PDBsum entry: 1hjv

Lectin

PDB-id: 1hjv

Biological unit = asymmetric unit,
as shown
(as defined in PDB file)

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

362 a.a. *

Ligands

NAG-NAG-NAG ×4

NAG-NAG-NAG-NAG ×4

NAG ×4

SO4 ×12

Waters ×302

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1hjv

Name:

Lectin

Title:

Crystal structure of hcgp-39 in complex with chitin tetramer

Structure:

Chitinase-3 like protein 1. Chain: a, b, c, d. Synonym: cartilage glycoprotein-39,gp-39,39 kda synovial protein, ykl-40

Source:

Homo sapiens. Human. Organism_taxid: 9606. Cell: chondrocytes

Biological unit:

Tetramer (from PDB file)

UniProt:

Chains A, B, C, D: P36222 (CH3L1_HUMAN)

Seq:

Struc:

Seq:

383 a.a.

Struc:

362 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Resolution:

2.75Å

R-factor:

0.212

R-free:

0.253

Authors:

D.R.Houston,A.D.Recklies,J.C.Krupa,D.M.F.Van Aalten

Key ref:

D.R.Houston et al. (2003). Structure and ligand-induced conformational change of the 39-kDa glycoprotein from human articular chondrocytes.. J Biol Chem, 278, 30206-30212. [PubMed id: 12775711] [DOI: 10.1074/jbc.M303371200]

Date:

28-Feb-03

Release date:

11-Mar-03

Related entries:

1hjw crystal structure of hcgp-39 in complex with chitin octamer
1hjx ligand-induced signalling and conformational change of the 39 kd glycoprotein from human articular chondrocytes
1hjy crystal structure of hcgp-39 in complex with chitin tetramer

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Surface

Key reference

DOI no: 10.1074/jbc.M303371200

J Biol Chem 278:30206-30212 (2003)

PubMed id: 12775711

Structure and ligand-induced conformational change of the 39-kDa glycoprotein from human articular chondrocytes.

D.R.Houston, A.D.Recklies, J.C.Krupa, D.M.van Aalten.

ABSTRACT

The 39-kDa human cartilage glycoprotein (HCGP39), a member of a novel family of chitinase-like lectins (Chilectins), is overexpressed in articular chondrocytes and certain cancers. Proposed functions of this protein include a role in connective tissue remodeling and defense against pathogens. Similar to other Chi-lectins, HCGP39 promotes the growth of connective tissue cells. The ability of HCGP39 to activate cytoplasmic signaling pathways suggests the presence of a ligand for this protein at the cell surface. There is currently no information regarding the identity of any physiological or pathological ligands of the Chi-lectins or the nature of the protein-ligand interaction. Here, we show that HCGP39 is able to bind chitooligosaccharides with micromolar affinity. Crystal structures of the native protein and a complex with GlcNAc8 show that the ligand is bound in identical fashion to family 18 chitinases. However, unlike the chitinases, binding of the oligosaccharide ligand to HCGP39 induces a large conformational change. Thus, HCGP39 could be a lectin that binds chitin-like oligosaccharide ligands and possibly plays a role in innate responses to chitinous pathogens, such as fungi and nematodes.

Selected figure(s)

Figure 2.
FIG. 2. Structural comparison of the Chi-lectins. The molecular surfaces calculated from the crystal structures of HCGP39, the human macrophage chitinase (HCHT) (18), Ym1 (30), and IDGF-2 (31), are compared for two properties. The top panel shows electrostatic surface potential, calculated with GRASP (47) (red, < -7.5 kiloteslas; blue, > +7.5 kiloteslas). The bottom panel shows sequence conservation, compared with the HCHT structure (magenta, conserved; gray, nonconserved). For HCHT, a model of GlcNAc[9], described previously (18), is also shown as a stick model.

Figure 3.
FIG. 3. A, electron density maps. The binding sites for the HCGP39 complex with GlcNAc[8] (NAG8) is compared with the HCHT-allosamidin complex. Ligands are shown as sticks with orange carbon. An unbiased (i.e. before including any ligand model) F[o] - F[c], [calc] map (magenta) is shown, contoured at 2.25 . Residues interacting with the ligand are shown as sticks with black carbons. Hydrogen bonds are shown as green dotted lines. B, conformational changes in the binding site. Molecular surfaces are shown for apo-HCGP39 (APO) and the complex with GlcNAc[8]. The solvent-exposed aromatics toward the nonreducing end of the ligand are shown as sticks with purple carbons. The residues undergoing conformational changes upon ligand binding (99-100 and 209-213) are shown as sticks with green carbons. The structure for the GlcNAc[6] ligand observed in the density is shown as sticks with orange carbons. C, conformational changes in the protein. The structure of apo-HCGP39 is shown in stereo as a gray ribbon, with key side chains shown as sticks with black carbons and label names starting with the letter a. For conformational changes of >1.0 Å, the backbone of the HCGP39-GlcNAc[8] complex is shown in green. The same side chains are shown as for apo-HCGP39, but with carbons colored green and label names starting with the letter h. The oligosaccharide is shown with orange carbons.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 30206-30212) copyright 2003.

Figures were selected by an automated process.