PDBsum entry 1vf8

Immune system

PDB id: 1vf8

Contents

Protein chain

373 a.a.

Waters ×528

References listed in PDB file

Key reference

• Title: The crystal structure of ym1 at 1.31 a resolution.
• Authors: M.L.Tsai, S.H.Liaw, N.C.Chang.
• Ref.: J Struct Biol, 2004, 148, 290-296. [DOI no: 10.1016/j.jsb.2004.07.002]
• PubMed id: 15522777

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.