4RZT

Lac repressor engineered to bind sucralose, sucralose-bound tetramer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Engineering an allosteric transcription factor to respond to new ligands.

Taylor, N.D.Garruss, A.S.Moretti, R.Chan, S.Arbing, M.A.Cascio, D.Rogers, J.K.Isaacs, F.J.Kosuri, S.Baker, D.Fields, S.Church, G.M.Raman, S.

(2016) Nat.Methods 13: 177-183

  • DOI: 10.1038/nmeth.3696
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Genetic regulatory proteins inducible by small molecules are useful synthetic biology tools as sensors and switches. Bacterial allosteric transcription factors (aTFs) are a major class of regulatory proteins, but few aTFs have been redesigned to resp ...

    Genetic regulatory proteins inducible by small molecules are useful synthetic biology tools as sensors and switches. Bacterial allosteric transcription factors (aTFs) are a major class of regulatory proteins, but few aTFs have been redesigned to respond to new effectors beyond natural aTF-inducer pairs. Altering inducer specificity in these proteins is difficult because substitutions that affect inducer binding may also disrupt allostery. We engineered an aTF, the Escherichia coli lac repressor, LacI, to respond to one of four new inducer molecules: fucose, gentiobiose, lactitol and sucralose. Using computational protein design, single-residue saturation mutagenesis or random mutagenesis, along with multiplex assembly, we identified new variants comparable in specificity and induction to wild-type LacI with its inducer, isopropyl β-D-1-thiogalactopyranoside (IPTG). The ability to create designer aTFs will enable applications including dynamic control of cell metabolism, cell biology and synthetic gene circuits.


    Organizational Affiliation

    Wyss Institute for Biologically-Inspired Engineering, Harvard University, Boston, Massachusetts, USA.,University of California Los Angeles-Department of Energy Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, California, USA.,Department of Genome Sciences, University of Washington, Seattle, Washington, USA.,Department of Medicine, University of Washington, Seattle, Washington, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA.,Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, USA.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA.,Systems Biology Institute, Yale University, West Haven, Connecticut, USA.,Department of Biochemistry, University of Washington, Seattle, Washington, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lac repressor
A, B, C, D
381Escherichia coli (strain K12)Mutation(s): 4 
Gene Names: lacI
Find proteins for P03023 (Escherichia coli (strain K12))
Go to UniProtKB:  P03023
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
40J
Query on 40J

Download SDF File 
Download CCD File 
A, B, C, D
1,6-dichloro-1,6-dideoxy-beta-D-fructofuranosyl 4-chloro-4-deoxy-alpha-D-galactopyranoside
sucralose
C12 H19 Cl3 O8
BAQAVOSOZGMPRM-QBMZZYIRSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.205 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 163.590α = 90.00
b = 74.080β = 119.91
c = 149.160γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
BUSTER-TNTrefinement
XSCALEdata scaling
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-23
    Type: Initial release
  • Version 1.1: 2016-01-06
    Type: Database references
  • Version 1.2: 2016-03-02
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Refinement description