title: The crystal structure of Ym1 at 1.31 A resolution.
abstract: Upon nematode infection, murine peritoneal macrophages synthesize and secrete large amounts of the Ym1 protein, which is a unique functional marker for alternatively activated macrophages in T(H)2-mediated inflammatory responses. Ym1 shares significant structural similarity to the family 18 chitinases. Previously, Ym1 has been studied with respect to its carbohydrate-binding ability and glycosyl hydrolysis activity and this has led to various inconclusive interpretations. Our present co-crystallization and soaking experiments with various glucosamine or N-acetylglucosamine oligomers yield only the uncomplexed Ym1. The refined Ym1 structure at 1.31A resolution clearly displays a water cluster forming an extensive hydrogen bond network with the "active-site" residues. This water cluster contributes notable electron density to lower resolution maps and this might have misled and given rise to a previous proposal for a monoglucosamine-binding site for Ym1. A structural comparison of family 18 glycosidase (-like) proteins reveals a lack of several conserved residues in Ym1, and illustrates the versatility of the divergent active sites. Therefore, Ym1 may lack N-acetylglucosamine-binding affinity, and this suggests that a new direction should be taken to unravel the function of Ym1.
authors.affiliation: Bioinformatics Program, National Yang-Ming University, Taipei 11221, Taiwan, ROC.
authors.forename: Meng-Ling
authors.initials: ML
authors.lastname: Tsai
authors.forename: Shwu-Huey
authors.initials: SH
authors.lastname: Liaw
authors.forename: Nan-Chi
authors.initials: NC
authors.lastname: Chang
mesh_terms: D000117:Acetylglucosamine / Q000737:chemistry; D000818:Animals; D001665:Binding Sites; D002241:Carbohydrates / Q000737:chemistry; D002688:Chitinases / Q000737:chemistry; D018360:Crystallography, X-Ray; D006026:Glycoside Hydrolases / Q000737:chemistry; D006868:Hydrolysis; D007249:Inflammation; D037102:Lectins / Q000737:chemistry*; D051379:Mice; D008958:Models, Molecular; D011485:Protein Binding; D017433:Protein Structure, Secondary; D018418:Th2 Cells; D014867:Water / Q000737:chemistry; D001619:beta-N-Acetylhexosaminidases / Q000737:chemistry*
chemical_list: D002241:Carbohydrates; D037102:Lectins; D014867:Water; D006026:Glycoside Hydrolases; D002688:Chitinases; C429541:Chil3 protein, mouse; D001619:beta-N-Acetylhexosaminidases; D000117:Acetylglucosamine