1UBZ

Crystal structure of Glu102-mutant human lysozyme doubly labeled with 2',3'-epoxypropyl beta-glycoside of N-acetyllactosamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-ray structural analysis of the ligand-recognition mechanism in the dual-affinity labeling of c-type lysozyme with 2',3'-epoxypropyl beta-glycoside of N-acetyllactosamine

Muraki, M.Harata, K.

(2003) J.MOL.RECOG. 16: 72-82

  • DOI: 10.1002/jmr.611
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In spite of the belonging to the same c-type lysozyme family, hen egg-white lysozyme (HEWL) was much less susceptible to the dual-affinity labeling with 2',3'-epoxypropyl beta-glycoside of N-acetyllactosamine (Galbeta1,4GlcNAc-Epo) than human lysozym ...

    In spite of the belonging to the same c-type lysozyme family, hen egg-white lysozyme (HEWL) was much less susceptible to the dual-affinity labeling with 2',3'-epoxypropyl beta-glycoside of N-acetyllactosamine (Galbeta1,4GlcNAc-Epo) than human lysozyme (HL). The three-dimensional structures of the HEWL labeled with single Galbeta1,4GlcNAc-Epo and the Glu102-mutant HL labeled with double Galbeta1,4GlcNAc-Epo were determined by X-ray crystallography at resolutions of 1.85 and 2.0 A, respectively. The overall conformation and the interaction mode of the carbohydrate ligand part in the singly labeled HEWL and the doubly labeled Glu102-mutant HL were basically identical to those of the correspondingly labeled wild-type HL with minor alterations in some stereochemical parameters. A detailed comparison of the structures revealed the key protein-carbohydrate and carbohydrate-carbohydrate interactions essential for the dual labeling. It was suggested that the difference in the efficiency of the dual labeling was caused by the structural difference between Gln104 in HL and Asn103 in HEWL. The relevance to our previous study and the carbohydrate-carbohydrate interaction on cell-surface membranes were discussed.


    Organizational Affiliation

    Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan. m-muraki@aist.go.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
A
130Homo sapiensMutation(s): 1 
Gene 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: 2 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.330α = 90.00
b = 61.000β = 90.00
c = 32.710γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
TRUNCATEdata reduction
X-PLORrefinement
CCP4data scaling
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2003-04-07 
  • Released Date: 2003-04-22 
  • Deposition Author(s): Muraki, M., Harata, K.

Revision History 

  • Version 1.0: 2003-04-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance