1WVL

Crystal Structure of Multimeric DNA-binding Protein Sac7d-GCN4 with DNA decamer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.276 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Design and characterization of a multimeric DNA binding protein using Sac7d and GCN4 as templates

Wu, S.W.Ko, T.P.Chou, C.C.Wang, A.H.

(2005) Proteins 60: 617-628

  • DOI: 10.1002/prot.20524
  • Primary Citation of Related Structures:  
    1WVL

  • PubMed Abstract: 
  • The protein Sac7d belongs to a class of small chromosomal proteins from the hyperthermophilic archaeon Sulfolobus acidocaldarius. Sac7d is extremely stable to heat, acid, and chemical agents. This protein is a monomer and it binds DNA without any particular sequence preference, while inducing a sharp kink in the DNA ...

    The protein Sac7d belongs to a class of small chromosomal proteins from the hyperthermophilic archaeon Sulfolobus acidocaldarius. Sac7d is extremely stable to heat, acid, and chemical agents. This protein is a monomer and it binds DNA without any particular sequence preference, while inducing a sharp kink in the DNA. By appending a leucine-zipper-like helical peptide derived from the yeast transcriptional activator GCN4 to the C-terminal end of Sac7d, the modified monomers (denoted S7dLZ) are expected to interact with each other via hydrophobic force to form a parallel dimer. The recombinant S7dLZ was expressed in Escherichia coli and purified by heating and ion-exchange chromatography. The formation of dimer was detected by gel-filtration chromatography and chemical cross-link. The results of surface plasmon resonance and circular dichroism experiments showed that the DNA-binding capacity was retained. Furthermore, X-ray diffraction analysis of single crystals of S7dLZ in complex with DNA decamer CCTATATAGG showed that the leucine-zipper segments of S7dLZ were associated into an antiparallel four-helix bundle. There are two DNA fragments bound to each S7dLZ tetramer in the crystal. This model works as a successful template that endows protein a new function without losing original properties.


    Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-binding proteins 7a/7b/7d, GCN4C [auth A], D [auth B]80Sulfolobus acidocaldariusMutation(s): 0 
UniProt
Find proteins for P13123 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
Explore P13123 
Go to UniProtKB:  P13123
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*CP*CP*TP*AP*TP*AP*TP*AP*GP*G)-3'A [auth C], B [auth D]10N/A
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.60 Å
    • R-Value Free: 0.269 
    • R-Value Work: 0.230 
    • R-Value Observed: 0.276 
    • Space Group: P 41 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 58.65α = 90
    b = 58.65β = 90
    c = 186.68γ = 90
    Software Package:
    Software NamePurpose
    CrystalCleardata collection
    XDSdata reduction
    CNSrefinement
    CrystalCleardata reduction
    XDSdata scaling
    CNSphasing

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    • Deposited Date: 2004-12-16 
    • Released Date: 2005-08-02 
    • Deposition Author(s): Wu, S.W., Wang, A.H.

    Revision History  (Full details and data files)

    • Version 1.0: 2005-08-02
      Type: Initial release
    • Version 1.1: 2008-04-30
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance