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Crystal Structure of the YchF Protein Reveals Binding Sites for GTP and Nucleic Acid

Alexey Teplyakov,^1* Galina Obmolova,¹ Seung Y. Chu,^1, John Toedt,¹ Edward Eisenstein,¹ Andrew J. Howard,² and Gary L. Gilliland^1*

Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute and the National Institute of Standards and Technology, Rockville, Maryland 20850,¹ Center for Synchrotron Radiation Research and Instrumentation, Biological, Chemical, and Physical Sciences Department, Illinois Institute of Technology, Chicago, Illinois 60616²

Received 13 January 2003/ Accepted 31 March 2003

The bacterial protein encoded by the gene ychF is 1 of 11 universally conserved GTPases and the only one whose function is unknown. The crystal structure determination of YchF was sought to help with the functional assignment of the protein. The YchF protein from Haemophilus influenzae was cloned and expressed, and the crystal structure was determined at 2.4 Å resolution. The polypeptide chain is folded into three domains. The N-terminal domain has a mononucleotide binding fold typical for the P-loop NTPases. An 80-residue domain next to it has a pronounced -helical coiled coil. The C-terminal domain features a six-stranded half-barrel that curves around an -helix. The crablike three-domain structure of YchF suggests the binding site for a double-stranded nucleic acid in the cleft between the domains. The structure of the putative GTP-binding site is consistent with the postulated guanine specificity of the protein. Fluorescence measurements have demonstrated the ability of YchF to bind a double-stranded nucleic acid and GTP. Taken together with other experimental data and genomic analysis, these results suggest that YchF may be part of a nucleoprotein complex and may function as a GTP-dependent translation factor.

Present address: Xencor Co., Monrovia, CA 91016.

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