Final answer:
The subject of the question 'Where did you put the keys?' is 'you,' and the main verb is 'put' with 'keys' being the direct object.
Step-by-step explanation:
In the sentence 'Where did you put the keys?', the subject is the pronoun 'you'. Despite the sentence being in the form of a question, which can sometimes make identifying the subject more challenging, the subject remains the person or entity performing the action. In questions with inverted word order, such as this one, the subject follows the helping verb 'did.' The main action or verb is 'put', and the keys are the direct object of the verb since they are receiving the action.