2PAF

Crystal Structure of the Lactose Repressor bound to anti-inducer ONPF in induced state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report



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:  
    2P9H, 2PAF, 2PE5

  • 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 how ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lactose operon repressor AB269Escherichia coliMutation(s): 0 
Gene Names: lacI
Find proteins for P03023 (Escherichia coli (strain K12))
Explore P03023 
Go to UniProtKB:  P03023
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NPF
Query on NPF

Download Ideal Coordinates CCD File 
A, B
2-nitrophenyl beta-D-fucopyranoside
C12 H15 N O7
SWRPIVXPHLYETN-BVWHHUJWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.199 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.541α = 90
b = 77.541β = 90
c = 212.456γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2007-03-27 
  • Released Date: 2007-06-19 
  • Deposition Author(s): Daber, R.

Revision History 

  • Version 1.0: 2007-06-19
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary