1NIV

MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM SNOWDROP (GALANTHUS NIVALIS) BULBS IN COMPLEX WITH MANNOSE-ALPHA 1,3-METHYL-D-MANNOSE

Summary for 1NIV

• Entry DOI: 10.2210/pdb1niv/pdb
• Descriptor: AGGLUTININ, alpha-D-mannopyranose-(1-3)-methyl alpha-D-mannopyranoside, methyl alpha-D-mannopyranoside (3 entities in total)
• Functional Keywords: lectin, mannose-binding
• Biological source: Galanthus nivalis (common snowdrop)
• Cellular location: Secreted (By similarity): P30617
• Total number of polymer chains: 2
• Total formula weight: 25774.21

Authors

Wright, C.S.,Hester, G. (deposition date: 1996-03-15, release date: 1996-10-14, Last modification date: 2024-10-30)

Primary citation

Hester, G.,Wright, C.S.
The mannose-specific bulb lectin from Galanthus nivalis (snowdrop) binds mono- and dimannosides at distinct sites. Structure analysis of refined complexes at 2.3 A and 3.0 A resolution.
J.Mol.Biol., 262:516-531, 1996

PubMed Abstract: Galanthus nivalis agglutinin (GNA, a 50 kDa tetramer) is a mannose-specific lectin of the Amaryllidaceae family of bulb lectins. Crystal structures of GNA complexed with methyl-alpha-D-mannose (MeMan) and mannose-alpha 1,3-D-mannose-alpha-OMe (MeMan-2) have been determined and analyzed in terms of internal structural symmetry and saccharide binding. The final model of the 2.29 A orthorhombic methyl-alpha-Man complex refined with an R-factor of 0.167 (all data) includes 12 bound sugar ligands and 327 water molecules. The four independent subunits (A, B, C and D) of the 222 tetramer and the three four-stranded beta-sheets (I,II and III) that constitute each subunit compare closely (r.m.s. delta = < 1.0 A). The 12 bound methyl-alpha-Man molecules refined with B-factors < 22 A2 and occupancies in the range of 0.5 to 1.0. The highest occupied site is located in beta-sheet I (site 1), where interactions from the dimer-related subunit contribute to complex stabilization. These subunit pairs (A-D and B-C) associate tightly with a buried surface area of 1738 A2 and 33 interchain hydrogen bonds resulting from C-terminal strand exchange. In comparison, the A-B and C-D subunit pairs have narrow interfaces (476 A2) and no direct H-bond contacts. The 3.0 A structure of the cubic Man-alpha 1,3-Man-OMe complex, determined by molecular replacement and refined with X-PLOR using NCS constraints and density modification methods, is less well ordered due to a high crystal solvent content (68%). Complexed disaccharide is responsible for the most crucial lattice contacts, which involve only one of the two independent subunits (A). The second subunit (C) shows a high degree of flexibility (Bav = 41.7 A2). The complete disaccharide molecule is visible in both subunits at site 3, which is the only extended site. The ligand is oriented with its reducing end positioned in the specificity pocket. The non-reducing manose is in contact through hydrogen bonding with a charged subsite (D37-K38) on the 2-fold-related subunit (A-B or C-D interfaces). Bound Man-alpha 1,3-MeMan is also well defined in site 2 of subunit A, as a result of favorable lattice contacts, while only the mannose residue bound in the specificity pocket is visible at site 2 of subunit C and site 1 of both subunits. Together these results suggest that strong binding correlates with the presence of subsidiary contacts coming either from a dimer-related subunit or from lattice interactions. Site 1 is most specific for terminal non-reducing or reducing mannose, while site 3 is extended and complementary to alpha-1,3 linked mannose oligosaccharides.

PubMed: 8893860
DOI: 10.1006/jmbi.1996.0532

Experimental method

X-RAY DIFFRACTION (3 Å)