1T8A

USE OF SEQUENCE DUPLICATION TO ENGINEER A LIGAND-TRIGGERED LONG-DISTANCE MOLECULAR SWITCH IN T4 Lysozyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

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: 11583-11586

  • DOI: 10.1073/pnas.0404482101
  • Primary Citation of Related Structures:  
  • Also Cited By: 2F2Q, 2F47, 2F32

  • PubMed Abstract: 
  • We have designed a molecular switch in a T4 lysozyme construct that controls a large-scale translation of a duplicated helix. As shown by crystal structures of the construct with the switch on and off, the conformational change is triggered by the bi ...

    We have designed a molecular switch in a T4 lysozyme construct that controls a large-scale translation of a duplicated helix. As shown by crystal structures of the construct with the switch on and off, the conformational change is triggered by the binding of a ligand (guanidinium ion) to a site that in the wild-type protein was occupied by the guanidino head group of an Arg. In the design template, a duplicated helix is flanked by two loop regions of different stabilities. In the "on" state, the N-terminal loop is weakly structured, whereas the C-terminal loop has a well defined conformation that is stabilized by means of nonbonded interactions with the Arg head group. The truncation of the Arg to Ala destabilizes this loop and switches the protein to the "off" state, in which the duplicated helix is translocated approximately 20 A. Guanidinium binding restores the key interactions, restabilizes the C-terminal loop, and restores the "on" state. Thus, the presence of an external ligand, which is unrelated to the catalytic activity of the enzyme, triggers the inserted helix to translate 20 A away from the binding site. The results illustrate a proposed mechanism for protein evolution in which sequence duplication followed by point mutation can lead to the establishment of new function.


    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
    • 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, OR 97403-1229, USA. brain@uoxray.uoregon.edu




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: 2 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.218 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 60.401α = 90.00
b = 60.401β = 90.00
c = 96.190γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description
  • Version 1.4: 2018-12-19
    Type: Data collection, Structure summary