X-ray structure of turkey egg lysozyme complex with di-N-acetyl-chitobiose. Recognition and binding of α-anomeric form

The crystalline complex of turkey-egg lysozyme (TEL) with di-N-acetylchitobiose (NAG2) was prepared by a soaking method and the structure was determined by X-ray analysis at 1.55 Å resolution. The structure was refined to an R value of 0.175 by simulated annealing and energy minimization. The α-anomer of NAG2 is located at subsite D with the orientation perpendicular to the direction of the active-site cleft. The anomeric residue is deeply inserted into the cleft and the O1—H hydroxyl group is hydrogen bonded to the carboxyl group of Glu35 which is a catalytic residue. The other sugar residue protrudes outside the cleft and is in van der Waals contact with the β-sheet region comprising of residues 43–53. The binding of NAG2 makes the active-site cleft 0.3–0.5 Å narrower and suppresses the thermal motion of two lobes constructing the cleft. The NAG2 molecule is bound in a manner not assumed in the catalytic action of the enzyme and the geometry of binding indicates that the α-anomer blocks the active center and acts only as an inhibitor.