Binding of N-acetylglucosamine oligosaccharides to hen egg-white lysozyme: a powder diffraction study.
The binding of N-acetylglucosamine oligosaccharides (NAGn, n = 2-6) to hen egg-white lysozyme (HEWL; EC 3.2.1.17) was investigated by X-ray powder diffraction at room temperature. Each NAGn examined was found to bind to lysozyme in rapid-precipitation preparations in 1.0 M NaCl pH 6.0 buffer. The location of each NAGn was easily found from difference Fourier maps generated from structure factors extracted during preliminary Rietveld refinements. Full NAGn-protein structures were subjected to combined Rietveld and stereochemical restraint refinements (Rwp = 2.28-2.59%; Rp = 1.81-2.04%; RF2 = 3.91-5.80%) and revealed binding modes for NAGn that depended on the length of the NAG oligosaccharide. The NAG2 ligand was found in the BC sites in the cleft of HEWL, NAG3 was found to bind in both the ABC and BCD sites in the ratio 35:65 and NAG4 and NAG5 bound to the ABCD and ABCDE sites, respectively, while NAG6 only bound to sites ABCDE, leaving the F site empty with the remaining saccharide ring located in a solvent region adjacent to the A site. All protein powder diffraction patterns in this study consisted of extremely sharp Bragg peaks consistent with approximately 1 microm crystallites that were devoid of line-broadening defects. Details of the stereochemical restraints used in these refinements and their impact on structural validation are also discussed.
Von Dreele
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XPS/IPNS Divisions, Argonne National Laboratory, Argonne, IL 60439, USA. vondreele@anl.gov
D000117:Acetylglucosamine / Q000737:chemistry*; D000465:Algorithms; D000818:Animals; D016880:Anisotropy; D001665:Binding Sites; D002645:Chickens; D018360:Crystallography, X-Ray; D004529:Egg White; D004583:Electrons; D005583:Fourier Analysis; D006863:Hydrogen-Ion Concentration; D008024:Ligands; D008958:Models, Molecular; D015233:Models, Statistical; D009113:Muramidase / Q000737:chemistry*; D009844:Oligosaccharides / Q000737:chemistry*; D033362:Powder Diffraction / Q000379:methods; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry; D013237:Stereoisomerism; D014961:X-Ray Diffraction / Q000379:methods
D008024:Ligands; D009844:Oligosaccharides; D011506:Proteins; D009113:Muramidase; D000117:Acetylglucosamine