By Gregory Zuckerman 

U.S. Bancorp is racking up profits with a bond-market maneuver that is pinching some investors holding high-yielding investments.

The Minneapolis company, which operates the fifth-largest U.S. commercial bank by assets, has made paper profits of about $53 million over the past three years forcing insurance companies, community banks and other investors to sell it Ginnie Mae-insured mortgage bonds at below-market prices, according to calculations by Performance Trust Capital Partners, LLC, a Chicago fixed-income investment firm.

U.S. Bancorp has been buying these bonds at par, or 100 cents on the dollar, though they had been trading about 15% higher at the time of the purchases, thanks in part to their above-market yields, investors say. The bank is entitled to buy the bonds at low prices because it serves as a trustee for pools of these bonds, which are sold to investors in the form of collateralized mortgage obligations, or pools of mortgages sliced into investments with different maturities, yields and risks.

According to the rules governing these investments, trustees can call, or redeem, the bonds when 99% of the value of the principal backing the pools has been paid down by borrowers, something that has happened with more frequency amid low rates. The maneuver is called a "1% cleanup call."

MetLife Inc. and TIAA-CREF are among those investors that had bonds redeemed by U.S. Bancorp, according to securities records. Representatives of MetLife and TIAA-CREF declined to comment.

Some investors have been surprised by the play, analysts say. A similar move over a decade ago by Fannie Mae sparked pushback by unhappy investors and was discontinued.

U.S. Bancorp's purchases come as at least one other trustee for similar Ginnie Mae bond pools-- Bank of New York Mellon Corp.--has elected not to pursue a similar buyback strategy, according to people close to the matter.

"Traders and investors thought the 1% cleanup wouldn't be called" in part because of the earlier backlash when Fannie Mae tried to call its own bonds in 2002, said Andrew Pace, vice president at Performance Trust, which works with institutional investors.

U.S. Bancorp's gains are a byproduct of the continued low-interest-rate environment, which can distort financial markets.

"The fact that they can and are taking advantage of this provision, even though not everyone else has in the past, makes investing a bit more challenging," says Anthony Van Daalen, who runs the $67 million Wright Current Income fund, which has seen some of its bonds purchased by U.S. Bancorp, forcing the fund to reinvest the money at lower interest rates. "They're within their rights, they see an opportunity and I suppose are taking advantage."

Investors forced to sell debt to U.S. Bancorp suffer because they no longer enjoy hefty interest payments from the Ginnie Mae bonds. Many of these bonds were issued in the 1990s with interest rates of 7% or 8% compared with bonds today issued with yields of 3% or less.

With rates still low, many investors have scoured the market for high-yielding debt, sometimes overlooking risks along the way, such as the call features attached to these bonds, traders say. That is why U.S. Bancorp's moves are attracting attention in some corners of the market.

It isn't clear if U.S. Bancorp has been profiting by selling the bonds in the marketplace or by holding them in its own portfolio or repackaging the repurchased debt in new structures sold to investors.

More than $355 million of bonds have been called by U.S. Bancorp since fall of 2012, investors say. In May alone, U.S. Bancorp made paper profits of about $4 million from these purchases; the bank could make about $35 million over the rest of 2015 calling bonds with a face value of about $230 million that are eligible or will become eligible for redemption, according to calculations by Performance Trust based on current prices for the bonds and the prices U.S. Bancorp paid.

Some investors say they were prepared for the potential redemption of the bonds and had placed a lower internal value on them, mitigating any losses in market value.

A U.S. Bancorp spokesman said: "The rights of the trustee to conduct a 1% cleanup call are clearly and fully disclosed in both the prospectus and the Ginnie Mae program guidelines."

The spokesman noted that U.S. Bancorp provides investors with 30-day notification about the termination of the trust.

John Getchis, senior vice president of the office of capital markets at Ginnie Mae, said that the cleanup-call provision is disclosed in the securities' offering materials and the call rights are part of a trustee's potential compensation for their work.

"Ginnie Mae has no financial interest in the call right nor control over the decision by the trustee whether to exercise the call right," Mr. Getchis said in an email.

A trustee for a CMO deal takes payments from the underlying mortgages and distributes them to investors with claims on various slices of the deal.

"This is perfectly legal but it's perfectly bitter for already yield-suffering investors," said Marilyn Cohen, president of Envision Capital, a bond-advisory firm in Los Angeles. She noted that retail, or individual, investors often are less capable of reading the fine print for some bond deals.

Joe Light contributed to this article.

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