4L7X

Crystal structure of the DIDO PHD finger in complex with H3K4me3

Summary for 4L7X

• Entry DOI: 10.2210/pdb4l7x/pdb
• Related: 4L58
• Descriptor: Death-inducer obliterator 1, Histone H3 peptide, ZINC ION, ... (4 entities in total)
• Functional Keywords: mitosis, chromatin, cell cycle, gene regulation
• Biological source: Homo sapiens (human); More
• Cellular location: Cytoplasm (By similarity): Q9BTC0
• Total number of polymer chains: 2
• Total formula weight: 8761.73

Authors

Tong, Q.,Gatchalian, J.,Kutateladze, T.G. (deposition date: 2013-06-14, release date: 2013-07-24)

Primary citation

Gatchalian, J.,Futterer, A.,Rothbart, S.B.,Tong, Q.,Rincon-Arano, H.,Sanchez de Diego, A.,Groudine, M.,Strahl, B.D.,Martinez-A, C.,van Wely, K.H.,Kutateladze, T.G.
Dido3 PHD Modulates Cell Differentiation and Division.
Cell Rep, 4:148-158, 2013

PubMed Abstract: Death Inducer Obliterator 3 (Dido3) is implicated in the maintenance of stem cell genomic stability and tumorigenesis. Here, we show that Dido3 regulates the expression of stemness genes in embryonic stem cells through its plant homeodomain (PHD) finger. Binding of Dido3 PHD to histone H3K4me3 is disrupted by threonine phosphorylation that triggers Dido3 translocation from chromatin to the mitotic spindle. The crystal structure of Dido3 PHD in complex with H3K4me3 reveals an atypical aromatic-cage-like binding site that contains a histidine residue. Biochemical, structural, and mutational analyses of the binding mechanism identified the determinants of specificity and affinity and explained the inability of homologous PHF3 to bind H3K4me3. Together, our findings reveal a link between the transcriptional control in embryonic development and regulation of cell division.

PubMed: 23831028
DOI: 10.1016/j.celrep.2013.06.014

Experimental method

X-RAY DIFFRACTION (1.35 Å)