2A70

Crystal structure of Emp47p carbohydrate recognition domain (CRD), monoclinic crystal form 2

Summary for 2A70

• Entry DOI: 10.2210/pdb2a70/pdb
• Related: 1GV9 1R1Z 2A6V 2A6W 2A6X 2A6Y 2A6Z 2A71
• Descriptor: Emp47p, 1,2-ETHANEDIOL (3 entities in total)
• Functional Keywords: beta sandwich, carbohydrate binding protein, cargo receptor, structural genomics, nppsfa, national project on protein structural and functional analyses, sugar binding protein
• Biological source: Saccharomyces cerevisiae (baker's yeast)
• Total number of polymer chains: 2
• Total formula weight: 50011.30

Authors

Satoh, T.,Sato, K.,Kanoh, A.,Yamashita, K.,Katoh, R.,Nakano, A.,Wakatsuki, S. (deposition date: 2005-07-04, release date: 2006-01-31, Last modification date: 2024-10-23)

Primary citation

Satoh, T.,Sato, K.,Kanoh, A.,Yamashita, K.,Yamada, Y.,Igarashi, N.,Kato, R.,Nakano, A.,Wakatsuki, S.
Structures of the carbohydrate recognition domain of Ca2+-independent cargo receptors Emp46p and Emp47p.
J.Biol.Chem., 281:10410-10419, 2006

PubMed 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.

PubMed: 16439369
DOI: 10.1074/jbc.M512258200

Experimental method

X-RAY DIFFRACTION (1.1 Å)