PDBsum entry 2gmm

Sugar binding protein

PDB id: 2gmm

Contents

Protein chains

227 a.a. *

Ligands

MAN-MAN ×2

SO4 ×2

Waters ×228

* Residue conservation analysis

PDB id:

2gmm

Name:

Sugar binding protein

Title:

Metal-free (apo) p. Angolensis seed lectin in complex with man- alpha(1-2)man

Structure:

Lectin. Chain: a, b

Source:

Pterocarpus angolensis. Organism_taxid: 182271. Tissue: seed

Resolution:

2.15Å R-factor: 0.185 R-free: 0.227

Authors:

A.Garcia-Pino,L.Buts,L.Wyns,R.Loris

Key ref:

A.Garcia-Pino et al. (2006). Interplay between metal binding and cis/trans isomerization in legume lectins: structural and thermodynamic study of P. angolensis lectin. J Mol Biol, 361, 153-167. PubMed id: 16824540 DOI: 10.1016/j.jmb.2006.06.006

Date:

07-Apr-06 Release date: 25-Jul-06

Protein chains

Q8GSD2  (Q8GSD2_PTEAG) -  Lectin (Fragment) from Pterocarpus angolensis

Seq: 260 a.a.

Struc: 227 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1016/j.jmb.2006.06.006

J Mol Biol 361:153-167 (2006)

PubMed id: 16824540

Interplay between metal binding and cis/trans isomerization in legume lectins: structural and thermodynamic study of P. angolensis lectin.

A.Garcia-Pino, L.Buts, L.Wyns, R.Loris.

ABSTRACT

The interplay between metal binding, carbohydrate binding activity, stability and structure of the lectin from Pterocarpus angolensis was investigated. Removal of the metals leads to a more flexible form of the protein with significantly less conformational stability. Crystal structures of this metal-free form show significant structural rearrangements, although some structural features that allow the binding of sugars are retained. We propose that substitution of an asparagine residue at the start of the C-terminal beta-strand of the legume lectin monomer hinders the trans-isomerization of the cis-peptide bond upon demetallization and constitutes an intramolecular switch governing the isomer state of the non-proline bond and ultimately the lectin phenotype.

Selected figure(s)

Figure 4.
Figure 4. Demetallization-induced structural changes on apo-PAL. (a) Stereo view of the superposition of holo-PAL (chain B from pdb entry 1ukg) on apo-PAL (chain B). The metal binding loop is coloured cyan for holo-PAL and blue for apo-PAL. (b) Stereo view of the superposition of the metal binding loop of holo-PAL (grey) on apo-PAL (in blue). Calcium ions are shown as yellow spheres and manganese ions as green spheres.

Figure 7.
Figure 7. A sequence-dependent intramolecular switch determines the cis/trans isomerization of metal-free legume lectins. (a) Stereo view of the carbohydrate binding sites and the C-terminal β-strands of apo-PAL (coloured according to atom type), apo-GS-IB4^15 (red) and apo-con A^11 (yellow) superimposed on each other. The hydrogen bonds between Asp208 and Asn104 in apo-con A are indicated by broken lines. (b) Stereo view of an equivalent superposition for apo-PAL (coloured according to atom type), ERGIC 53^38 (blue), Arcelin-1^36 (light green) and Arcelin-5^35 (dark green).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 361, 153-167) copyright 2006.

Figures were selected by the author.

Author's comment

We have identified a sequence dependent conformational switch in the legume lectin and ERGIC families of proteins that determines whether or not metal ions are necessary to induce a non-proline cis-peptide bond in the primary binding site of the protein.
Abel Garcia-Pino