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7 year oldPresident Donald Trump said Mr Pruitt had done "an outstanding job, and I will always be thankful to him".
But Mr Pruitt has been embroiled in allegations of ethics violations for months.
His deputy Andrew Wheeler will take over as acting head of the agency, Mr Trump said.
The long list of Scott Pruitt controversiesNewer articles
<p>The EU suspended €93 billion in planned tariffs on US goods Tuesday after striking a last-minute deal with Washington, averting a trade clash. Brussels warned the measures...