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PDBsum entry 4l7x
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Cell cycle, gene regulation
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PDB id
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4l7x
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PDB id:
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| Name: |
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Cell cycle, gene regulation
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Title:
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Crystal structure of the dido phd finger in complex with h3k4me3
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Structure:
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Death-inducer obliterator 1. Chain: a. Fragment: phd-type zinc finger domain residues 266-325. Synonym: dio-1, hdido1, death-associated transcription factor 1, datf-1. Engineered: yes. Histone h3 peptide. Chain: u. Synonym: h3k4me3 peptide.
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Gene: dido1, c20orf158, datf1, kiaa0333. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: peptide was synthesized.
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Resolution:
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1.35Å
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R-factor:
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0.133
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R-free:
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0.142
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Authors:
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Q.Tong,J.Gatchalian,T.G.Kutateladze
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Key ref:
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J.Gatchalian
et al.
(2013).
Dido3 PHD modulates cell differentiation and division.
Cell Rep,
4,
148-158.
PubMed id:
DOI:
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Date:
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14-Jun-13
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Release date:
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24-Jul-13
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PROCHECK
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Headers
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References
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Q9BTC0
(DIDO1_HUMAN) -
Death-inducer obliterator 1 from Homo sapiens
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Seq:
Struc:
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2240 a.a.
58 a.a.*
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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*
PDB and UniProt seqs differ
at 2 residue positions (black
crosses)
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DOI no:
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Cell Rep
4:148-158
(2013)
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PubMed id:
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Dido3 PHD modulates cell differentiation and division.
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J.Gatchalian,
A.Fütterer,
S.B.Rothbart,
Q.Tong,
H.Rincon-Arano,
A.Sánchez de Diego,
M.Groudine,
B.D.Strahl,
C.Martínez-A,
K.H.van Wely,
T.G.Kutateladze.
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ABSTRACT
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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.
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