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PDBsum entry 1d6p
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Protein-Carbohydrate interactions in human lysozyme probed by combining site-Directed mutagenesis and affinity labeling.
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Authors
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M.Muraki,
K.Harata,
N.Sugita,
K.I.Sato.
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Ref.
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Biochemistry, 2000,
39,
292-299.
[DOI no: ]
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PubMed id
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Abstract
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The synergism between apolar and polar interactions in the carbohydrate
recognition by human lysozyme (HL) was probed by site-directed mutagenesis and
affinity labeling. The three-dimensional structures of the Tyr63-->Leu mutant
HL labeled with 2',3'-epoxypropyl beta-glycoside of N,N'-diacetylchitobiose
(L63-HL/NAG-NAG-EPO complex) and the Asp102-->Glu mutant HL labeled with the
2',3'-epoxypropyl beta-glycoside of N-acetyllactosamine were revealed by X-ray
diffraction at 2.23 and 1.96 A resolution, respectively. Compared to the
wild-type HL labeled with the 2', 3'-epoxypropyl beta-glycoside of
N,N'-diacetylchitobiose, the N-acetylglucosamine residue at subsite B of the
L63-HL/NAG-NAG-EPO complex markedly moved away from the 63rd residue, with
substantial loss of hydrogen-bonding interactions. Evidently, the stacking
interaction with the aromatic side chain of Tyr63 is essential in positioning
the N-acetylglucosamine residue in the productive binding mode. On the other
hand, the position of the galactose residue in subsite B of HL is almost
unchanged by the mutation of Asp102 to Glu. Most hydrogen bonds, including the
one between the carboxylate group of Glu102 and the axial 4-OH group of the
galactose residue, were maintained by local movement of the backbone from
residues 102-104. In both structures, the conformation of the disaccharide was
conserved, reflecting an intrinsic conformational rigidity of the disaccharides.
The structural analysis suggested that CH-pi interactions played an important
role in the recognition of the carbohydrate residue at subsite B of HL.
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Secondary reference #1
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Title
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Dual affinity labeling of the active site of human lysozyme with an n-Acetyllactosamine derivative: first ligand assisted recognition of the second ligand.
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Authors
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M.Muraki,
K.Harata,
N.Sugita,
K.I.Sato.
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Ref.
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Biochemistry, 1999,
38,
540-548.
[DOI no: ]
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PubMed id
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Secondary reference #2
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Title
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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.
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Authors
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M.Muraki,
K.Harata,
N.Sugita,
K.Sato.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 1998,
54,
834-843.
[DOI no: ]
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PubMed id
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Figure 8.
Fig. 8. Stereoview of the omit
difference (Fo - Fc) electron-
density map (contoured at 2.5~)
shown with the refined position
of the ligand and Asp53 of HL
superimposed.
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Figure 9.
Fig. 9. Schematic drawing of the possible hydrogen-bonding interac-
tions between the protein and ligand in the
HL/MAN-NAG-EPO
complex. Hydrogen-bonded contacts of less than 3.5 ,~ are shown
with broken lines. All HL residues belong to the same molecule.
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The above figures are
reproduced from the cited reference
with permission from the IUCr
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Secondary reference #3
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Title
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Origin of carbohydrate recognition specificity of human lysozyme revealed by affinity labeling.
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Authors
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M.Muraki,
K.Harata,
N.Sugita,
K.Sato.
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Ref.
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Biochemistry, 1996,
35,
13562-13567.
[DOI no: ]
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PubMed id
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Secondary reference #4
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Title
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Dissection of the functional role of structural elements of tyrosine-63 in the catalytic action of human lysozyme.
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Authors
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M.Muraki,
K.Harata,
Y.Jigami.
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Ref.
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Biochemistry, 1992,
31,
9212-9219.
[DOI no: ]
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PubMed id
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