1PYI

CRYSTAL STRUCTURE OF A PPR1-DNA COMPLEX: DNA RECOGNITION BY PROTEINS CONTAINING A ZN2CYS6 BINUCLEAR CLUSTER


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.330 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a PPR1-DNA complex: DNA recognition by proteins containing a Zn2Cys6 binuclear cluster.

Marmorstein, R.Harrison, S.C.

(1994) Genes Dev. 8: 2504-2512


  • PubMed Abstract: 
  • PPR1 is a yeast transcription factor that contains a six-cysteine, two-zinc (Zn) domain, homologous to a similar structure in GAL4. Like GAL4, it binds to DNA sites with conserved CGG triplets symmetrically placed near each end. Whereas the GAL4 site ...

    PPR1 is a yeast transcription factor that contains a six-cysteine, two-zinc (Zn) domain, homologous to a similar structure in GAL4. Like GAL4, it binds to DNA sites with conserved CGG triplets symmetrically placed near each end. Whereas the GAL4 site has 11 intervening base pairs, the PPR1 site has 6. The crystal structure of a 95-residue fragment of PPR1 in specific complex with DNA shows that the protein binds to a symmetrical 14-bp recognition site as a nonsymmetrical homodimer. An amino-terminal Zn domain interacts with a conserved CGG triplet near each end of the site through major groove contacts, and the carboxy-terminal residues mediate dimerization through a coiled-coil element and an extended strand. A linker region, connecting the Zn domain and the coiled-coil, folds into a beta-hairpin. This hairpin packs differently on the two subunits and leads to a striking asymmetry, which is largely restricted to the dimerization and linker regions of the protein. Comparison with the GAL4-DNA structure shows that their specificities for sites of different length are determined by the preferred folds of their respective linker segments and by residues at the amino-terminal ends of their coiled-coils. None of these residues contact DNA in PPR1, and they contact only the sugar phosphate backbone in GAL4. We propose that this novel mode of DNA site selection is employed by other proteins that contain a Zn2Cys6 binuclear cluster.


    Related Citations: 
    • DNA Recognition by GAL4: Structure of a Protein-DNA Complex
      Marmorstein, R.,Carey, M.,Ptashne, M.,Harrison, S.C.
      (1992) Nature 356: 408


    Organizational Affiliation

    Harvard University, Department of Biochemistry and Molecular Biology, Cambridge, Massachusetts.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (PYRIMIDINE PATHWAY REGULATOR 1)
A, B
96Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PPR1
Find proteins for P07272 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07272
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*CP*GP*GP*CP*AP*AP*TP*TP*GP*CP*CP*GP*A)-3')D,E14N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.330 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 53.800α = 90.00
b = 92.600β = 90.00
c = 174.700γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-02-27
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance