Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 19934.31 
• Atom Count: 1443 
• Residue Count: 175 
• Unique protein chains: 1

1T8A

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

• DOI: 10.2210/pdb1T8A/pdb

• Classification: HYDROLASE
• Organism(s): Enterobacteria phage T4
• Expression System: Escherichia coli
• Mutation(s): 4 


• Deposited: 2004-05-11 Released: 2004-08-17 
• Deposition Author(s): Yousef, M.S., Baase, W.A., Matthews, B.W.

---

Experimental Data Snapshot

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

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

• PubMed: 15286283 
• DOI: 10.1073/pnas.0404482101
• Primary Citation of Related Structures:  
  1T97
• 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 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. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Lysozyme	A	175	Enterobacteria phage T4	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
HED	A	2-HYDROXYETHYL DISULFIDE C4 H10 O2 S2 KYNFOMQIXZUKRK-UHFFFAOYSA-N
GAI	A	GUANIDINE C H5 N3 ZRALSGWEFCBTJO-UHFFFAOYSA-N

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 = 60.401	α = 90.00
b = 60.401	β = 90.00
c = 96.190	γ = 120.00

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-05-11 
• Released Date: 2004-08-17 
• Deposition Author(s): Yousef, M.S., Baase, W.A., Matthews, B.W.

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