X-ray structure of human lysozyme labelled with 2',3'-epoxypropyl beta-glycoside of man-beta1,4-GlcNAc. Structural change and recognition specificity at subsite B.
Human lysozyme (HL) labelled with the 2',3'-epoxypropyl beta-glycoside of Man-beta1,4-GlcNAc was crystallized at pH 4.5. The cell dimensions were a = 36.39, b = 116.38, c = 30.91 A and the space group was P212121. The unit cell contained four molecules (Vm = 2.18 A3 Da-1). The crystal structure was determined by molecular replacement and refined to an R value of 0.168 for 7060 reflections [|Fo| > 3sigma(F)] in the resolution range 8.0-2.1 A. A prominent shift of the Calpha-atom positions by up to 3.8 A in the region of residues 45-50 was observed compared with wild-type HL. Owing to the conformational change in this region the intermolecular contacts were altered remarkably compared to wild-type HL, explaining the difference in molecular packing. The Man-beta1,4-GlcNAc moiety occupied subsites B and C in the substrate-binding site of HL. Several differences in the hydrogen-bonded contacts between the ligand part and the protein part were observed for HL labelled with the 2',3'-epoxypropyl beta-glycoside of Man-beta1,4-GlcNAc compared with HL labelled with the corresponding derivatives of GlcNAc-beta1, 4-GlcNAc and Gal-beta1,4-GlcNAc. In contrast to the replacement of GlcNAc with Gal, the replacement of GlcNAc with Man did not sacrifice the stacking interactions with the side-chain group of Tyr63 as determined by the parallelism of the apolar face of the carbohydrate residue and the aromatic plane of the Tyr63 side chain. The 2',3'-epoxypropyl beta-glycoside of Man-beta1,4-GlcNAc exhibited almost the same affinity towards HL as Gal-beta1,4-GlcNAc, a much lower affinity than that of GlcNAc-beta1,4-GlcNAc. The difference in the protein-ligand interactions was discussed in relation to the carbo-hydrate-residue recognition specificity at subsite B of HL. The results suggested that Gln104 was a determinant for the strong recognition of GlcNAc residue at subsite B in HL.
Muraki
M
M
Biomolecules Department, National Institute of Bioscience and Human Technology, Tsukuba, Ibaraki 305, Japan.
Harata
K
K
Sugita
N
N
Sato
K i
Ki
D000345:Affinity Labels / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D003460:Crystallization; D018360:Crystallography, X-Ray; D004187:Disaccharides / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D006860:Hydrogen Bonding; D008024:Ligands; D008958:Models, Molecular; D009113:Muramidase / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D013379:Substrate Specificity
C115879:2',3'-epoxypropyl mannopyranosyl-1-4-N-acetylaminoglucopyranoside; D000345:Affinity Labels; D004187:Disaccharides; D008024:Ligands; D009113:Muramidase