PDBsum entry 1vf8

Immune system

PDB id: 1vf8

Contents

Protein chain

373 a.a. *

Waters ×528

* Residue conservation analysis

PDB id:

1vf8

Name:

Immune system

Title:

The crystal structure of ym1 at 1.31 a resolution

Structure:

Secretory protein. Chain: a. Synonym: ym1

Source:

Mus musculus. House mouse. Organism_taxid: 10090

Resolution:

1.31Å R-factor: 0.175 R-free: 0.197

Authors:

S.H.Liaw,M.L.Tsai,N.C.Chang

Key ref:

M.L.Tsai et al. (2004). The crystal structure of Ym1 at 1.31 A resolution. J Struct Biol, 148, 290-296. PubMed id: 15522777 DOI: 10.1016/j.jsb.2004.07.002

Date:

09-Apr-04 Release date: 15-Mar-05

Protein chain

O35744  (CHIL3_MOUSE) -  Chitinase-like protein 3 from Mus musculus

Seq: 398 a.a.

Struc: 373 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.1.52 - beta-N-acetylhexosaminidase.
• Reaction: Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides.

DOI no: 10.1016/j.jsb.2004.07.002

J Struct Biol 148:290-296 (2004)

PubMed id: 15522777

The crystal structure of Ym1 at 1.31 A resolution.

M.L.Tsai, S.H.Liaw, N.C.Chang.

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.