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PDBsum entry 2kwk
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Metal binding protein
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PDB id
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2kwk
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Contents |
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* Residue conservation analysis
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PDB id:
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| Name: |
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Metal binding protein
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Title:
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Solution structures of the double phd fingers of human transcriptional protein dpf3b bound to a h3 peptide wild type
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Structure:
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Histone peptide. Chain: b. Engineered: yes. Zinc finger protein dpf3. Chain: a. Fragment: phd-types 1 and 2 residues 261-372. Synonym: zinc finger protein cer-d4, brg1-associated factor 45c, baf45c. Engineered: yes
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Source:
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Synthetic: yes. Other_details: the peptide was chemically synthesized. Homo sapiens. Human. Organism_taxid: 9606. Gene: dpf3, baf45c, cerd4. Expressed in: escherichia coli. Expression_system_taxid: 511693.
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NMR struc:
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20 models
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Authors:
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L.Zeng,Q.Zhang,S.Li,A.N.Plotnikov,M.J.Walsh,M.Zhou
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Key ref:
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L.Zeng
et al.
(2010).
Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b.
Nature,
466,
258-262.
PubMed id:
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Date:
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12-Apr-10
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Release date:
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14-Jul-10
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PROCHECK
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Headers
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References
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Enzyme class:
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Chains B, A:
E.C.?
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Nature
466:258-262
(2010)
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PubMed id:
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Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b.
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L.Zeng,
Q.Zhang,
S.Li,
A.N.Plotnikov,
M.J.Walsh,
M.M.Zhou.
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ABSTRACT
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Histone lysine acetylation and methylation have an important role during gene
transcription in a chromatin context. Knowledge concerning the types of protein
modules that can interact with acetyl-lysine has so far been limited to
bromodomains. Recently, a tandem plant homeodomain (PHD) finger (PHD1-PHD2, or
PHD12) of human DPF3b, which functions in association with the BAF chromatin
remodelling complex to initiate gene transcription during heart and muscle
development, was reported to bind histones H3 and H4 in an acetylation-sensitive
manner, making it the first alternative to bromodomains for acetyl-lysine
binding. Here we report the structural mechanism of acetylated histone binding
by the double PHD fingers of DPF3b. Our three-dimensional solution structures
and biochemical analysis of DPF3b highlight the molecular basis of the
integrated tandem PHD finger, which acts as one functional unit in the
sequence-specific recognition of lysine-14-acetylated histone H3 (H3K14ac).
Whereas the interaction with H3 is promoted by acetylation at lysine 14, it is
inhibited by methylation at lysine 4, and these opposing influences are
important during transcriptional activation of the mouse DPF3b target genes
Pitx2 and Jmjd1c. Binding of this tandem protein module to chromatin can thus be
regulated by different histone modifications during the initiation of gene
transcription.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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C.A.Musselman,
M.E.Lalonde,
J.Côté,
and
T.G.Kutateladze
(2012).
Perceiving the epigenetic landscape through histone readers.
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Nat Struct Mol Biol,
19,
1218-1227.
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S.Eustermann,
J.C.Yang,
M.J.Law,
R.Amos,
L.M.Chapman,
C.Jelinska,
D.Garrick,
D.Clynes,
R.J.Gibbons,
D.Rhodes,
D.R.Higgs,
and
D.Neuhaus
(2011).
Combinatorial readout of histone H3 modifications specifies localization of ATRX to heterochromatin.
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Nat Struct Mol Biol,
18,
777-782.
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PDB code:
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S.Iwase,
B.Xiang,
S.Ghosh,
T.Ren,
P.W.Lewis,
J.C.Cochrane,
C.D.Allis,
D.J.Picketts,
D.J.Patel,
H.Li,
and
Y.Shi
(2011).
ATRX ADD domain links an atypical histone methylation recognition mechanism to human mental-retardation syndrome.
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Nat Struct Mol Biol,
18,
769-776.
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PDB codes:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
