2LT7

Solution NMR structure of Kaiso zinc finger DNA binding domain in complex with Kaiso binding site DNA


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

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:  
    4F6M, 4F6N, 2LT7

  • 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

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transcriptional regulator KaisoA133Homo sapiensMutation(s): 0 
Gene Names: ZBTB33KAISOZNF348
Find proteins for Q86T24 (Homo sapiens)
Explore Q86T24 
Go to UniProtKB:  Q86T24
NIH Common Fund Data Resources
PHAROS:  Q86T24
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*TP*GP*CP*TP*TP*CP*CP*TP*GP*CP*CP*AP*AP*TP*AP*AP*CP*G)-3')B [auth D]19N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*CP*GP*TP*TP*AP*TP*TP*GP*GP*CP*AP*GP*GP*AP*AP*GP*CP*AP*C)-3')C [auth E]19N/A
      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: SOLUTION NMR
      • Conformers Calculated: 100 
      • Conformers Submitted: 20 
      • Selection Criteria: structures with the lowest energy 
      • OLDERADO: 2LT7 Olderado

      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: 2012-09-19
        Changes: Database references
      • Version 1.2: 2012-10-03
        Changes: Database references