260L

AN ADAPTABLE METAL-BINDING SITE ENGINEERED INTO T4 LYSOZYME


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Use of a non-rigid region in T4 lysozyme to design an adaptable metal-binding site.

Wray, J.W.Baase, W.A.Ostheimer, G.J.Zhang, X.J.Matthews, B.W.

(2000) Protein Eng. 13: 313-321

  • Primary Citation of Related Structures:  257L, 258L, 259L, 1EPY

  • PubMed Abstract: 
  • It is not easy to find candidate sites within a given protein where the geometry of the polypeptide chain matches that of metal-binding sites in known protein structures. By choosing a location in T4 lysozyme that is inherently flexible, it was possi ...

    It is not easy to find candidate sites within a given protein where the geometry of the polypeptide chain matches that of metal-binding sites in known protein structures. By choosing a location in T4 lysozyme that is inherently flexible, it was possible to engineer a two-histidine site that binds different divalent cations. Crystallographic analysis shows that the geometry of binding of zinc is distorted tetrahedral while that of cobalt and nickel is octahedral. Insofar as spectroscopic data can be measured, they indicate that similar modes of coordination are retained in solution. The two substitutions, Thr21 --> His and Thr142 --> His, lie, respectively, on the surface of the N- and C-terminal domains on opposite sides of the active site cleft. The design takes advantage of hinge-bending motion which allows the binding site to adapt to the most favorable ligand geometry for the metal. Introduction of the two histidines increases the melting temperature of the protein by 2.0 degrees C at pH 7.4. Metal binding further increases the melting temperature, but only by a small amount (up to 1.5 degrees C). A third substitution, Gln141 --> His, which could act as a third ligand in principle, does not do so, demonstrating the difficulty in mimicking naturally occurring metal-binding sites.


    Related Citations: 
    • Structure of a Stabilizing Disulfide Bridge Mutant that Closes the Active Site Cleft of T4 Lysozyme
      Jacobson, R.,Matsumura, M.,Faber, H.R.,Matthews, B.W.
      (1992) Protein Sci. 1: 46
    • Structure of Bacteriophage T4 Lysozyme Refined at 1.7 Angstrom Resolution
      Weaver, L.H.,Matthews, B.W.
      (1987) J.Mol.Biol. 193: 189
    • Control of Enzyme Activity by an Engineered Disulfide Bond
      Matsumura, M.,Matthews, B.W.
      (1989) Science 243: 792


    Organizational Affiliation

    Institute of Molecular Biology, Howard Hughes Medical Institute and Department of Physics, 1229 University of Oregon, Eugene,OR 97403-1229, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (LYSOZYME)
A
164Enterobacteria phage T4Gene Names: E
EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
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
NI
Query on NI

Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.190 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 62.170α = 90.00
b = 62.170β = 90.00
c = 96.780γ = 120.00
Software Package:
Software NamePurpose
TNTphasing
SDMSdata reduction
SDMSdata scaling
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-09-11
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance