4M9E

Structure of Klf4 zinc finger DNA binding domain in complex with methylated DNA

Summary for 4M9E

• Entry DOI: 10.2210/pdb4m9e/pdb
• Descriptor: Krueppel-like factor 4, DNA (5'-D(*GP*AP*GP*GP*(5CM)P*GP*TP*GP*GP*C)-3'), DNA (5'-D(*GP*CP*CP*AP*(5CM)P*GP*CP*CP*TP*C)-3'), ... (7 entities in total)
• Functional Keywords: dna methylation, transcription factor, cellular reprogramming, c2h2 zinc finger, dna binding, transcription-dna complex, transcription/dna
• Biological source: Mus musculus (mouse); More
• Cellular location: Nucleus: Q60793
• Total number of polymer chains: 3
• Total formula weight: 16896.21

Authors

Liu, Y.,Olanrewaju, Y.O.,Blumenthal, R.M.,Zhang, X.,Cheng, X. (deposition date: 2013-08-14, release date: 2014-02-12, Last modification date: 2023-09-20)

Primary citation

Liu, Y.,Olanrewaju, Y.O.,Zheng, Y.,Hashimoto, H.,Blumenthal, R.M.,Zhang, X.,Cheng, X.
Structural basis for Klf4 recognition of methylated DNA.
Nucleic Acids Res., 42:4859-4867, 2014

PubMed Abstract: Transcription factor Krüppel-like factor 4 (Klf4), one of the factors directing cellular reprogramming, recognizes the CpG dinucleotide (whether methylated or unmodified) within a specific G/C-rich sequence. The binding affinity of the mouse Klf4 DNA-binding domain for methylated DNA is only slightly stronger than that for an unmodified oligonucleotide. The structure of the C-terminal three Krüppel-like zinc fingers (ZnFs) of mouse Klf4, in complex with fully methylated DNA, was determined at 1.85 Å resolution. An arginine and a glutamate interact with the methyl group. By comparison with two other recently characterized structures of ZnF protein complexes with methylated DNA, we propose a common principle of recognition of methylated CpG by C2H2 ZnF proteins, which involves a spatially conserved Arg-Glu pair.

PubMed: 24520114
DOI: 10.1093/nar/gku134

Experimental method

X-RAY DIFFRACTION (1.851 Å)