1LMT

STRUCTURE OF A CONFORMATIONALLY CONSTRAINED ARG-GLY-ASP SEQUENCE INSERTED INTO HUMAN LYSOZYME


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of a conformationally constrained Arg-Gly-Asp sequence inserted into human lysozyme.

Yamada, T.Song, H.Inaka, K.Shimada, Y.Kikuchi, M.Matsushima, M.

(1995) J.Biol.Chem. 270: 5687-5690


  • PubMed Abstract: 
  • To examine the effect of a conformational constraint introduced into the Arg-Gly-Asp (RGD) sequence on cell adhesion activity, we constructed a mutant protein by inserting an RGD-containing sequence flanked by two Cys residues between Val74 and Asn75 ...

    To examine the effect of a conformational constraint introduced into the Arg-Gly-Asp (RGD) sequence on cell adhesion activity, we constructed a mutant protein by inserting an RGD-containing sequence flanked by two Cys residues between Val74 and Asn75 of human lysozyme. The CRGDSC-inserted lysozyme was expressed in yeast, purified, and designated as Cys-RGD4. Using baby hamster kidney cells, Cys-RGD4 was shown to possess even higher cell adhesion activity than that of the RGDS-inserted lysozyme, RGD4. The Cys-RGD4 protein was co-crystallized with a lysozyme inhibitor, tri-N-acetylchitotriose, and the three-dimensional structure was determined at 1.6-A resolution by x-ray crystallography. In contrast to RGD4, the inserted RGD-containing region of Cys-RGD4 was well defined. The structural analysis revealed that the two inserted Cys residues form a new disulfide bond in Cys-RGD4, as expected, and that the RGD region assumes a type II' beta-turn conformation of Gly-Asp with a hydrogen bond between the C = O of Arg and the H-N of Ser. In addition, it was confirmed that two more hydrogen bonds are present in the RGD region of the Cys-RGD4 lysozyme. These results suggest that the conformation of the RGD-containing region is rigid and stable in the Cys-RGD4 molecule and that the type II' beta-turn structure of RGD is essential for binding to integrins with high affinity.


    Related Citations: 
    • Structural and Functional Analyses of the Arg-Gly-Asp Sequence Introduced Into Human Lysozyme
      Yamada, T.,Matsushima, M.,Inaka, K.,Ohkubo, T.,Uyeda, A.,Maeda, T.,Titani, K.,Sekiguchi, K.,Kikuchi, M.
      (1993) J.Biol.Chem. 268: 10588


    Organizational Affiliation

    Protein Engineering Research Institute, Osaka, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HUMAN LYSOZYME
A
136Homo 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 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: 1.6 Å
  • R-Value Work: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.490α = 90.00
b = 61.460β = 90.00
c = 33.420γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
X-PLORmodel building
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-03-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other