1D6Q

HUMAN LYSOZYME E102 MUTANT LABELLED WITH 2',3'-EPOXYPROPYL GLYCOSIDE OF N-ACETYLLACTOSAMINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Protein-carbohydrate interactions in human lysozyme probed by combining site-directed mutagenesis and affinity labeling.

Muraki, M.Harata, K.Sugita, N.Sato, K.I.

(2000) Biochemistry 39: 292-299

  • Primary Citation of Related Structures:  1D6P

  • PubMed Abstract: 
  • 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' ...

    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.


    Related Citations: 
    • Origin of Carbohydrate Recognition Specificity of Human Lysozyme Revealed by Affinity Labeling
      Muraki, M.,Harata, K.,Sugita, N.,Sato, K.
      (1996) Biochemistry 35: 13562
    • Dual Affinity Labeling of the Active Site of Human Lysozyme with an N- Acetyllactosamine Derivative: First Ligand Assisited Recognition of the Second Ligand
      Muraki, M.,Harata, K.,Sugita, N.,Sato, K.
      (1999) Biochemistry 38: 540
    • Dissection of teh Functional Role of Structural Elements of Tyrosine-63 in the Catalytic Action of Human Lysozyme
      Muraki, M.,Harata, K.,Jigami, Y.
      (1992) Biochemistry 31: 9212
    • X-ray Structure of Human Lysozyme Labelled with 2',3'-Epoxypropyl b-Glycoside of Man-b1,4-GlcNAc. Structural Change and Recognition Specificity at Subsite B
      Muraki, M.,Harata, K.,Sugita, N.,Sato, K.
      (1998) Acta Crystallogr.,Sect.D 54: 834


    Organizational Affiliation

    Biomolecules Department, National Institute of Bioscience and Human-Technology, 1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan. muraki@nibh.go.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSOZYME
A
130Homo sapiensGene Names: LYZ (LZM)
EC: 3.2.1.17
Find proteins for P61626 (Homo sapiens)
Go to Gene View: LYZ
Go to UniProtKB:  P61626
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
GAL
Query on GAL

Download SDF File 
Download CCD File 
A
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.790α = 90.00
b = 61.240β = 90.00
c = 33.020γ = 90.00
Software Package:
Software NamePurpose
MADNESSdata reduction
MERGEFdata scaling
X-PLORmodel building
X-PLORphasing
MERGEFdata reduction
X-PLORrefinement
MADNESSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-01-21
    Type: Initial release
  • Version 1.1: 2008-04-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description
  • Version 1.4: 2017-10-11
    Type: Data collection