2F47

Xray crystal structure of T4 lysozyme mutant L20/R63A liganded to methylguanidinium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 
    • 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
    • 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


    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
MGX
Query on MGX

Download SDF File 
Download CCD File 
A
1-METHYLGUANIDINE
C2 H7 N3
CHJJGSNFBQVOTG-UHFFFAOYSA-N
 Ligand Interaction
BME
Query on BME

Download SDF File 
Download CCD File 
A
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MGXKd: 148000000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.206 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 60.685α = 90.00
b = 60.685β = 90.00
c = 95.482γ = 120.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction

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