1VF8

The Crystal Structure of Ym1 at 1.31 A Resolution

Summary for 1VF8

• Entry DOI: 10.2210/pdb1vf8/pdb
• Related: 1E9L
• Descriptor: secretory protein (2 entities in total)
• Functional Keywords: ym1, chitinase, chi-lectin, structural plasticity, functional versatility, immune system
• Biological source: Mus musculus (house mouse)
• Cellular location: Secreted: O35744
• Total number of polymer chains: 1
• Total formula weight: 42365.52

Authors

Liaw, S.H.,Tsai, M.L.,Chang, N.C. (deposition date: 2004-04-09, release date: 2005-03-15, Last modification date: 2024-10-16)

Primary citation

Tsai, M.L.,Liaw, S.H.,Chang, N.C.
The crystal structure of Ym1 at 1.31 A resolution
J.Struct.Biol., 148:290-296, 2004

PubMed 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.

PubMed: 15522777
DOI: 10.1016/j.jsb.2004.07.002

Experimental method

X-RAY DIFFRACTION (1.31 Å)