PDBsum entry 1v6m

Sugar binding protein

PDB id: 1v6m

Contents

Protein chains

(+ 2 more) 232 a.a. *

Metals

_MN ×8

_CA ×8

Waters ×360

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Structural plasticity of peanut lectin: an X-Ray analysis involving variation in ph, Ligand binding and crystal structure.

Authors

S.Kundhavai natchiar, A.Arockia jeyaprakash, T.N.Ramya, C.J.Thomas, K.Suguna, A.Surolia, M.Vijayan.

Ref.

Acta Crystallogr D Biol Crystallogr, 2004, 60, 211-219. [DOI no: 10.1107/S090744490302849X]

PubMed id

14747696

Abstract

Until recently, it has only been possible to grow crystals of peanut lectin when complexed with sugar ligands. It is now shown that it is possible to grow peanut lectin crystals at acidic pH in the presence of oligopeptides corresponding to a loop in the lectin molecule. Crystals have also been prepared in the presence of these peptides as well as lactose. Low-pH crystal forms of the lectin-lactose complex similar to those obtained at neutral pH have also been grown. Thus, crystals of peanut lectin grown under different environmental conditions, at two pH values with and without sugar bound to the lectin, are now available. They have been used to explore the plasticity and hydration of the molecule. A detailed comparison between different structures shows that the lectin molecule is sturdy and that the effect of changes in pH, ligand binding and environment on it is small. The region involving the curved front beta-sheet and the loops around the second hydrophobic core is comparatively rigid. The back beta-sheet involved in quaternary association, which exhibits considerable variability, is substantially flexible, as is the sugar-binding region. The numbers of invariant water molecules in the hydration shell are small and they are mainly involved in metal coordination or in stabilizing unusual structural features. Small consistent movements occur in the combining site upon sugar binding, although the site is essentially preformed.

Figure 1.
Figure 1 Schematic representation of the two tetramers in the monoclinic crystals. S and L indicate the occupation of the combining site by lactose and a loop from a neighbouring molecule, respectively. Four combining sites are unoccupied. P represents the molecular dyad. R1 and R2 represent the twofold axes that relate A and D, and B and C, respectively. P, R1 and R2 do not intersect, but pass through a line represented by Q. In the orthorhombic crystals, which grow only in the presence of sugar, the crystallographic asymmetric unit contains one tetramer in which all the subunits are sugar-bound.

Figure 2.
Figure 2 Rigid (blue), flexible (green) and most flexible (red) regions in a PNA subunit. Pink and cyan balls represent metal ions. Red balls represent invariant water molecules obtained through the superposition of 16 subunits along with their hydration shells. The lactose molecule is in ball-and-stick representation. This and the subsequent figures were prepared using MOLSCRIPT (Kraulis, 1991[Kraulis, P. (1991). J. Appl. Cryst. 24, 946-950.]).

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2004, 60, 211-219) copyright 2004.

Secondary reference #1

Title

Crystal structures of the peanut lectin-Lactose complex at acidic ph: retention of unusual quaternary structure, Empty and carbohydrate bound combining sites, Molecular mimicry and crystal packing directed by interactions at the combining site.

Authors

R.Ravishankar, C.J.Thomas, K.Suguna, A.Surolia, M.Vijayan.

Ref.

Proteins, 2001, 43, 260-270. [DOI no: 10.1002/prot.1037]

PubMed id

11288176

Figure 1.
Figure 1. a: Stereo view of the omit map corresponding to the sugar molecule in subunit A of the monoclinic form. The map is contoured at 3.5 . Water molecules are indicated by crosses. Surrounding peptide stretches are also shown. b: Stereo view of the difference Fourier map contoured at 2.7 in the unoccupied binding site of subunit D.

Figure 2.
Figure 2. Stereoview of the quaternary association in the ABCD tetramer of the monoclinic form. P is a molecular dyad that relates the AD and BC dimers. R1 and R2 are local twofolds of the AD and BC dimers, respectively, and are inclined by 73° and -73°, respectively, with respect to P. They are skewed by 12 Å on either side of P. Q is an irrational screw axis, perpendicular to and passing through P, R1, and R2, which relates subunits C and A (146° and 24 Å) and D and B (-146° and -24 Å).

The above figures are reproduced from the cited reference with permission from John Wiley & Sons, Inc.