4EOT

Crystal structure of the MafA homodimer bound to the consensus MARE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A Novel DNA Binding Mechanism for maf Basic Region-Leucine Zipper Factors Inferred from a MafA-DNA Complex Structure and Binding Specificities.

Lu, X.Guanga, G.P.Wan, C.Rose, R.B.

(2012) Biochemistry 51: 9706-9717

  • DOI: 10.1021/bi301248j
  • Primary Citation of Related Structures:  
    4EOT

  • PubMed Abstract: 
  • MafA is a proto-oncoprotein and is critical for insulin gene expression in pancreatic β-cells. Maf proteins belong to the AP1 superfamily of basic region-leucine zipper (bZIP) transcription factors. Residues in the basic helix and an ancillary N-terminal domain, the Extended Homology Region (EHR), endow maf proteins with unique DNA binding properties: binding a 13 bp consensus site consisting of a core AP1 site (TGACTCA) flanked by TGC sequences and binding DNA stably as monomers ...

    MafA is a proto-oncoprotein and is critical for insulin gene expression in pancreatic β-cells. Maf proteins belong to the AP1 superfamily of basic region-leucine zipper (bZIP) transcription factors. Residues in the basic helix and an ancillary N-terminal domain, the Extended Homology Region (EHR), endow maf proteins with unique DNA binding properties: binding a 13 bp consensus site consisting of a core AP1 site (TGACTCA) flanked by TGC sequences and binding DNA stably as monomers. To further characterize maf DNA binding, we determined the structure of a MafA-DNA complex. MafA forms base-specific hydrogen bonds with the flanking G(-5)C(-4) and central C(0)/G(0) bases, but not with the core-TGA bases. However, in vitro binding studies utilizing a pulse-chase electrophoretic mobility shift assay protocol revealed that mutating either the core-TGA or flanking-TGC bases dramatically increases the binding off rate. Comparing the known maf structures, we propose that DNA binding specificity results from positioning the basic helix through unique phosphate contacts. The EHR does not contact DNA directly but stabilizes DNA binding by contacting the basic helix. Collectively, these results suggest a novel multistep DNA binding process involving a conformational change from contacting the core-TGA to contacting the flanking-TGC bases.


    Organizational Affiliation

    Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription factor MafAA, B95Homo sapiensMutation(s): 0 
Gene Names: MAFA
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NHW3 (Homo sapiens)
Explore Q8NHW3 
Go to UniProtKB:  Q8NHW3
PHAROS:  Q8NHW3
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*CP*CP*GP*GP*TP*GP*CP*TP*GP*AP*GP*TP*CP*AP*GP*CP*AP*GP*G)-3'C19N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*CP*CP*CP*TP*GP*CP*TP*GP*AP*CP*TP*CP*AP*GP*CP*AP*CP*CP*G)-3'D19N/A
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      SO4
      Query on SO4

      Download Ideal Coordinates CCD File 
      E [auth A], F [auth A], G [auth B]SULFATE ION
      O4 S
      QAOWNCQODCNURD-UHFFFAOYSA-L
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.85 Å
      • R-Value Free: 0.260 
      • R-Value Work: 0.221 
      • R-Value Observed: 0.223 
      • Space Group: P 31 2 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 116.1α = 90
      b = 116.1β = 90
      c = 85.08γ = 120
      Software Package:
      Software NamePurpose
      XDSdata scaling
      PHASERphasing
      PHENIXrefinement
      XDSdata reduction
      XSCALEdata scaling

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2012-11-28
        Type: Initial release
      • Version 1.1: 2012-12-26
        Changes: Database references