Tokyo, strangely, is a city in Japan (5)
I believe the answer is:
kyoto
'a city in japan' is the definition.
(I've seen this in another clue)
'tokyo strangely' is the wordplay.
'strangely' indicates an anagram.
'tokyo' anagrammed gives 'KYOTO'.
'is' acts as a 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" .)