4HPI

Crystal Structure of Hen Egg White Lysozyme complex with GN2-M

Summary for 4HPI

• Entry DOI: 10.2210/pdb4hpi/pdb
• Related: 4HP0
• Descriptor: Lysozyme C, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-1-DEOXYNOJIRIMYCIN (3 entities in total)
• Functional Keywords: lysozyme, carbohydrate, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Gallus gallus (bantam,chickens)
• Cellular location: Secreted: P00698
• Total number of polymer chains: 1
• Total formula weight: 14900.72

Authors

Umemoto, N.,Numata, T.,Ohnuma, T.,Fukamizo, T. (deposition date: 2012-10-23, release date: 2013-01-16, Last modification date: 2024-10-09)

Primary citation

Ogata, M.,Umemoto, N.,Ohnuma, T.,Numata, T.,Suzuki, A.,Usui, T.,Fukamizo, T.
A novel transition-state analogue for lysozyme, 4-O-beta-tri-N-acetylchitotriosyl moranoline, provided evidence supporting the covalent glycosyl-enzyme intermediate.
J.Biol.Chem., 288:6072-6082, 2013

PubMed Abstract: 4-O-β-Di-N-acetylchitobiosyl moranoline (2) and 4-O-β-tri-N-acetylchitotriosyl moranoline (3) were produced by lysozyme-mediated transglycosylation from the substrates tetra-N-acetylchitotetraose, (GlcNAc)4, and moranoline, and the binding modes of 2 and 3 to hen egg white lysozyme (HEWL) was examined by inhibition kinetics, isothermal titration calorimetry (ITC), and x-ray crystallography. Compounds 2 and 3 specifically bound to HEWL, acting as competitive inhibitors with Ki values of 2.01 × 10(-5) and 1.84 × 10(-6) m, respectively. From ITC analysis, the binding of 3 was found to be driven by favorable enthalpy change (ΔHr°), which is similar to those obtained for 2 and (GlcNAc)4. However, the entropy loss (-TΔSr°) for the binding of 3 was smaller than those of 2 and (GlcNAc)4. Thus the binding of 3 was found to be more favorable than those of the others. Judging from the Kd value of 3 (760 nm), the compound appears to have the highest affinity among the lysozyme inhibitors identified to date. X-ray crystal structure of HEWL in a complex with 3 showed that compound 3 binds to subsites -4 to -1 and the moranoline moiety adopts an undistorted (4)C1 chair conformation almost overlapping with the -1 sugar covalently bound to Asp-52 of HEWL (Vocadlo, Davies, G. J., Laine, R., and Withers, S. G. (2001) Nature 412, 835-838). From these results, we concluded that compound 3 serves as a transition-state analogue for lysozyme providing additional evidence supporting the covalent glycosyl-enzyme intermediate in the catalytic reaction.

PubMed: 23303182
DOI: 10.1074/jbc.M112.439281

Experimental method

X-RAY DIFFRACTION (1.19 Å)