3QMB

Structural Basis of Selective Binding of Nonmethylated CpG Islands by the CXXC Domain of CFP1

Summary for 3QMB

• Entry DOI: 10.2210/pdb3qmb/pdb
• Related: 3QMC 3QMD 3QMG 3QMH 3QMI
• Descriptor: CpG-binding protein, 5'-D(*GP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*C)-3', ZINC ION, ... (5 entities in total)
• Functional Keywords: structural genomics consortium, sgc, cxxc-type zn finger, dna binding, unmethylated cpg motifs, nucleus speckle, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Homo sapiens (human); More
• Cellular location: Nucleus speckle : Q9P0U4
• Total number of polymer chains: 3
• Total formula weight: 17027.62

Authors

Lam, R.,Xu, C.,Bian, C.B.,Kania, J.,Bountra, C.,Weigelt, J.,Arrowsmith, C.H.,Edwards, A.M.,Bochkarev, A.,Min, J.,Structural Genomics Consortium (SGC) (deposition date: 2011-02-04, release date: 2011-02-23, Last modification date: 2024-02-21)

Primary citation

Xu, C.,Bian, C.,Lam, R.,Dong, A.,Min, J.
The structural basis for selective binding of non-methylated CpG islands by the CFP1 CXXC domain.
Nat Commun, 2:227-227, 2011

PubMed Abstract: CFP1 is a CXXC domain-containing protein and an essential component of the SETD1 histone H3K4 methyltransferase complex. CXXC domain proteins direct different chromatin-modifying activities to various chromatin regions. Here, we report crystal structures of the CFP1 CXXC domain in complex with six different CpG DNA sequences. The crescent-shaped CFP1 CXXC domain is wedged into the major groove of the CpG DNA, distorting the B-form DNA, and interacts extensively with the major groove of the DNA. The structures elucidate the molecular mechanism of the non-methylated CpG-binding specificity of the CFP1 CXXC domain. The CpG motif is confined by a tripeptide located in a rigid loop, which only allows the accommodation of the non-methylated CpG dinucleotide. Furthermore, we demonstrate that CFP1 has a preference for a guanosine nucleotide following the CpG motif.

PubMed: 21407193
DOI: 10.1038/ncomms1237

Experimental method

X-RAY DIFFRACTION (2.06 Å)