Crystal structure of a β-prism II lectin from Remusatia vivipara

Abstract

The crystal structure of a β-prism II (BP2) fold lectin from Remusatia vivipara, a plant of traditional medicinal value, has been determined at a resolution of 2.4 Å. This lectin (RVL, Remusatia vivipara lectin) is a dimer with each protomer having two distinct BP2 domains without a linker between them. It belongs to the "monocot mannose-binding" lectin family, which consists of proteins of high sequence and structural similarity. Though the overall tertiary structure is similar to that of lectins from snowdrop bulbs and garlic, crucial differences in the mannose-binding regions and oligomerization were observed. Unlike most of the other structurally known proteins in this family, only one of the three carbohydrate recognition sites (CRSs) per BP2 domain is found to be conserved. RVL does not recognize simple mannose moieties. RVL binds to only N-linked complex glycans like those present on the gp120 envelope glycoprotein of HIV and mannosylated blood proteins like fetuin, but not to simple mannose moieties. The molecular basis for these features and their possible functional implications to understand the different levels of carbohydrate affinities in this structural family have been investigated through structure analysis, modeling and binding studies. Apart from being the first structure of a lectin to be reported from the Araceae/Arum family, this protein also displays a novel mode of oligomerization among BP2 lectins.

Crystal Structure of Colocasia esculenta Tuber Agglutinin at 1.74 Å Resolution and Its Quaternary Interactions

“…of 0.4380. This new solution seemed even more probable/trusted as both the dimers formed tetramers through their B chains (as in [16]) in the arrangement resulting from these rotations and translations within the P222 1 unit cell (Figure 3). Only one of the two dimers had shown this property in the previous solutions found by MOLREP.…”

“…We believe in the advice of keeping as much X-ray data as possible as long as the shells are high in completeness, though much of the data is weak, as this is beneficial regarding the accuracy of the structure [22]. As a result, our R value for the 49,194 reflections is 0.344, as opposed to 0.209 for RVL [16]. The refined structure in 5D5G has no bond length, bond angle, chirality or planarity outliers and has 0.9% Ramachandran outliers.…”

“…The structure solution and analyses were carried out using various modules of CCP4i; the structures were solved using molecular replacement [15] using the crystal structure of the two domain RVL (PDB ID: 3R0E) [16] having 94.6% sequence identity to CEA. The model was monitored and modified using the molecular graphics program Coot within the CCP4i package, substituting the side chains for the residues differing between CEA and RVL.…”

“…Among previously solved crystal structures, Remusatia vivipara lectin (RVL, PDB ID: 3R0E, 25,784 reflns, 2.40 Å) [16] has the highest sequence identity of 93.8% with the Colocasia esculenta agglutinin. Other lectins like Scafet (32% or lower), PCL (45% or lower) and CVL Figure 1: MALDI-TOF mass spectrometric analysis of the CEA crystal performed after dissolving it in water.…”

“…However, the RVL crystallized in a tetragonal space group P4 1 and its 2.4 Å structure included 3510 protein atoms and 129 water molecules [16].…”