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PDBsum entry 3jvm
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Signaling protein
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PDB id
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3jvm
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References listed in PDB file
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Key reference
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Title
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Structures of the dual bromodomains of the p-Tefb activating protein brd4 at atomic resolution.
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Authors
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F.Vollmuth,
W.Blankenfeldt,
M.Geyer.
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Ref.
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J Biol Chem, 2009,
284,
36547-36556.
[DOI no: ]
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PubMed id
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Abstract
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Brd4 is a member of the bromodomains and extra terminal domain (BET) family
proteins that recognize acetylated chromatin structures through their
bromodomains and act as transcriptional activators. Brd4 functions as an
associated factor and positive regulator of P-TEFb, a Cdk9-Cyclin T heterodimer
that stimulates transcriptional elongation by RNA polymerase II. Here, the
crystal structures of the two bromodomains of Brd4 (BD1 and BD2) were determined
at 1.5 and 1.2 A resolution, respectively. Complex formation of BD1 with a
histone H3 tail polypeptide encompassing residues 12-19 showed binding of the
Nz-acetylated lysine 14 to the conserved asparagine 140 of Brd4. In contrast, in
BD2 the N-terminal linker sequence was found to interact with the binding site
for acetylated lysines of the adjacent molecule to form continuous strings in
the crystal lattice. This assembly shows for the first time a different binding
ligand than acetylated lysine indicating that also other sequence compositions
may be able to form similar interaction networks. Isothermal titration
calorimetry revealed best binding of BD1 to H3 and of BD2 to H4 acetylated
lysine sequences, suggesting alternating histone recognition specificities.
Intriguingly, an acetylated lysine motif from Cyclin T1 bound similarly well to
BD2. While the structure of Brd2 BD1 suggested its dimer formation, both Brd4
bromodomains appeared monomeric in solution as shown by size exclusion
chromatography and mutational analyses.
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Figure 3.
Electrostatic surface potential of the two Brd4 bromodomains.
Displayed is the electrostatic surface potential from −15
k[B]T (red) to +15 k[B]T (blue) for BD1 (A) and BD2 (B). The
binding site for acetylated lysines is indicated by arrows.
Acidic residues on helices α[Z″] to α[A] and the BC loop
form negatively charged surfaces surrounding the interaction
cleft of both bromodomains (right panel).
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Figure 5.
Structural basis of H3-K(ac)14 binding to Brd4 BD1. A,
complex structure of the bromodomain 42–166 with the peptide
GGK(ac)A from H3 (green). B, hydrogen bonds between the H3
peptide and the essential asparagine Asn-140 in BD1 define the
interaction network. Several water molecules (colored red) in
the binding cavity of the bromodomain surround the acetyl moiety.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2009,
284,
36547-36556)
copyright 2009.
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