3NV3

Crystal structure of human galectin-9 C-terminal CRD in complex with biantennary oligosaccharide

Summary for 3NV3

• Entry DOI: 10.2210/pdb3nv3/pdb
• Related: 3NV1 3NV2 3NV4
• Descriptor: Galectin 9 short isoform variant, beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose, NICKEL (II) ION, ... (4 entities in total)
• Functional Keywords: sugar binding, sugar binding protein
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 1
• Total formula weight: 16334.16

Authors

Yoshida, H.,Kamitori, S. (deposition date: 2010-07-07, release date: 2010-09-22, Last modification date: 2023-11-01)

Primary citation

Yoshida, H.,Teraoka, M.,Nishi, N.,Nakakita, S.,Nakamura, T.,Hirashima, M.,Kamitori, S.
X-ray structures of human galectin-9 C-terminal domain in complexes with a biantennary oligosaccharide and sialyllactose
J.Biol.Chem., 285:36969-36976, 2010

PubMed Abstract: Galectin-9, a tandem-repeat-type β-galactoside-specific animal lectin with two carbohydrate recognition domains (CRDs) at the N- and C-terminal ends, is involved in chemoattraction, apoptosis, and the regulation of cell differentiation and has anti-allergic effects. Its ability to recognize carbohydrates is essential for its biological functions. Human galectin-9 (hG9) has high affinity for branched N-glycan-type oligosaccharides (dissociation constants of 0.16-0.70 μM) and linear β1-3-linked poly-N-acetyllactosamines (0.09-8.3 μM) and significant affinity for the α2-3-sialylated oligosaccharides (17-34 μM). Further, its N-terminal CRD (hG9N) and C-terminal CRD (hG9C) differ in specificity. To elucidate this unique feature of hG9, x-ray structures of hG9C in the free form and in complexes with N-acetyllactosamine, the biantennary pyridylaminated oligosaccharide, and α2-3-sialyllactose were determined. They are the first x-ray structural analysis of C-terminal CRD of the tandem-repeat-type galectin. The results clearly revealed the mechanism by which branched and α2-3-sialylated oligosaccharides are recognized and explained the difference in specificity between hG9N and hG9C. Based on structural comparisons with other galectins, we propose that the wide entrance for ligand binding and the shallow binding site of hG9C are favorable for branched oligosaccharides and that Arg(221) is responsible for recognizing sialylated oligosaccharides.

PubMed: 20861009
DOI: 10.1074/jbc.M110.163402

Experimental method

X-RAY DIFFRACTION (1.57 Å)