Houghton Mifflin Harcourt Publishing Co., the publisher of authors from Mark Twain to J.R.R. Tolkien, sought bankruptcy protection to eliminate more than $3 billion in debt.

The company, based in Boston, listed assets and debt of more than $1 billion each in Chapter 11 documents filed today in US Bankruptcy Court in Manhattan.

(On May 11, Houghton disclosed a deal with creditors to wipe out $3.1 billion in debt in return for stakes in the company, which it said would lift heavy interest payment obligations without the need for cutbacks. Houghton has been struggling with debt since the company’s owner, Irish investor Barry O’Callaghan, borrowed heavily to buy Houghton Mifflin in 2006 and Harcourt in 2007. Under Houghton’s plan, the financial restructuring was to be processed as a so-called pre-packaged Chapter 11 bankruptcy. When the plan was disclosed, Houghton went to great lengths to assure employees, vendors, and customers that the company was not on the verge of going out of business, or in the process of being liquidated. )

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Houghton said May 11 it received support from more than 70 percent of lenders to restructure its debt. The company has about $2.85 billion of loans maturing in the next two years, according to data compiled by Bloomberg.

Under the proposed plan, Houghton’s long-term bank loan and bond debt would convert to all of the equity in the reorganized company, according to a May 11 statement. Existing shareholders will receive warrants for 5 percent of the new stock if they vote in favor of the plan.

Houghton provides educational products and services to about 60 million students in 120 countries, according to its website. The company also prints and distributes electronic books owned by one of Amazon.com Inc.’s publishing arms, under an agreement announced in January.

The accord allows Amazon, the world’s largest Internet retailer, to market books to people who don’t visit its site and provides Houghton with a new source of revenue as sales decline at brick-and-mortar bookstores.

Moody’s Investors Service in May cut Houghton’s corporate credit grade to Ca, the second-lowest rating and reserved for borrowers that “offer very poor financial security.” In March, Moody’s said the company’s capital structure was “unsustainable without a significant rebound in earnings.”

Houghton’s origins date to 1832, according to the company. Among its authors are Ralph Waldo Emerson and Jonathan Safran Foer, and the company’s titles include the “Curious George” and “Lord of the Rings” books.

(In a statement issued Monday, Houghton said: “Today, Houghton Mifflin Harcourt filed a ‘pre-packaged’ comprehensive financial restructuring plan that will strengthen the company financially so we can continue to invest in our business and ensure we are well positioned for the future. This plan, which is supported by a majority of our key financial stakeholders, will eliminate $3.1 billion of debt through a debt to equity transaction, and reduce our annual cash interest costs. The company today lodged voluntary petitions for reorganization under Chapter 11 in the US Bankruptcy Court for the Southern District of New York. With a more appropriate capital structure to support our strategic plan and business objectives, we will have greater financial flexibility to pursue growth opportunities. Houghton Mifflin Harcourt will maintain normal day-to-day business operations throughout the restructuring process, and we expect no disruptions to our relationships with our customers, agents, authors, employees, business partners, and suppliers. Our customers will continue to receive the high quality content they have come to expect from us, and service without interruption. Additionally, our plan provides for our suppliers and vendors to be paid in full during and after this process and for our employees to continue receiving their usual pay and benefits. Because of the high level of support we have obtained from our lenders, bondholders and shareholders for our plan, we seek to complete this financial restructuring quickly, likely by the end of June 2012. )