1EFA

CRYSTAL STRUCTURE OF THE LAC REPRESSOR DIMER BOUND TO OPERATOR AND THE ANTI-INDUCER ONPF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.247 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A closer view of the conformation of the Lac repressor bound to operator.

Bell, C.E.Lewis, M.

(2000) Nat.Struct.Mol.Biol. 7: 209-214

  • DOI: 10.1038/73317

  • PubMed Abstract: 
  • Crystal structures of the Lac repressor, with and without isopropyithiogalactoside (IPTG), and the repressor bound to operator have provided a model for how the binding of the inducer reduces the affinity of the repressor for the operator. However, b ...

    Crystal structures of the Lac repressor, with and without isopropyithiogalactoside (IPTG), and the repressor bound to operator have provided a model for how the binding of the inducer reduces the affinity of the repressor for the operator. However, because of the low resolution of the operator-bound structure (4.8 A), the model for the allosteric transition was presented in terms of structural elements rather than in terms of side chain interactions. Here we have constructed a dimeric Lac repressor and determined its structure at 2.6 A resolution in complex with a symmetric operator and the anti-inducer orthonitrophenylfucoside (ONPF). The structure enables the induced (IPTG-bound) and repressed (operator-bound) conformations of the repressor to be compared in atomic detail. An extensive network of interactions between the DNA-binding and core domains of the repressor suggests a possible mechanism for the allosteric transition.


    Related Citations: 
    • Crystal structure of lac repressor core tetramer and its implications for DNA looping
      Friedman, A.M.,Fischmann, T.O.,Steitz, T.A.
      (1995) Science 268: 1721
    • Refined structure of lac repressor headpiece (1-56) determined by relaxation matrix calculations from 2D and 3D NOE data: change of tertiary structure upon binding to the lac operator
      Slijper, M.,Bonvin, A.M.,Boelens, R.,Kaptein, R.
      (1996) J.Mol.Biol. 259: 761
    • The solution structure of lac repressor headpiece 62 complexed to a symmetrical lac operator sequence determined by NMR and restrained molecular dynamics
      Spronk, C.A.E.M.,Bonvin, A.M.J.J.,Radha, P.K.,Melacini, G.,Boelens, R.
      (1999) Structure 7: 1483
    • Crystal structure of the lactose operon repressor and its complexes with DNA and inducer
      Lewis, M.,Chang, G.,Horton, N.C.,Kercher, M.A.,Pace, H.C.
      (1996) Science 271: 1247


    Organizational Affiliation

    The Johnson Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, 37th and Hamilton walk, Philadelphia, Pennsylvania 19102-6059, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LAC REPRESSOR
A, B, C
333Escherichia 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(*GP*AP*AP*T*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*T)-3')D,E21N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NPF
Query on NPF

Download SDF File 
Download CCD File 
A, B, C
ORTHONITROPHENYL-BETA-D-FUCOPYRANOSIDE
C12 H15 N O7
SWRPIVXPHLYETN-BVWHHUJWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.247 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 251.438α = 90.00
b = 251.438β = 90.00
c = 204.791γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
AMoREphasing
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2000-02-07 
  • Released Date: 2000-03-06 
  • Deposition Author(s): Bell, C.E., Lewis, M.

Revision History 

  • Version 1.0: 2000-03-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model