2F2Q

High resolution crystal strcuture of T4 lysozyme mutant L20R63/A liganded to guanidinium ion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Guanidinium derivatives bind preferentially and trigger long-distance conformational changes in an engineered T4 lysozyme.

Yousef, M.S.Bischoff, N.Dyer, C.M.Baase, W.A.Matthews, B.W.

(2006) Protein Sci. 15: 853-861

  • DOI: 10.1110/ps.052020606
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The binding of guanidinium ion has been shown to promote a large-scale translation of a tandemly duplicated helix in an engineered mutant of T4 lysozyme. The guanidinium ion acts as a surrogate for the guanidino group of an arginine side chain. Here ...

    The binding of guanidinium ion has been shown to promote a large-scale translation of a tandemly duplicated helix in an engineered mutant of T4 lysozyme. The guanidinium ion acts as a surrogate for the guanidino group of an arginine side chain. Here we determine whether methyl- and ethylguanidinium provide better mimics. The results show that addition of the hydrophobic moieties to the ligand enhances the binding affinity concomitant with reduction in ligand solubility. Crystallographic analysis confirms that binding of the alternative ligands to the engineered site still drives the large-scale conformational change. Thermal analysis and NMR data show, in comparison to guanidinium, an increase in protein stability and in ligand affinity. This is presumably due to the successive increase in hydrophobicity in going from guanidinium to ethylguanidinium. A fluorescence-based optical method was developed to sense the ligand-triggered helix translation in solution. The results are a first step in the de novo design of a molecular switch that is not related to the normal function of the protein.


    Related Citations: 
    • Long-distance conformational changes in a protein engineered by modulated sequence duplication
      Sagermann, M.,Gay, L.,Matthews, B.W.
      (2003) Proc.Natl.Acad.Sci.USA 100: 9191
    • Use of sequence duplication to engineer a ligand-triggered, long-distance molecular switch in T4 lysozyme
      Yousef, M.S.,Baase, W.A.,Matthews, B.W.
      (2004) Proc.Natl.Acad.Sci.USA 101: 11583
    • Structural characterization of an engineered tandem repeat contrasts the importance of context and sequence in protein folding
      Sagermann, M.,Baase, W.A.,Matthews, B.W.
      (1999) Proc.Natl.Acad.Sci.USA 96: 6078


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme
A
175Enterobacteria phage T4Mutation(s): 4 
Gene Names: E
EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Small Molecules
Ligands 3 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
HED
Query on HED

Download SDF File 
Download CCD File 
A
2-HYDROXYETHYL DISULFIDE
C4 H10 O2 S2
KYNFOMQIXZUKRK-UHFFFAOYSA-N
 Ligand Interaction
GAI
Query on GAI

Download SDF File 
Download CCD File 
A
GUANIDINE
C H5 N3
ZRALSGWEFCBTJO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.200 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 60.712α = 90.00
b = 60.712β = 90.00
c = 95.352γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-04-25
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description
  • Version 1.4: 2018-12-19
    Type: Data collection, Structure summary