PDBsum entry 3jvm

Signaling protein

PDB id: 3jvm

Contents

Protein chain

116 a.a. *

Ligands

BME ×2

EDO ×2

Waters ×223

* Residue conservation analysis

PDB id:

3jvm

Name:

Signaling protein

Title:

Crystal structure of bromodomain 2 of mouse brd4

Structure:

Bromodomain-containing protein 4. Chain: a. Fragment: bromodomain 2, unp residues 349-464. Synonym: mitotic chromosome-associated protein, mcap. Engineered: yes

Source:

Mus musculus. Mouse. Organism_taxid: 10090. Gene: brd4. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.20Å R-factor: 0.117 R-free: 0.151

Authors:

F.Vollmuth,W.Blankenfeldt,M.Geyer

Key ref:

F.Vollmuth et al. (2009). Structures of the dual bromodomains of the P-TEFb activating protein Brd4 at atomic resolution. J Biol Chem, 284, 36547-36556. PubMed id: 19828451 DOI: 10.1074/jbc.M109.033712

Date:

17-Sep-09 Release date: 13-Oct-09

Protein chain

Q9ESU6  (BRD4_MOUSE) -  Bromodomain-containing protein 4 from Mus musculus

Seq: 1400 a.a.

Struc: 116 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1074/jbc.M109.033712

J Biol Chem 284:36547-36556 (2009)

PubMed id: 19828451

Structures of the dual bromodomains of the P-TEFb activating protein Brd4 at atomic resolution.

F.Vollmuth, W.Blankenfeldt, M.Geyer.

ABSTRACT

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.

Selected figure(s)

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).

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.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 36547-36556) copyright 2009.

Figures were selected by the author.