1NPL

MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM DAFFODIL (NARCISSUS PSEUDONARCISSUS) BULBS IN COMPLEX WITH MANNOSE-ALPHA1,3-MANNOSE

Summary for 1NPL

• Entry DOI: 10.2210/pdb1npl/pdb
• Related PRD ID: PRD_900112
• Descriptor: PROTEIN (AGGLUTININ), alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose, PHOSPHATE ION, ... (4 entities in total)
• Functional Keywords: lectin, agglutinin, mannobiose, mannose-alpha1, 3-mannose, daffodil, sugar binding protein
• Biological source: Narcissus pseudonarcissus (daffodil)
• Total number of polymer chains: 1
• Total formula weight: 13863.65

Authors

Sauerborn, M.K.,Wright, L.M.,Reynolds, C.D.,Grossmann, J.G.,Rizkallah, P.J. (deposition date: 1998-12-17, release date: 1998-12-23, Last modification date: 2020-07-29)

Primary citation

Sauerborn, M.K.,Wright, L.M.,Reynolds, C.D.,Grossmann, J.G.,Rizkallah, P.J.
Insights into carbohydrate recognition by Narcissus pseudonarcissus lectin: the crystal structure at 2 A resolution in complex with alpha1-3 mannobiose.
J.Mol.Biol., 290:185-199, 1999

PubMed Abstract: Carbohydrate recognition by monocot mannose-binding lectins was studied via the crystal structure determination of daffodil (Narcissus pseudonarcissus) lectin. The lectin was extracted from daffodil bulbs, and crystallised in the presence of alpha-1,3 mannobiose. Molecular replacement methods were used to solve the structure using the partially refined model of Hippeastrum hybrid agglutinin as a search model. The structure was refined at 2.0 A resolution to a final R -factor of 18.7 %, and Rfreeof 26.7 %. The main feature of the daffodil lectin structure is the presence of three fully occupied binding pockets per monomer, arranged around the faces of a triangular beta-prism motif. The pockets have identical topology, and can bind mono-, di- or oligosaccharides. Strand exchange forms tightly bound dimers, and higher aggregation states are achieved through hydrophobic patches on the surface, completing a tetramer with internal 222-symmetry. There are therefore 12 fully occupied binding pockets per tetrameric cluster. The tetramer persists in solution, as shown with small-angle X-ray solution scattering. Extensive sideways and out-of-plane interactions between tetramers, some mediated via the ligand, make up the bulk of the lattice contacts.A fourth binding site was also observed. This is unique and has not been observed in similar structures. The site is only partially occupied by a ligand molecule due to the much lower binding affinity. A comparison with the Galanthus nivalis agglutinin/mannopentaose complex suggests an involvement of this site in the recognition mechanism for naturally occurring glycans.

PubMed: 10388566
DOI: 10.1006/jmbi.1999.2862

Experimental method

X-RAY DIFFRACTION (2 Å)