2PE5

Crystal Structure of the Lac Repressor bound to ONPG in repressed state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural analysis of lac repressor bound to allosteric effectors

Daber, R.Stayrook, S.Rosenberg, A.Lewis, M.

(2007) J.Mol.Biol. 370: 609-619

  • DOI: 10.1016/j.jmb.2007.04.028
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The lac operon is a model system for understanding how effector molecules regulate transcription and are necessary for allosteric transitions. The crystal structures of the lac repressor bound to inducer and anti-inducer molecules provide a model for ...

    The lac operon is a model system for understanding how effector molecules regulate transcription and are necessary for allosteric transitions. The crystal structures of the lac repressor bound to inducer and anti-inducer molecules provide a model for how these small molecules can modulate repressor function. The structures of the apo repressor and the repressor bound to effector molecules are compared in atomic detail. All effectors examined here bind to the repressor in the same location and are anchored to the repressor through hydrogen bonds to several hydroxyl groups of the sugar ring. Inducer molecules form a more extensive hydrogen-bonding network compared to anti-inducers and neutral effector molecules. The structures of these effector molecules suggest that the O6 hydroxyl on the galactoside is essential for establishing a water-mediated hydrogen bonding network that bridges the N-terminal and C-terminal sub-domains. The altered hydrogen bonding can account in part for the different structural conformations of the repressor, and is vital for the allosteric transition.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, 37th and Hamilton Walk, Philadelphia, PA 19104-6059, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Lactose operon repressor
A, B, C
330Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: lacI
Find proteins for P03023 (Escherichia coli (strain K12))
Go to UniProtKB:  P03023
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*DAP*DAP*DTP*DTP*DGP*DTP*DGP*DAP*DGP*DCP*DGP*DCP*DTP*DCP*DAP*DCP*DAP*DAP*DTP*DT)-3')D,E,F20synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
145
Query on 145

Download SDF File 
Download CCD File 
A, B, C
1-O-[O-NITROPHENYL]-BETA-D-GALACTOPYRANOSE
C12 H15 N O8
KUWPCJHYPSUOFW-YBXAARCKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.233 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 253.080α = 90.00
b = 253.080β = 90.00
c = 203.247γ = 120.00
Software Package:
Software NamePurpose
MAR345data collection
DENZOdata reduction
REFMACrefinement
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-03-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-18
    Type: Refinement description, Source and taxonomy