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J. Biol. Chem., Vol. 276, Issue 20, 17507-17514, May 18, 2001

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The Crystal Structure of a Novel Mammalian Lectin, Ym1, Suggests a Saccharide Binding Site^*

Yuh-Ju Sun^§, Nan-Chi A. Chang^¶, Shuen-Iu Hung^¶, Alice Chien Chang^**, Chia-Cheng Chou, and Chwan-Deng Hsiao^§§

From the  Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China, the ^§ Department of Life Sciences, National Tsing-Hua University, Hsinchu, Taiwan 300, Republic of China, the ^¶ Institute of Microbiology & Immunology and ^** Institute of Neuroscience, School of Life Science, National Yang-Ming University, Taipei, Taiwan 112, Republic of China, and the  Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan 114, Republic of China

Ym1, a secretory protein synthesized by activated murine peritoneal macrophages, is a novel mammalian lectin with a binding specificity to GlcN. Lectins are responsible for carbohydrate recognition and for mediating cell-cell and cell-extracellular matrix interactions in microbes, plants, and animals. Glycosaminoglycan heparin/heparan sulfate binding ability was also detected in Ym1. We report here the three-dimensional structure of Ym1 at 2.5-Å resolution by x-ray crystallography. The crystal structure of Ym1 consists of two globular domains, a / triose-phosphate isomerase barrel domain and a small  +  folding domain. A notable electron density of sugar is detected in the Ym1 crystal structure. The saccharide is located inside the triose-phosphate isomerase domain at the COOH terminal end of the -strands. Both hydrophilic and hydrophobic interactions are noted in the sugar-binding site in Ym1. Despite the fact that Ym1 is not a chitinase, structurally, Ym1 shares significant homology with chitinase A of Serratia marcescens. Ym1 and chitinase A have a similar carbohydrate binding cleft. This study provides new structure information, which will lead to better understanding of the biological significance of Ym1 and its putative gene members.

The atomic coordinates and the structure factors (code 1E9L) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).

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