4HP0

Crystal Structure of Hen Egg White Lysozyme in complex with GN3-M

4HP0 の概要

• エントリーDOI: 10.2210/pdb4hp0/pdb
• 関連するPDBエントリー: 4HPI
• 関連するBIRD辞書のPRD_ID: PRD_900017
• 分子名称: Lysozyme C, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-1-DEOXYNOJIRIMYCIN (3 entities in total)
• 機能のキーワード: lysozyme, carbohydrate, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• 由来する生物種: Gallus gallus (bantam,chickens)
• 細胞内の位置: Secreted: P00698
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 15103.91

構造登録者

Umemoto, N.,Numata, T.,Ohnuma, T.,Fukamizo, T. (登録日: 2012-10-23, 公開日: 2013-01-16, 最終更新日: 2024-10-30)

主引用文献

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

実験手法

X-RAY DIFFRACTION (1.19 Å)