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J. Biol. Chem., Vol. 280, Issue 19, 19213-19220, May 13, 2005

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The Shwachman-Bodian-Diamond Syndrome Protein Family Is Involved in RNA Metabolism^*

From the ^aOntario Center for Structural Proteomics, the ^bBanting and Best Department of Medical Research, and the ^eStructural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L6, Canada, the ^cDepartment of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, the ^dNortheast Structural Genomics Consortium, and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, the ^fDivision of Molecular and Structural Biology, Ontario Cancer Institute, Toronto, Ontario M5G 2M9, Canada, the ^gDepartment of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 2M9, Canada, the ^hProtein Design Group, Centro Nacional de Biotecnologia (CNB-CSIC), Cantoblanco, E-28049 Madrid, Spain, the ⁱBioinformatics Group, Ontario Genomics Innovation Centre, Ottawa Health Research Institute, Ottawa, Ontario K1H 8L6, Canada, the ^jDepartment of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73190, the ^kEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD United Kingdom, and the ^lProgram in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada

A combination of structural, biochemical, and genetic studies in model organisms was used to infer a cellular role for the human protein (SBDS) responsible for Shwachman-Bodian-Diamond syndrome. The crystal structure of the SBDS homologue in Archaeoglobus fulgidus, AF0491, revealed a three domain protein. The N-terminal domain, which harbors the majority of disease-linked mutations, has a novel three-dimensional fold. The central domain has the common winged helix-turn-helix motif, and the C-terminal domain shares structural homology with known RNA-binding domains. Proteomic analysis of the SBDS sequence homologue in Saccharomyces cerevisiae, YLR022C, revealed an association with over 20 proteins involved in ribosome biosynthesis. NMR structural genomics revealed another yeast protein, YHR087W, to be a structural homologue of the AF0491 N-terminal domain. Sequence analysis confirmed them as distant sequence homologues, therefore related by divergent evolution. Synthetic genetic array analysis of YHR087W revealed genetic interactions with proteins involved in RNA and rRNA processing including Mdm20/Nat3, Nsr1, and Npl3. Our observations, taken together with previous reports, support the conclusion that SBDS and its homologues play a role in RNA metabolism.

Received for publication, December 22, 2004 , and in revised form, January 24, 2005.

The atomic coordinates and structure factors (code 1P9Q and 1NYN) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).

NMR data (code 5695) on chemical shifts have been deposited in the BioMagResBank, Madison, WI.

^* This work was supported by Genome Canada, the Ontario Research and Development Challenge Fund, and the National Institutes of Health Protein Structure Initiative (Grants P50-GM62413-02 to the NE Structural Genomics Consortium and P50-GM62414 to the Midwest Center for Structural Genomics). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

^m To whom correspondence should be addressed: Banting and Best Dept. of Medical Research, C. H. Best Institute, University of Toronto, 112 College St., Toronto, ON M5G 1L6, Canada. Tel.: 416-946-3436; Fax: 416-946-0588; E-mail: aled.edwards{at}utoronto.ca.

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