4F6N

Crystal structure of Kaiso zinc finger DNA binding protein in complex with methylated CpG site DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular basis for recognition of methylated and specific DNA sequences by the zinc finger protein Kaiso.

Buck-Koehntop, B.A.Stanfield, R.L.Ekiert, D.C.Martinez-Yamout, M.A.Dyson, H.J.Wilson, I.A.Wright, P.E.

(2012) Proc Natl Acad Sci U S A 109: 15229-15234

  • DOI: 10.1073/pnas.1213726109
  • Primary Citation of Related Structures:  
    2LT7, 4F6M, 4F6N

  • PubMed Abstract: 
  • Methylation of CpG dinucleotides in DNA is a common epigenetic modification in eukaryotes that plays a central role in maintenance of genome stability, gene silencing, genomic imprinting, development, and disease. Kaiso, a bifunctional Cys(2)His(2) zinc finger protein implicated in tumor-cell proliferation, binds to both methylated CpG (mCpG) sites and a specific nonmethylated DNA motif (TCCTGCNA) and represses transcription by recruiting chromatin remodeling corepression machinery to target genes ...

    Methylation of CpG dinucleotides in DNA is a common epigenetic modification in eukaryotes that plays a central role in maintenance of genome stability, gene silencing, genomic imprinting, development, and disease. Kaiso, a bifunctional Cys(2)His(2) zinc finger protein implicated in tumor-cell proliferation, binds to both methylated CpG (mCpG) sites and a specific nonmethylated DNA motif (TCCTGCNA) and represses transcription by recruiting chromatin remodeling corepression machinery to target genes. Here we report structures of the Kaiso zinc finger DNA-binding domain in complex with its nonmethylated, sequence-specific DNA target (KBS) and with a symmetrically methylated DNA sequence derived from the promoter region of E-cadherin. Recognition of specific bases in the major groove of the core KBS and mCpG sites is accomplished through both classical and methyl CH···O hydrogen-bonding interactions with residues in the first two zinc fingers, whereas residues in the C-terminal extension following the third zinc finger bind in the opposing minor groove and are required for high-affinity binding. The C-terminal region is disordered in the free protein and adopts an ordered structure upon binding to DNA. The structures of these Kaiso complexes provide insights into the mechanism by which a zinc finger protein can recognize mCpG sites as well as a specific, nonmethylated regulatory DNA sequence.


    Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transcriptional regulator KaisoA133Homo sapiensMutation(s): 0 
Gene Names: ZBTB33KAISOZNF348
UniProt & NIH Common Fund Data Resources
Find proteins for Q86T24 (Homo sapiens)
Explore Q86T24 
Go to UniProtKB:  Q86T24
PHAROS:  Q86T24
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*TP*GP*TP*CP*AP*CP*(5CM)P*GP*(5CM)P*GP*TP*CP*TP*AP*TP*AP*CP*G)-3')B [auth D]19Homo sapiens
    Protein Feature View
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    • Reference Sequence
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    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*CP*GP*TP*AP*TP*AP*GP*AP*(5CM)P*GP*(5CM)P*GP*GP*TP*GP*AP*CP*AP*C)-3')C [auth E]19Homo sapiens
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.80 Å
      • R-Value Free: 0.261 
      • R-Value Work: 0.228 
      • R-Value Observed: 0.230 
      • Space Group: F 2 2 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 44.049α = 90
      b = 183.402β = 90
      c = 230.138γ = 90
      Software Package:
      Software NamePurpose
      Blu-Icedata collection
      PHASERphasing
      REFMACrefinement
      HKL-2000data reduction
      HKL-2000data scaling

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2012-09-05
        Type: Initial release
      • Version 1.1: 2012-09-26
        Changes: Database references
      • Version 1.2: 2012-10-03
        Changes: Database references