1E9L
The crystal structure of novel mammalian lectin Ym1 suggests a saccharide binding site
Summary for 1E9L
| Entry DOI | 10.2210/pdb1e9l/pdb |
| Descriptor | YM1 SECRETORY PROTEIN, 2-amino-2-deoxy-beta-D-glucopyranose (3 entities in total) |
| Functional Keywords | macrophage secretory protein, inflammation, lectin, inducible, secretory |
| Biological source | MUS MUSCULUS (HOUSE MOUSE) |
| Total number of polymer chains | 1 |
| Total formula weight | 42544.69 |
| Authors | Hsiao, C.D.,Sun, Y.J. (deposition date: 2000-10-21, release date: 2001-03-01, Last modification date: 2024-10-23) |
| Primary citation | Sun, Y.J.,Chang, N.C.,Hung, S.I.,Chang, A.C.,Chou, C.C.,Hsiao, C.D. The Crystal Structure of a Novel Mammalian Lectin, Ym1, Suggests a Saccharide Binding Site J.Biol.Chem., 276:17507-, 2001 Cited by PubMed Abstract: 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-A resolution by x-ray crystallography. The crystal structure of Ym1 consists of two globular domains, a beta/alpha triose-phosphate isomerase barrel domain and a small alpha + beta 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 beta-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. PubMed: 11278670DOI: 10.1074/JBC.M010416200 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.5 Å) |
Structure validation
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