PDBsum entry: 1e9l

Macrophage secretory protein

PDB id: 1e9l

Contents

Protein chain

372 a.a. *

Ligands

GCS

Waters ×642

* Residue conservation analysis

PDB id:

1e9l

Name:

Macrophage secretory protein

Title:

The crystal structure of novel mammalian lectin ym1 suggests a saccharide binding site

Structure:

Ym1 secretory protein. Chain: a

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Strain: icr. Cell: peritoneal exudate cells(macrophages). Cellular_location: cytoplasm. Gene: ym1. Other_details: oral infections of mice with trichinella spiralis induce peritoneal exudate cells to secrete ym1

Resolution:

2.5Å R-factor: 0.198 R-free: 0.272

Authors:

C.D.Hsiao,Y.J.Sun

Key ref:

Y.J.Sun et al. (2001). The crystal structure of a novel mammalian lectin, Ym1, suggests a saccharide binding site. J Biol Chem, 276, 17507-17514. PubMed id: 11278670 DOI: 10.1074/jbc.M010416200

Date:

21-Oct-00 Release date: 01-Mar-01

Protein chain

O35744  (CH3L3_MOUSE) -  Chitinase-3-like protein 3

Seq: 398 a.a.

Struc: 372 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular region (2 terms)
• Biological process: carbohydrate metabolic process (3 terms)
• Biochemical function: catalytic activity (7 terms)

DOI no: 10.1074/jbc.M010416200

J Biol Chem 276:17507-17514 (2001)

PubMed id: 11278670

The crystal structure of a novel mammalian lectin, Ym1, suggests a saccharide binding site.

Y.J.Sun, N.C.Chang, S.I.Hung, A.C.Chang, C.C.Chou, C.D.Hsiao.

ABSTRACT

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.

Selected figure(s)

Figure 1.
Fig. 1. Ribbon diagrams (60, 61) of Ym1 in side view orientation (a) and top view orientation (b). The proposed saccharide substrate-binding site is shown as a ball and stick. The -helices are shown as cylinders in violet, and the -strands are shown as arrows in cyan. The amino and carboxyl termini are labeled.

Figure 6.
Fig. 6. Electrostatic surface potential of the TIM domain of Ym1 and chitosanase (Protein Data Bank number 1CHK) displayed by the program GRASP (54). The putative saccharide binding site of both Ym1 and chitosanase shows a relatively strong electronegative character. Negative potentials (<10 kiloteslas) are colored in deep red, and positive potentials (>10 kiloteslas) are colored in deep blue. The neutral surface potential regions are depicted in white. The orientation of Ym1 is the same as in Fig. 1b.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 17507-17514) copyright 2001.

Figures were selected by an automated process.