LONDON, Sept 17 (Reuters) - An Amsterdam court on Thursday froze a stake held by Exem Energy, a company owned by the husband of Angola's former first daughter Isabel dos Santos, in a dispute over a deal struck with Angolan state oil firm Sonangol in 2006.

The dos Santos family has faced legal battles around the world since José Eduardo, who installed two of his children as heads of key state enterprises during four decades of rule, stepped down as Angolan president in 2017.

Dutch law firm Van Doorne, which represented Isabel's husband Sindika Dokolo in the dispute between Sonangol and Exem, did not respond to a request for comment on the Amsterdam appeal court's ruling, which was posted on its website on Thursday.

A representative for Isabel dos Santos did not immediately reply to a Reuters request for comment. She has repeatedly denied any wrongdoing by the family and says she faces a political "witch hunt" by Angola's new leadership.

The former Sonangol chairwoman lives outside Angola, where her assets were seized last year in an ongoing investigation.

The dispute, which is being heard in Amsterdam after both sides agreed on arbitration, concerns Sonangol's sale of a 40% stake in holding company Esperaza to Exem in 2006.

Sonangol later rejected the deal and returned the funds.

This sale agreement goes to the heart of Angolan allegations that the Dos Santos family manipulated its influence over government institutions for their own gain.

Exem was required to pay only 11.3 million euros up front and the remaining 85%, 63.8 million euros, was financed by Sonangol through loans, court documents showed.

"There was no commercial reason to give 40% of the newly acquired Esperaza to Exem," Emmanuel Gaillard of law firm Shearman & Sterling, which is representing Sonangol, said.

In its ruling, which applies for the duration of the proceedings, the appeals court in Amsterdam froze Exem's stake, removed Exem's representative from Esperaza's board and ordered dividends to be paid into an escrow account.

The court also ordered an investigation into the way in which Sonangol agreed, shortly before Angola's new leadership sacked Isabel Dos Santos in 2017, that Exem's loan repayment could be made in Kwanza, Angola's relatively weak currency.

(Additional reporting by Anthony Deutsch and Toby Sterling in Amsterdam; Editing by Alexander Smith)