Crystal structure of the legume lectin-like domain of an ERGIC-53-like protein from Entamoeba histolytica

Abstract

ERGIC-53-like proteins are type I membrane proteins that belong to the class of intracellular cargo receptors and are known to be indispensable for the intracellular transport of glycoproteins. They are implicated in transporting glycoproteins between the endoplasmic reticulum and the Golgi body. The crystal structure of the legume lectin-like domain of an ERGIC-53-like protein from Entamoeba histolytica has been determined at 2.4 Å resolution. Although the overall structure of the domain resembles those of its mammalian and yeast orthologs (ERGIC-53 and Emp46, respectively), there are significant changes in the carbohydrate-binding site. A sequence-based search revealed the presence of several homologs of ERGIC-53 in different species of Entamoeba. This is the first report of the structural characterization of a member of this class of proteins from a protozoan and serves to further knowledge and understanding regarding the species-specific differences.

Keywords: ERGIC-53-like proteins; Entamoeba histolytica; intracellular cargo receptors; legume lectin-like domains; membrane proteins.

Figure 1

Cartoon representation of EntERGIC displaying the various domains. The box below displays the domains, with residue numbers demarcating the boundaries.

Figure 2

The overall structure of EntLec with the loops involved in carbohydrate and metal binding depicted; loop A is in blue, loop B is in green, loop C is in red, the variable loop D is in purple and loop E is in cyan. The Cys residues forming disulfide bonds are marked and the disulfide bonds are displayed in yellow in stick representation.

Figure 3

Comparison of EntLec with other lectins. EntLec (in cyan) superposed on (a) ERGIC-53 (PDB entry 4gky; Zheng et al., 2013 ▸), (b) the carbohydrate-binding site of ERGIC-53, (c) pea lectin (PDB entry 2bqp; Pletnev et al., 1997 ▸), (d) the carbohydrate-binding site of pea lectin and (e) Emp46 (PDB entry 2a6w; Satoh et al., 2006 ▸). (f) K⁺-bound loop E from Emp46. Water molecules and ions are represented as spheres. Glucose and mannose molecules are shown in pink.

Figure 4

The unique disulfide bond in loop A. An enlarged image of this disulfide bond is shown with the F _o − F _c OMIT map contoured at the 3σ level.

Figure 5

Surface-charge comparison. (a) ERGIC-53 (PDB entry 1r1z; Velloso et al., 2003 ▸), (b) Emp46 (PDB entry 2a6w; Satoh et al., 2006 ▸), (c) pea lectin (PDB entry 2bqp; Pletnev et al., 1997 ▸), (d) VIP36 (PDB entry 2duo; Satoh et al., 2007 ▸), (e) EntLec. The top and bottom panels display surface charges on the front and back β-sheets, respectively. A blue colour indicates positively charged residues and red indicates negatively charged residues. The scale used is from −10 kT/e to +10 kT/e.