One may be put out by it (5)
I believe the answer is:
ether
'it' is the definition.
The definition suggests a singular noun which matches the answer.
'one may be put out' is the wordplay.
'one' becomes 'the' (both can introduce a definite example of something).
'may' becomes 'er' (I can't justify this - if you can you should give a lot more credence to this answer).
'be put out' indicates putting letters inside.
'the' going within 'er' is 'ETHER'.
'by' acts as a link.
Can you help me to learn more?
(Other definitions for ether that I've seen before include "Once widely-used anaesthetic" , "It could knock you out" , "Solvent; clear sky (poet.)" , "Rare atmosphere" , "Colourless volatile highly inflammable liquid" .)