2LT7

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

• PDB DOI:  https://doi.org/10.2210/pdb2LT7/pdb
• NAKB: 2LT7
• BMRB: 18462

• Classification: METAL BINDING PROTEIN/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-05-15 Released: 2012-09-05 
• Deposition Author(s): Buck-Koehntop, B.A., Stanfield, R.L., Ekiert, D.C., Martinez-Yamout, M.A., Dyson, H., Wilson, I.A., Wright, P.E.

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Experimental Data Snapshot

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

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

• PubMed: 22949637 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 27.93 kDa 
• Atom Count: 1,903 
• Modelled Residue Count: 171 
• Deposited Residue Count: 171 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator Kaiso	A	133	Homo sapiens	Mutation(s): 0  Gene Names: ZBTB33, KAISO, ZNF348
UniProt & NIH Common Fund Data Resources
Find proteins for Q86T24 (Homo sapiens) Explore Q86T24  Go to UniProtKB:  Q86T24
PHAROS:  Q86T24

Entity ID: 2
Molecule	Chains	Length	Organism	Image
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]	19	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
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]	19	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A], E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-05 
Deposition Author(s): Buck-Koehntop, B.A., Stanfield, R.L., Ekiert, D.C., Martinez-Yamout, M.A., Dyson, H., Wilson, I.A., Wright, P.E.

Revision History  

• 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