PDBsum entry 1wmz

Sugar binding protein

PDB id: 1wmz

Contents

Protein chains

140 a.a. *

Ligands

NGA ×3

A2G

Metals

_CA ×12

Waters ×400

* Residue conservation analysis

PDB id:

1wmz

Name:

Sugar binding protein

Title:

Crystal structure of c-type lectin cel-i complexed with n-acetyl-d- galactosamine

Structure:

Lectin cel-i, n-acetyl-d-galactosamine-specific c-type. Chain: a, b, c, d. Synonym: c-type lectin cel-i

Source:

Cucumaria echinata. Organism_taxid: 40245

Biol. unit:

Tetramer (from PQS)

Resolution:

1.70Å R-factor: 0.160 R-free: 0.186

Authors:

H.Sugawara,M.Kusunoki,G.Kurisu,T.Fujimoto,H.Aoyagi,T.Hatakeyama

Key ref:

H.Sugawara et al. (2004). Characteristic recognition of N-acetylgalactosamine by an invertebrate C-type Lectin, CEL-I, revealed by X-ray crystallographic analysis. J Biol Chem, 279, 45219-45225. PubMed id: 15319425 DOI: 10.1074/jbc.M408840200

Date:

22-Jul-04 Release date: 07-Sep-04

Protein chains

Q7M462  (Q7M462_CUCEC) -  Lectin CEL-I, N-acetyl-D-galactosamine-specific C-type from Cucumaria echinata

Seq: 140 a.a.

Struc: 140 a.a.

DOI no: 10.1074/jbc.M408840200

J Biol Chem 279:45219-45225 (2004)

PubMed id: 15319425

Characteristic recognition of N-acetylgalactosamine by an invertebrate C-type Lectin, CEL-I, revealed by X-ray crystallographic analysis.

H.Sugawara, M.Kusunoki, G.Kurisu, T.Fujimoto, H.Aoyagi, T.Hatakeyama.

ABSTRACT

CEL-I is a C-type lectin, purified from the sea cucumber Cucumaria echinata, that shows a high specificity for N-acetylgalactosamine (GalNAc). We determined the crystal structures of CEL-I and its complex with GalNAc at 2.0 and 1.7 A resolution, respectively. CEL-I forms a disulfide-linked homodimer and contains two intramolecular disulfide bonds, although it lacks one intramolecular disulfide bond that is widely conserved among various C-type carbohydrate recognition domains (CRDs). Although the sequence similarity of CEL-I with other C-type CRDs is low, the overall folding of CEL-I was quite similar to those of other C-type CRDs. The structure of the complex with GalNAc revealed that the basic recognition mode of GalNAc was very similar to that for the GalNAc-binding mutant of the mannose-binding protein. However, the acetamido group of GalNAc appeared to be recognized more strongly by the combination of hydrogen bonds to Arg115 and van der Waals interaction with Gln70. Mutational analyses, in which Gln70 and/or Arg115 were replaced by alanine, confirmed that these residues contributed to GalNAc recognition in a cooperative manner.

Selected figure(s)

Figure 1.
FIG. 1. Stereo view of the ribbon model of CEL-I (protomer A). The -helices, -strands, loops, and intramolecular disulfide bonds are shown in purple, blue, gray, and green, respectively. Bound calcium ions are shown by cyan spheres. Secondary structures were determined by the program PROMOTIF (45). Fig. 1 was drawn by the program MOLSCRIPT (46) and rendered by the program Raster3D (47).

Figure 6.
FIG. 6. Comparison of the carbohydrate-binding modes of CEL-I and the GalNAc-binding mutant of MBP. A, electron density map around the GalNAc-binding site of CEL-I (protomer 1A). A 2F[obs] - F[calc] omit map is drawn at the 1.5 level. Carbon, oxygen, nitrogen, and calcium atoms are shown in green, red, blue, and purple, respectively. B, overlapped structures of CEL-I (protomer 1A) and the mutant MBP around the bound GalNAc. C, overlapped structures of CEL-I (protomer 1A) and the mutant MBP around the acetamido group. GalNAc, the calcium ion, and its binding residues in CEL-I and the MBP mutant are superimposed. Carbon, calcium atoms, and residue numbers of CEL-I and the mutant MBP are shown in green and yellow, respectively. Hydrogen and coordination bonds are indicated by dots. The GalNAc-binding site structure of protomer 2A is similar to this site. Fig. 6 was drawn by the program PyMOL (49).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 45219-45225) copyright 2004.

Figures were selected by the author.