title: Molecular basis for recognition of methylated and specific DNA sequences by the zinc finger protein Kaiso.
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.
authors.affiliation: Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
authors.forename: Bethany A
authors.initials: BA
authors.lastname: Buck-Koehntop
authors.forename: Robyn L
authors.initials: RL
authors.lastname: Stanfield
authors.forename: Damian C
authors.initials: DC
authors.lastname: Ekiert
authors.forename: Maria A
authors.initials: MA
authors.lastname: Martinez-Yamout
authors.forename: H Jane
authors.initials: HJ
authors.lastname: Dyson
authors.forename: Ian A
authors.initials: IA
authors.lastname: Wilson
authors.forename: Peter E
authors.initials: PE
authors.lastname: Wright
mesh_terms: D001483:Base Sequence; D015820:Cadherins / Q000737:chemistry; D002843:Chromatin / Q000737:chemistry; D018899:CpG Islands; D018360:Crystallography, X-Ray / Q000379:methods; D004247:DNA / Q000737:chemistry; D019175:DNA Methylation; D006801:Humans; D006863:Hydrogen-Ion Concentration; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D014157:Transcription Factors / Q000737:chemistry* / Q000235:genetics; D016335:Zinc Fingers
chemical_list: D015820:Cadherins; D002843:Chromatin; D014157:Transcription Factors; C492254:ZBTB33 protein, human; D004247:DNA