Sugar recognition by lactoferrin: Crystal structure of the complex formed between C-lobe of bovine lactoferrin and a pentasaccharide at 2.38 A resolution

Department of Biophysics, All India Institute of Medical Sciences
○Rishi Jain Nagendra Singh Talat Jabeen Sujata Sharma Asha Bhusan Tej P Singh

Lactoferrin is an 80 kDa iron-binding glycoprotein. The single polypeptide chain of 691 amino acid residues is folded into two globular N-lobe and C-lobe. The present study reports the crystal structure of the complex of a proteolytically generated bovine C-lobe by proteinase K with a pentasaccharide at 2.38 A resolution. The crystal belongs to space group space group P21 with unit cell dimensions a = 62.9 , b = 50.5 , c = 65.8 , β = 107.5°. Final model contains 2605 protein atoms; 1 Fe3+, 3 Zn2+ and 1 CO32- ions, 13 sugar residues(N-linked), 5 NAG residues and 276 water molecules. There were three zinc atoms were observed at sites involving Tyr342, His588, and Glu659. This is the first time that a novel ligand binding site has been observed in lactoferrins. The pentasaccharide binds at a very distinct site. This site is located near C-terminal end of the C-lobe, which is formed by residues Leu651, Gly652, Thr430, Tyr660, Thr663, Glu659, and Lys498. The pentasaccharide interacts with C-lobe residues. The main feature of the present structure is the presence of a pentasaccharide at a novel binding site on C-lobe of the bovine lactoferrin. The site is formed by a number of hydrophobic and polar residues. The pentasaccharide forms extensive hydrogen bonding interactions with the protein molecule. The main residues involved in the interactions are Leu 651, Gly 652, Thr 430, Tyr 660, Glu 659, Thr 663 and Lys 498. The pentasaccharide fits exactly in the shape of the new binding site. The binding of pentasaccharide can explain several function of lactoferrin which involved interactions with surface sugar molecules on other proteins. This site is most probably involved in protein-protein interaction with other molecules.