1FYU

Crystal structure of erythrina corallodendron lectin in hexagonal crystal form

Summary for 1FYU

• Entry DOI: 10.2210/pdb1fyu/pdb
• Related: 1ax0 1ax1 1ax2 1axy 1axz 1LTE
• Related PRD ID: PRD_900008
• Descriptor: LECTIN, beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose, MANGANESE (II) ION, ... (5 entities in total)
• Functional Keywords: lectin, protein-carbohydrate complex, sugar binding protein
• Biological source: Erythrina corallodendron
• Total number of polymer chains: 2
• Total formula weight: 56712.64

Authors

Elgavish, S.,Shaanan, B. (deposition date: 2000-10-03, release date: 2000-10-25, Last modification date: 2023-08-09)

Primary citation

Elgavish, S.,Shaanan, B.
Chemical characteristics of dimer interfaces in the legume lectin family.
Protein Sci., 10:753-761, 2001

PubMed Abstract: The Erythrina corallodendron lectin (EcorL) crystallizes in monoclinic and hexagonal crystal forms. Comparison of the newly determined hexagonal form (PDB code 1fyu) with the monoclinic form shows that the dimeric structure of EcorL reflects the inherent biological structure of the protein and is not an artifact of the crystal packing. To further understand the factors determining the dimerization modes of legume lectins, EcorL, concanavalin A (ConA), and Griffonia simplicifolia (GS4) were taken as representatives of the three unique dimers found in the family. Six virtual homodimers were generated. The hydropathy, amino acid composition, and solvation energy were calculated for all nine homodimers. Each of the three native dimers has a distinct chemical composition. EcorL has a dominant hydrophobic component, and ConA has a strong polar component, but in GS4 the three components contribute equally to the interface. This distribution pattern at the interface is unique to the native dimers and distinct from the partition observed in the virtual dimers. Amino acid composition of other members of the family that dimerize like EcorL or ConA maintain the same pattern of amino acids distribution observed in EcorL and ConA. However, lectins that dimerize like GS4 do not show a particularly distinct distribution. In all cases, the calculated solvation energy of the native dimer was lower than that of the virtual dimers, suggesting that the observed mode of dimerization is the most stable organization for the given sequence and tertiary structure. The dimerization type cannot be predicted by sequence analysis.

PubMed: 11274466
DOI: 10.1110/ps.44001

Experimental method

X-RAY DIFFRACTION (2.6 Å)