PDBsum entry: 2z49

Toxin

PDB-id: 2z49

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

432 a.a. *

Ligands

AMG ×10

Metal ions

_MG ×4

_CA ×10

Waters ×740

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

2z49

Name:

Toxin

Title:

Crystal structure of hemolytic lectin cel-iii complexed with methyl-alpha-d-galactopylanoside

Structure:

Hemolytic lectin cel-iii. Chain: a, b. Fragment: residues in database 11-442

Source:

Cucumaria echinata. Organism_taxid: 40245

UniProt:

Chains A, B: Q868M7 (Q868M7_CUCEC)

Seq:

Struc:

Seq:

442 a.a.

Struc:

432 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 14 residue positions (black crosses)

Resolution:

1.95Å

R-factor:

0.193

R-free:

0.239

Authors:

T.Hatakeyama,H.Unno,S.Eto,H.Hidemura,T.Uchida,Y.Kouzuma

Key ref:

T.Hatakeyama et al. (2007). C-type lectin-like carbohydrate recognition of the hemolytic lectin CEL-III containing ricin-type -trefoil folds.. J Biol Chem, 282, 37826-37835. [PubMed id: 17977832] [DOI: 10.1074/jbc.M705604200]

Date:

13-Jun-07

Release date:

30-Oct-07

Related entries:

1vcl
2z48

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1074/jbc.M705604200

J Biol Chem 282:37826-37835 (2007)

PubMed id: 17977832

C-type lectin-like carbohydrate recognition of the hemolytic lectin CEL-III containing ricin-type -trefoil folds.

T.Hatakeyama, H.Unno, Y.Kouzuma, T.Uchida, S.Eto, H.Hidemura, N.Kato, M.Yonekura, M.Kusunoki.

ABSTRACT

CEL-III is a Ca(2+)-dependent hemolytic lectin, isolated from the marine invertebrate Cucumaria echinata. The three-dimensional structure of CEL-III/GalNAc and CEL-III/methyl alpha-galactoside complexes was solved by x-ray crystallographic analysis. In these complexes, five carbohydrate molecules were found to be bound to two carbohydrate-binding domains (domains 1 and 2) located in the N-terminal 2/3 portion of the polypeptide and that contained beta-trefoil folds similar to ricin B-chain. The 3-OH and 4-OH of bound carbohydrate molecules were coordinated with Ca(2+) located at the subdomains 1alpha, 1gamma, 2alpha, 2beta, and 2gamma, simultaneously forming hydrogen bond networks with nearby amino acid side chains, which is similar to carbohydrate binding in C-type lectins. The binding of carbohydrates was further stabilized by aromatic amino acid residues, such as tyrosine and tryptophan, through a stacking interaction with the hydrophobic face of carbohydrates. The importance of amino acid residues in the carbohydrate-binding sites was confirmed by the mutational analyses. The orientation of bound GalNAc and methyl alpha-galactoside was similar to the galactose moiety of lactose bound to the carbohydrate-binding site of the ricin B-chain, although the ricin B-chain does not require Ca(2+) ions for carbohydrate binding. The binding of the carbohydrates induced local structural changes in carbohydrate-binding sites in subdomains 2alpha and 2beta. Binding of GalNAc also induced a slight change in the main chain structure of domain 3, which could be related to the conformational change upon binding of specific carbohydrates to induce oligomerization of the protein.

Selected figure(s)

Figure 1.
FIGURE 1. Structure of carbohydrate-binding site (1 ) with bound GalNAc and Me- -Gal. 2F[o] - F[c] electron density maps are contoured at 1.2 in GalNAc (A) and Me- -Gal (B) complexes. The Ca^2+ ions are shown as magenta spheres.

Figure 2.
FIGURE 2. Overall structure of the CEL-III/GalNAc complex (A) and its carbohydrate-binding domains (domains 1 and 2) (B). Bound GalNAc molecules are indicated by yellow stick models. Ca^2+ and Mg^2+ ions are shown as purple and orange balls, respectively. Five GalNAc molecules are bound at subdomains 1 , 1 , 2 , 2β, and 2 . Only subdomain 1β contains no Ca^2+ ion and no GalNAc. An additional GalNAc molecule nonspecifically bound to CEL-III (Fig. 4C) is not depicted.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 37826-37835) copyright 2007.

Figures were selected by the author.