PDBsum entry 2a6y

Sugar binding protein

PDB id: 2a6y

Contents

Protein chain

231 a.a. *

Ligands

SO4 ×2

Waters ×301

* Residue conservation analysis

PDB id:

2a6y

Name:

Sugar binding protein

Title:

Crystal structure of emp47p carbohydrate recognition domain (crd), tetragonal crystal form

Structure:

Emp47p (form1). Chain: a. Fragment: residues 1-254. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.42Å R-factor: 0.134 R-free: 0.192

Authors:

T.Satoh,K.Sato,A.Kanoh,K.Yamashita,R.Kato,A.Nakano,S.Wakatsuki

Key ref:

T.Satoh et al. (2006). Structures of the carbohydrate recognition domain of Ca2+-independent cargo receptors Emp46p and Emp47p. J Biol Chem, 281, 10410-10419. PubMed id: 16439369 DOI: 10.1074/jbc.M512258200

Date:

04-Jul-05 Release date: 31-Jan-06

Protein chain

P43555  (EMP47_YEAST) -  Protein EMP47 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 445 a.a.

Struc: 231 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DOI no: 10.1074/jbc.M512258200

J Biol Chem 281:10410-10419 (2006)

PubMed id: 16439369

Structures of the carbohydrate recognition domain of Ca2+-independent cargo receptors Emp46p and Emp47p.

T.Satoh, K.Sato, A.Kanoh, K.Yamashita, Y.Yamada, N.Igarashi, R.Kato, A.Nakano, S.Wakatsuki.

ABSTRACT

Emp46p and Emp47p are type I membrane proteins, which cycle between the endoplasmic reticulum (ER) and the Golgi apparatus by vesicles coated with coat protein complexes I and II (COPI and COPII). They are considered to function as cargo receptors for exporting N-linked glycoproteins from the ER. We have determined crystal structures of the carbohydrate recognition domains (CRDs) of Emp46p and Emp47p of Saccharomyces cerevisiae, in the absence and presence of metal ions. Both proteins fold as a beta-sandwich, and resemble that of the mammalian ortholog, p58/ERGIC-53. However, the nature of metal binding is distinct from that of Ca(2+)-dependent p58/ERGIC-53. Interestingly, the CRD of Emp46p does not bind Ca(2+) ion but instead binds K(+) ion at the edge of a concave beta-sheet whose position is distinct from the corresponding site of the Ca(2+) ion in p58/ERGIC-53. Binding of K(+) ion to Emp46p appears essential for transport of a subset of glycoproteins because the Y131F mutant of Emp46p, which cannot bind K(+) ion fails to rescue the transport in disruptants of EMP46 and EMP47 genes. In contrast the CRD of Emp47p binds no metal ions at all. Furthermore, the CRD of Emp46p binds to glycoproteins carrying high mannosetype glycans and the is promoted by binding not the addition of Ca(2+) or K(+) ion in These results suggest that Emp46p can be regarded as a Ca(2+)-independent intracellular lectin at the ER exit sites.

Selected figure(s)

Figure 3.
FIGURE 3. Electrostatic surface potential representations of Emp46p (A and B) and Emp47p (C and D). The surface models of Emp46p and Emp47p are shown in the same orientations as in Fig. 1 and colored according to the electrostatic surface potential (blue, positive; red, negative; scale from -10 to +10 kT/e).

Figure 4.
FIGURE 4. K^+ ion binding site and its conformational changes upon K^+ ion binding of Emp46p. A, K^+ ion binding site of Emp46p. Residues coordinating the K^+ ion are shown in ball- and-stick models. The magenta sphere indicates the K^+ ion. Water molecules are shown as W1 and W2. Pink spheres indicate Ca^2+ ions at the Ca1 and Ca2 sites in p58/ERGIC-53 (14). An anomalous Fourier map (blue mesh) is contoured at 15 . B, comparison between the metal-free and K^+-bound Emp46p structures. Residues coordinating the K^+ and those with significant conformational changes are shown in ball- and -stick models. The metal-free and K^+-bound structures are colored in cyan and yellow, respectively. C, comparison between the metal-free and Y131F Emp46p structures. The metal-free and Y131F structures are colored in cyan and green, respectively.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 10410-10419) copyright 2006.

Figures were selected by an automated process.