5KE9

mouse Klf4 E446P ZnF1-3 and TpG/CpA sequence DNA complex structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Distinctive Klf4 mutants determine preference for DNA methylation status.

Hashimoto, H.Wang, D.Steves, A.N.Jin, P.Blumenthal, R.M.Zhang, X.Cheng, X.

(2016) Nucleic Acids Res 44: 10177-10185

  • DOI: 10.1093/nar/gkw774
  • Primary Citation of Related Structures:  
    5KEB, 5KEA, 5KE8, 5KE7, 5KE9, 5KE6

  • PubMed Abstract: 
  • Reprogramming of mammalian genome methylation is critically important but poorly understood. Klf4, a transcription factor directing reprogramming, contains a DNA binding domain with three consecutive C2H2 zinc fingers. Klf4 recognizes CpG or TpG within a specific sequence ...

    Reprogramming of mammalian genome methylation is critically important but poorly understood. Klf4, a transcription factor directing reprogramming, contains a DNA binding domain with three consecutive C2H2 zinc fingers. Klf4 recognizes CpG or TpG within a specific sequence. Mouse Klf4 DNA binding domain has roughly equal affinity for methylated CpG or TpG, and slightly lower affinity for unmodified CpG. The structural basis for this key preference is unclear, though the side chain of Glu446 is known to contact the methyl group of 5-methylcytosine (5mC) or thymine (5-methyluracil). We examined the role of Glu446 by mutagenesis. Substituting Glu446 with aspartate (E446D) resulted in preference for unmodified cytosine, due to decreased affinity for 5mC. In contrast, substituting Glu446 with proline (E446P) increased affinity for 5mC by two orders of magnitude. Structural analysis revealed hydrophobic interaction between the proline's aliphatic cyclic structure and the 5-methyl group of the pyrimidine (5mC or T). As in wild-type Klf4 (E446), the proline at position 446 does not interact directly with either the 5mC N4 nitrogen or the thymine O4 oxygen. In contrast, the unmethylated cytosine's exocyclic N4 amino group (NH 2 ) and its ring carbon C5 atom hydrogen bond directly with the aspartate carboxylate of the E446D variant. Both of these interactions would provide a preference for cytosine over thymine, and the latter one could explain the E446D preference for unmethylated cytosine. Finally, we evaluated the ability of these Klf4 mutants to regulate transcription of methylated and unmethylated promoters in a luciferase reporter assay.


    Organizational Affiliation

    Genetics and Molecular Biology Graduate Program, Laney Graduate School, Emory University, Atlanta, GA 30322, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Krueppel-like factor 4A93Mus musculusMutation(s): 1 
Gene Names: Klf4EzfGklfZie
UniProt & NIH Common Fund Data Resources
Find proteins for Q60793 (Mus musculus)
Explore Q60793 
Go to UniProtKB:  Q60793
IMPC:  MGI:1342287
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*AP*GP*GP*TP*GP*TP*GP*GP*C)-3')B10synthetic construct
    Protein Feature View
    Expand
    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*GP*CP*CP*AP*CP*AP*CP*CP*TP*C)-3')C10synthetic construct
      Protein Feature View
      Expand
      • Reference Sequence
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      ZN
      Query on ZN

      Download Ideal Coordinates CCD File 
      D [auth A], E [auth A], F [auth A]ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.34 Å
      • R-Value Free: 0.272 
      • R-Value Work: 0.214 
      • R-Value Observed: 0.217 
      • Space Group: P 43 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 51.44α = 90
      b = 51.44β = 90
      c = 130.594γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      HKL-2000data reduction
      HKL-2000data scaling
      PHASERphasing

      Structure Validation

      View Full Validation Report




      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM049245

      Revision History  (Full details and data files)

      • Version 1.0: 2016-09-14
        Type: Initial release
      • Version 1.1: 2016-09-21
        Changes: Database references
      • Version 1.2: 2016-12-14
        Changes: Database references
      • Version 1.3: 2017-09-20
        Changes: Author supporting evidence
      • Version 1.4: 2019-12-25
        Changes: Author supporting evidence