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: 2.90 Å
  • R-Value Work: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.6 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

  • DOI: https://doi.org/10.1126/science.7973627
  • Primary Citation of Related Structures:  
    1PNR, 2PUA, 2PUB, 2PUC, 2PUD

  • 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 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.


  • Organizational Affiliation

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


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PURINE REPRESSORB [auth A]340Escherichia coliMutation(s): 1 
Gene Names: PURR
UniProt
Find proteins for P0ACP7 (Escherichia coli (strain K12))
Explore P0ACP7 
Go to UniProtKB:  P0ACP7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ACP7
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*AP*CP*GP*CP*AP*AP*AP*CP*GP*TP*TP*TP*GP*CP*GP*T )-3')A [auth B]17synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6MP
Query on 6MP

Download Ideal Coordinates CCD File 
C [auth A]6-METHYLPURINE
C6 H6 N4
SYMHUEFSSMBHJA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Work: 0.166 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 175.65α = 90
b = 94.68β = 90
c = 81.83γ = 90
Software Package:
Software NamePurpose
TNTrefinement
SDMSdata reduction
SDMSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-05-06
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-03-08
    Changes: Structure summary
  • Version 1.4: 2018-04-04
    Changes: Data collection
  • Version 1.5: 2021-11-03
    Changes: Database references, Derived calculations
  • Version 1.6: 2024-02-21
    Changes: Data collection