PDBsum entry: 1vcl

Toxin

PDB-id: 1vcl

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

432 a.a. *

Ligands

BTB

Metal ions

_CL ×2

_CA ×10

_MG ×4

Waters ×846

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1vcl

Name:

Toxin

Title:

Crystal structure of hemolytic lectin cel-iii

Structure:

Hemolytic lectin cel-iii. Chain: a, b

Source:

Cucumaria echinata. Organism_taxid: 40245

UniProt:

Chains A, B: Q868M7 (Q868M7_9ECHN)

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:

1.70Å

R-factor:

0.167

R-free:

0.201

Authors:

T.Uchida,T.Yamasaki,S.Eto,H.Sugawara,G.Kurisu,A.Nakagawa, M.Kusunoki,T.Hatakeyama

Key ref:

T.Uchida et al. (2004). Crystal structure of the hemolytic lectin CEL-III isolated from the marine invertebrate Cucumaria echinata: implications of domain structure for its membrane pore-formation mechanism.. J Biol Chem, 279, 37133-37141. [PubMed id: 15194688] [DOI: 10.1074/jbc.M404065200]

Date:

09-Mar-04

Release date:

07-Sep-04

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1074/jbc.M404065200

J Biol Chem 279:37133-37141 (2004)

PubMed id: 15194688

Crystal structure of the hemolytic lectin CEL-III isolated from the marine invertebrate Cucumaria echinata: implications of domain structure for its membrane pore-formation mechanism.

T.Uchida, T.Yamasaki, S.Eto, H.Sugawara, G.Kurisu, A.Nakagawa, M.Kusunoki, T.Hatakeyama.

ABSTRACT

CEL-III is a Ca(2+)-dependent and galactose-specific lectin purified from the sea cucumber, Cucumaria echinata, which exhibits hemolytic and hemagglutinating activities. Six molecules of CEL-III are assumed to oligomerize to form an ion-permeable pore in the cell membrane. We have determined the crystal structure of CELIII by using single isomorphous replacement aided by anomalous scattering in lead at 1.7 A resolution. CEL-III consists of three distinct domains as follows: the N-terminal two carbohydrate-binding domains (1 and 2), which adopt beta-trefoil folds such as the B-chain of ricin and are members of the (QXW)(3) motif family; and domain 3, which is a novel fold composed of two alpha-helices and one beta-sandwich. CEL-III is the first Ca(2+)-dependent lectin structure with two beta-trefoil folds. Despite sharing the structure of the B-chain of ricin, CEL-III binds five Ca(2+) ions at five of the six subdomains in both domains 1 and 2. Considering the relatively high similarity among the five subdomains, they are putative binding sites for galactose-related carbohydrates, although it remains to be elucidated whether bound Ca(2+) is directly involved in interaction with carbohydrates. The paucity of hydrophobic interactions in the interfaces between the domains and biochemical data suggest that these domains rearrange upon carbohydrate binding in the erythrocyte membrane. This conformational change may be responsible for oligomerization of CEL-III molecules and hemolysis in the erythrocyte membranes.

Selected figure(s)

Figure 2.
FIG. 2. Three-dimensional structure and topology diagram of CEL-III. A, ribbon model of a CEL-III molecule. Domains 1-3 are colored blue, green, and orange, respectively. The color gradation is shown from bright (e.g. subdomain ) to dark (subdomain ) colors along the polypeptide chain from the N to the C termini in domains 1 and 2. -Helices and 3[10] helices are colored red. Cys residues are depicted as ball-and-stick models (yellow indicates sulfur atoms, and gray indicates carbon atoms). Calcium, magnesium, and chloride ions are shown as purple, orange, and green balls, respectively. Numbers 1-32 indicate the serial numbers of -strands, 1- 32. H1-H7 designate 3[10] helices and H8-H9 -helices. Numbers and Greek letters in boxes indicate subdomains. Figs. 2A, 3, 4, 5A, 6A-C, and 7B-C were made using the programs MOLSCRIPT (50) and RASTER3D (51). B, topology diagram of CEL-III. Color coding is the same as in A. Disulfide bonds are shown as double yellow circles.

Figure 4.
FIG. 4. Ribbon models of -trefoil domains for CEL-III (A) and the B-chain of ricin (B). The color coding is the same as in Fig. 2A.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 37133-37141) copyright 2004.

Figures were selected by the author.