2ERG

Crystal Structure of Leu3 DNA-binding domain with a single H50C mutation complexed with a 15mer DNA duplex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.273 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of a Leu3-DNA complex: recognition of everted CGG half-sites by a Zn2Cys6 binuclear cluster protein.

Fitzgerald, M.X.Rojas, J.R.Kim, J.M.Kohlhaw, G.B.Marmorstein, R.

(2006) Structure 14: 725-735

  • DOI: https://doi.org/10.1016/j.str.2005.11.025
  • Primary Citation of Related Structures:  
    2ER8, 2ERE, 2ERG

  • PubMed Abstract: 

    Gal4 is the prototypical Zn2Cys6 binuclear cluster transcriptional regulator that binds as a homodimer to DNA containing inverted CGG half-sites. Leu3, a member of this protein family, binds to everted (opposite polarity to inverted) CGG half-sites, and an H50C mutation within the Leu3 Zn2Cys6 binuclear motif abolishes its transcriptional repression function without impairing DNA binding. We report the X-ray crystal structures of DNA complexes with Leu3 and Leu3(H50C) and solution DNA binding studies of selected Leu3 mutant proteins. These studies reveal the molecular details of everted CGG half-site recognition, and suggest a role for the H50C mutation in transcriptional repression. Comparison with the Gal4-DNA complex shows an unexpected conservation in the DNA recognition mode of inverted and everted CGG half-sites, and points to a critical function of a linker region between the Zn2Cys6 binuclear cluster and dimerization regions in DNA binding specificity. Broader implications of these findings are discussed.


  • Organizational Affiliation

    The Wistar Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Regulatory protein LEU3C [auth A],
D [auth B]
72Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: LEU3
UniProt
Find proteins for P08638 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P08638 
Go to UniProtKB:  P08638
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08638
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*TP*TP*GP*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*CP*A)-3'A [auth C],
B [auth D]
15N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.273 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.768α = 90
b = 66.768β = 90
c = 122.745γ = 120
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-04-04
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-23
    Changes: Data collection, Refinement description