2DUO

Crystal structure of VIP36 exoplasmic/lumenal domain, Ca2+-bound form

Summary for 2DUO

• Entry DOI: 10.2210/pdb2duo/pdb
• Related: 1GV9 1R1Z 2DUP 2DUQ 2DUR 2DUS
• Descriptor: Vesicular integral-membrane protein VIP36, CALCIUM ION, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: beta sandwich, carbohydrate binding protein, cargo receptor, protein transport
• Biological source: Canis lupus familiaris (dog)
• Cellular location: Golgi apparatus membrane; Single-pass type I membrane protein: P49256
• Total number of polymer chains: 2
• Total formula weight: 58332.78

Authors

Satoh, T.,Cowieson, N.P.,Kato, R.,Wakatsuki, S. (deposition date: 2006-07-25, release date: 2007-07-24, Last modification date: 2024-10-30)

Primary citation

Satoh, T.,Cowieson, N.P.,Hakamata, W.,Ideo, H.,Fukushima, K.,Kurihara, M.,Kato, R.,Yamashita, K.,Wakatsuki, S.
Structural basis for recognition of high mannose type glycoproteins by mammalian transport lectin VIP36
J.Biol.Chem., 282:28246-28255, 2007

PubMed Abstract: VIP36 functions as a transport lectin for trafficking certain high mannose type glycoproteins in the secretory pathway. Here we report the crystal structure of VIP36 exoplasmic/luminal domain comprising a carbohydrate recognition domain and a stalk domain. The structures of VIP36 in complex with Ca(2+) and mannosyl ligands are also described. The carbohydrate recognition domain is composed of a 17-stranded antiparallel beta-sandwich and binds one Ca(2+) adjoining the carbohydrate-binding site. The structure reveals that a coordinated Ca(2+) ion orients the side chains of Asp(131), Asn(166), and His(190) for carbohydrate binding. This result explains the Ca(2+)-dependent carbohydrate binding of this protein. The Man-alpha-1,2-Man-alpha-1,2-Man, which corresponds to the D1 arm of high mannose type glycan, is recognized by eight residues through extensive hydrogen bonds. The complex structures reveal the structural basis for high mannose type glycoprotein recognition by VIP36 in a Ca(2+)-dependent and D1 arm-specific manner.

PubMed: 17652092
DOI: 10.1074/jbc.M703064200

Experimental method

X-RAY DIFFRACTION (1.8 Å)