one of the duties the Secretary of State:"Negotiates, interprets & terminates treaties & agreements"
see: Duties of the Secretary of State
Under the Constitution, the President of the United States determines U.S. foreign policy. The Secretary of State, appointed by the President with the advice and consent of the Senate, is the Presidents chief foreign affairs adviser. The Secretary carries out the Presidents foreign policies through the State Department and the Foreign Service of the United States.
However, as is the case with all trade agreements, such as the Transpacific Partnership, the Office of the United States Trade Representative has takes the lead in the negotiations of these agreements. Note that The Office of the United States Trade Representative is part of
the Executive Office of the President. That means that The Office of the United States Trade Representative - is answerable directly to the President. Meaning it is the President who determines what the foreign policy, including trade agreements, of the United States will be.