2PUA

CRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER, PURR, BOUND TO DNA: MINOR GROOVE BINDING BY ALPHA HELICES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices.

Schumacher, M.A.Choi, K.Y.Zalkin, H.Brennan, R.G.

(1994) Science 266: 763-770

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The three-dimensional structure of a ternary complex of the purine repressor, PurR, bound to both its corepressor, hypoxanthine, and the 16-base pair purF operator site has been solved at 2.7 A resolution by x-ray crystallography. The bipartite struc ...

    The three-dimensional structure of a ternary complex of the purine repressor, PurR, bound to both its corepressor, hypoxanthine, and the 16-base pair purF operator site has been solved at 2.7 A resolution by x-ray crystallography. The bipartite structure of PurR consists of an amino-terminal DNA-binding domain and a larger carboxyl-terminal corepressor binding and dimerization domain that is similar to that of the bacterial periplasmic binding proteins. The DNA-binding domain contains a helix-turn-helix motif that makes base-specific contacts in the major groove of the DNA. Base contacts are also made by residues of symmetry-related alpha helices, the "hinge" helices, which bind deeply in the minor groove. Critical to hinge helix-minor groove binding is the intercalation of the side chains of Leu54 and its symmetry-related mate, Leu54', into the central CpG-base pair step. These residues thereby act as "leucine levers" to pry open the minor groove and kink the purF operator by 45 degrees.


    Related Citations: 
    • Structure-Based Redesign of Corepressor Specificity of the Escherichia Coli Purine Repressor by Substitution of Residue 190
      Lu, F.,Schumacher, M.A.,Arvidson, D.N.,Haldimann, A.,Wanner, B.L.,Zalkin, H.,Brennan, R.G.
      (1998) Biochemistry 37: 971


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Oregon Health Sciences University, Portland 97201-3098.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PURINE REPRESSOR
A
340Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: purR
Find proteins for P0ACP7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ACP7
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*AP*CP*GP*CP*AP*AP*AP*CP*GP*TP*TP*TP*GP*CP*GP*T )-3')B17synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6MP
Query on 6MP

Download SDF File 
Download CCD File 
A
6-METHYLPURINE
C6 H6 N4
SYMHUEFSSMBHJA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Work: 0.166 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 175.650α = 90.00
b = 94.680β = 90.00
c = 81.830γ = 90.00
Software Package:
Software NamePurpose
SDMSdata scaling
TNTrefinement
SDMSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-05-06
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-03-08
    Type: Structure summary
  • Version 1.4: 2018-04-04
    Type: Data collection