1REM

HUMAN LYSOZYME WITH MAN-B1,4-GLCNAC COVALENTLY ATTACHED TO ASP53

Summary for 1REM

• Entry DOI: 10.2210/pdb1rem/pdb
• Descriptor: LYSOZYME, beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, NITRATE ION, ... (5 entities in total)
• Functional Keywords: lysozyme, muramidase, hydrolase (o-glycosyl), man-b1, 4-glcnac, hydrolase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 1
• Total formula weight: 15242.14

Authors

Muraki, M.,Harata, K.,Sugita, N.,Sato, K. (deposition date: 1998-01-14, release date: 1998-07-15, Last modification date: 2024-10-23)

Primary citation

Muraki, M.,Harata, K.,Sugita, N.,Sato, K.
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.
Acta Crystallogr.,Sect.D, 54:834-843, 1998

PubMed Abstract: 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.

PubMed: 9757098
DOI: 10.1107/S090744499800122X

Experimental method

X-RAY DIFFRACTION (2.1 Å)