The crystal structure of a novel mammalian lectin, Ym1, suggests a saccharide binding site.
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.
Sun
Y J
YJ
Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China.
Chang
N C
NC
Hung
S I
SI
Chang
A C
AC
Chou
C C
CC
Hsiao
C D
CD
D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D050260:Carbohydrate Metabolism; D002241:Carbohydrates / Q000737:chemistry*; D002688:Chitinases / Q000737:chemistry; D018360:Crystallography, X-Ray / Q000379:methods; D005916:Globulins / Q000737:chemistry; D005944:Glucosamine / Q000378:metabolism; D037102:Lectins / Q000737:chemistry* / Q000378:metabolism; D017737:Macrophages, Peritoneal / Q000502:physiology*; D008322:Mammals; D051379:Mice; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010940:Plant Proteins / Q000737:chemistry; D014674:Plant Proteins, Dietary / Q000737:chemistry; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D001619:beta-N-Acetylhexosaminidases
D002241:Carbohydrates; D005916:Globulins; D037102:Lectins; D010940:Plant Proteins; D014674:Plant Proteins, Dietary; C066193:narbonin; C007110:concanavalin B protein, Canavalia ensiformis; D002688:Chitinases; C429541:Chil3 protein, mouse; D001619:beta-N-Acetylhexosaminidases; D005944:Glucosamine