PDBsum entry 1x1v

Sugar binding protein

PDB id: 1x1v

Contents

Protein chains

138 a.a.

Ligands

MMA ×5

HEZ ×6

Metals

_ZN ×3

Waters ×498

References listed in PDB file

Key reference

Title

Unusual sugar specificity of banana lectin from musa paradisiaca and its probable evolutionary origin. Crystallographic and modelling studies.

Authors

D.D.Singh, K.Saikrishnan, P.Kumar, A.Surolia, K.Sekar, M.Vijayan.

Ref.

Glycobiology, 2005, 15, 1025-1032.

PubMed id

15958419

Abstract

The crystal structure of a complex of methyl-alpha-D-mannoside with banana lectin from Musa paradisiaca reveals two primary binding sites in the lectin, unlike in other lectins with beta-prism I fold which essentially consists of three Greek key motifs. It has been suggested that the fold evolved through successive gene duplication and fusion of an ancestral Greek key motif. In other lectins, all from dicots, the primary binding site exists on one of the three motifs in the three-fold symmetric molecule. Banana is a monocot, and the three motifs have not diverged enough to obliterate sequence similarity among them. Two Greek key motifs in it carry one primary binding site each. A common secondary binding site exists on the third Greek key. Modelling shows that both the primary sites can support 1-2, 1-3, and 1-6 linked mannosides with the second residue interacting in each case primarily with the secondary binding site. Modelling also readily leads to a bound branched mannopentose with the nonreducing ends of the two branches anchored at the two primary binding sites, providing a structural explanation for the lectin's specificity for branched alpha-mannans. A comparison of the dimeric banana lectin with other beta-prism I fold lectins, provides interesting insights into the variability in their quaternary structure.

Secondary reference #1

Title

Purification, Crystallization and preliminary X-Ray structure analysis of the banana lectin from musa paradisiaca.

Authors

D.D.Singh, K.Saikrishnan, P.Kumar, Z.Dauter, K.Sekar, A.Surolia, M.Vijayan.

Ref.

Acta Crystallogr D Biol Crystallogr, 2004, 60, 2104-2106. [DOI no: 10.1107/S0907444904024114]

PubMed id

15502341

Figure 2.
Figure 2 Overall fold of the banana (M. paradisiaca) lectin dimer at the current stage of refinement. Also shown is the pseudo-twofold axis that relates the two subunits of the dimer. The three loops that interact with the sugar are coloured identically (blue) in the two subunits.

The above figure is reproduced from the cited reference with permission from the IUCr

Secondary reference #2

Title

Structural basis for the carbohydrate specificities of artocarpin: variation in the length of a loop as a strategy for generating ligand specificity.

Authors

A.A.Jeyaprakash, A.Srivastav, A.Surolia, M.Vijayan.

Ref.

J Mol Biol, 2004, 338, 757-770. [DOI no: 10.1016/j.jmb.2004.03.040]

PubMed id

15099743

Figure 3.
Figure 3. Stereo view of the superposition of the sugar-binding region of mannotriose complex (violet) on that in the Me-a-Man complex (green). Interactions between the mannotriose and the lectin are shown.

Figure 5.
Figure 5. Surface representation of the sugar-binding site with modelled (a) Mana1-2Man (conformers I; blue, II; pink), (b) Mana1-6Man (conformers I; blue, II; gold, III; brown), (c) Gn[2]Mn[3] and (d) horseradish peroxidase oligosaccharide.

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #3

Title

Crystal structures of artocarpin, A moraceae lectin with mannose specificity, And its complex with methyl-Alpha-D-Mannose: implications to the generation of carbohydrate specificity.

Authors

J.V.Pratap, A.A.Jeyaprakash, P.G.Rani, K.Sekar, A.Surolia, M.Vijayan.

Ref.

J Mol Biol, 2002, 317, 237-247. [DOI no: 10.1006/jmbi.2001.5432]

PubMed id

11902840

Figure 1.
Figure 1. Structure of artocarpin. (a) Schematic representation showing hydrogen bonds. (b) The subunit with the three Greek keys coloured differently. (c) Quaternary structure with the four subunits coloured differently. Figures 1(b) 4 were prepared using BOBSCRIPT. [44]

Figure 3.
Figure 3. (a) Stereo view of the sugar molecule in the A subunit with the 2|F[o]| -|F[c]| map contoured at 1s and (b) hydrogen bonds observed between the protein and sugar.

The above figures are reproduced from the cited reference with permission from Elsevier