1WET

STRUCTURE OF THE PURR-GUANINE-PURF OPERATOR COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Observed: 0.176 

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This is version 1.3 of the entry. See complete history


Literature

The X-ray structure of the PurR-guanine-purF operator complex reveals the contributions of complementary electrostatic surfaces and a water-mediated hydrogen bond to corepressor specificity and binding affinity.

Schumacher, M.A.Glasfeld, A.Zalkin, H.Brennan, R.G.

(1997) J Biol Chem 272: 22648-22653

  • DOI: 10.1074/jbc.272.36.22648
  • Primary Citation of Related Structures:  
    1WET

  • PubMed Abstract: 
  • The purine repressor, PurR, is the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. This dimeric transcription factor is activated to bind to cognate DNA operator sites by initially binding either of its physiologically relevant, high affinity corepressors, hypoxanthine (Kd = 9 ...

    The purine repressor, PurR, is the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. This dimeric transcription factor is activated to bind to cognate DNA operator sites by initially binding either of its physiologically relevant, high affinity corepressors, hypoxanthine (Kd = 9.3 microM) or guanine (Kd = 1.5 microM). Here, we report the 2.5-A crystal structure of the PurR-guanine-purF operator ternary complex and complete the atomic description of 6-oxopurine-induced repression by PurR. As anticipated, the structure of the PurR-guanine-purF operator complex is isomorphous to the PurR-hypoxanthine-purF operator complex, and their protein-DNA and protein-corepressor interactions are nearly identical. The former finding confirms the use of an identical allosteric DNA-binding mechanism whereby corepressor binding 40 A from the DNA-binding domain juxtaposes the hinge regions of each monomer, thus favoring the formation and insertion of the critical minor groove-binding hinge helices. Strikingly, the higher binding affinity of guanine for PurR and the ability of PurR to discriminate against 2-oxopurines do not result from direct protein-ligand interactions, but rather from a water-mediated contact with the exocyclic N-2 of guanine, which dictates the presence of a donor group on the corepressor, and the better electrostatic complementarity of the guanine base and the corepressor-binding pocket.


    Related Citations: 
    • 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

    Organizational Affiliation

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



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (PURINE REPRESSOR)B [auth A]340Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0ACP7 (Escherichia coli (strain K12))
Explore P0ACP7 
Go to UniProtKB:  P0ACP7
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*AP*CP*GP*AP*AP*AP*AP*CP*GP*TP*TP*TP*TP*CP*GP*T )-3')A [auth B]17N/A
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    GUN
    Query on GUN

    Download Ideal Coordinates CCD File 
    C [auth A]GUANINE
    C5 H5 N5 O
    UYTPUPDQBNUYGX-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.60 Å
    • R-Value Observed: 0.176 
    • Space Group: C 2 2 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 175.99α = 90
    b = 95.08β = 90
    c = 81.51γ = 90
    Software Package:
    Software NamePurpose
    TNTrefinement

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1997-11-21
      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: 2018-04-04
      Changes: Data collection