanese capital before 1868" , "Japan's old capital" , "Japanese city of treaty on climate change" , "City of agreement on global warming" .)