Human bromodomain containing protein 4 - domain 1

Target ID:

BRD4A

Aliases:

CAPHUNKIMCAP

Deposition Date:

Tuesday 6th February 2007

Families:

Bromodomain

Related Diseases:

CancerSignallingChromatin and epigenetics

Structure type:

apo

Download Coordinates:

2OSS

Authors:

P.FILIPPAKOPOULOS,T.KEATES,P.SAVITSKY,N.BURGESS,A.C.W.PIKE,E.UGOCHUKWU,F.VON DELFT,C.H.ARROWSMITH,A.EDWARDS,J.WEIGELT,M.SUNDSTROM,S.KNAPP,STRUCTURAL GENOMICS CONSORTIUM (SGC)

Site:

Oxford

ICM Datapack:

ICM Datapack

2OSS

tabs

Structure Details

BRD4 belongs to the BET subclass of proteins, which are distinguished by two N-terminal bromodomains and one ET (Extra Terminal) domain. Bromodomains are acetyl-lysine targeting modules commonly found in chromatin-modifying complexes. BET family members bind to mitotic chromosomes and regulate gene activity through cell cycle progression. Bromodomains in BRD4 bind to specific acetylated lysines in histones H3 and H4 and BRD4 has been isolated in complex with the replication factor complex (RFC). Mouse embryos izygous for BRD4 are non-viable due to an early post-implantation defect, suggesting that BRD4 is required for fundamental cellular processes. Disruption of BRD4 function in cell lines has been shown to inhibit progression to S phase.

In many virus-infected cells, the viral genome is similarly packaged into chromatin and chromatin targeting has been shown to be also critical for viral gene expression. BRD4 has been implicated in viral genome segregation and was found associated with E2, a protein encoded by human papillomaviruses (HPVs) and a regulator of the viral E6 oncoprotein. In addition, gene rearrangements of BRD4 have been detected in several aggressive carcinoma. Here we determined the structure of the first Bromodomain of BRD4 at 1.3 Ã… resolution.

Materials and Methods

BRD4 domain 1

PDB:2OSS

Revision

Revision Type:created
Revised by:created
Revision Date:created
Entry Clone Accession:NP_490597.1
Entry Clone Source:FivePrime
SGC Clone Accession:
Tag:Tag sequence: mhhhhhhssgvdlgtenlyfq*s(m) , TEV-cleavable (*) N-terminal his6 tag
Host:BL21 (DE3)

Construct

Prelude:
Sequence:mhhhhhhssgvdlgtenlyfqsmNPPPPE TSNPNKPKRQTNQLQYLLRVVLKTLWKHQ FAWPFQQPVDAVKLNLPDYYKIIKTPMDM GTIKKRLENNYYWNAQECIQDFNTMFTNC YIYNKPGDDIVLMAEALEKLFLQKINELP TEE
Vector:pNIC28-Bsa4

Growth

Medium:LB
Antibiotics:
Procedure:Grow starter cultures from freshly transformed colonies in 10 ml LB , 50 mg/ml kanamycin. This started culture was diluted 1:1000 in fresh media and was grown at 37°C to a OD600 of 0.4 and than transferred to 18°C. Expression was induced at an OD600 of 0.6 - 0.7 using 1 mM IPTG (final concentration). Cells were harvested after 4h by centrifugation (15min, 6500rpm on a JLA 8.100 rotor), transferred to 50-ml tubes, and frozen at -20°C.

Purification

Procedure
Column 1 : DE52/Ni-NTA
Procedure (Gravity feed chromatography): A DE52 column (10gr suspended in 100ml of 2.5M NaCl) was equilibrated with 100ml of Loading Buffer. A 5ml NiNTA column was equilibrated with 20ml of Loading Buffer. The lysed sample was applied to the DE-52 column and washed through with 50 ml loading buffer. The flow through was applied to the 5 ml Ni-NTA column which was washed with 2x10ml of wash buffer and eluted with elution buffer in 5 ml aliquots (Step elution using 50, 100, 150, 200 and 250 mM imidazole in the Elution Buffer).

Enzymatic treatment : Treated the IMAC elution(s) with TEV protease overnight.

Column 2: SEC (AKTA-prime)
Procedure (Gel Filtration): Fractions containing BRD4A collected from IMAC and treated with TEV protease overnight (identified by SDS PAGE) were concentrated to about 1.5ml and directly applied to a S75 16/60 column equilibrated in 10 mM Hepes pH 7.5, 100 m NaCl. The flow rate was 1ml/min and the pure protein eluted at 74-86min.

Concentration : The combined samples from the SEC column (identified by SDS PAGE) were concentrated using centricons with 10 kDa cut off.

Extraction

Procedure
The cell pellets (5 gr wet wt) were re-suspended in 50 ml extraction buffer containing a Protease Inhibitor Coctail tablet (Roche), and lysed in a high pressure cell disrupter. The supernatant was centrifuged for 45 minutes at 53k g in a JA 25.5 rotor.
Concentration:
Ligand
MassSpec:LC-ESI-MStof confirmed the correct mass of 15084 expected for this construct after TEV treatment.
Crystallization:Crystals were grown at 4°C in 150nl sitting drops mixing 75 nl of BRD4A (9 mg/ml in 10mM Hepes pH 7.5, 100mM NaCl ,10mM DTT) with 75 nl of a solution containing 0.2M NaNO3, 20% PEG3350 and 10% EtGly. Cryo protection was achieved by adding to the crystallization mix Ethylene Glycole (20% final w/v).
NMR Spectroscopy:
Data Collection:Resolution: 1.35 Å; X-ray source: Synchrotron SLS -X10, single wavelength.
Data Processing:

References

Abbate, E. A., Voitenleitner, C., and Botchan, M. R. (2006). Structure of the papillomavirus DNA-tethering complex E2:Brd4 and a peptide that ablates HPV chromosomal association. Mol Cell 24, 877-889.
French, C. A., Miyoshi, I., Aster, J. C., Kubonishi, I., Kroll, T. G., Dal Cin, P., Vargas, S. O., Perez-Atayde, A. R., and Fletcher, J. A. (2001). BRD4 bromodomain gene rearrangement in aggressive carcinoma with translocation t(15;19). Am J Pathol 159, 1987-1992.
Houzelstein, D., Bullock, S. L., Lynch, D. E., Grigorieva, E. F., Wilson, V. A., and Beddington, R. S. (2002). Growth and early postimplantation defects in mice deficient for the bromodomain-containing protein Brd4. Mol Cell Biol 22, 3794-3802.
Ilves, I., Maemets, K., Silla, T., Janikson, K., and Ustav, M. (2006). Brd4 is involved in multiple processes of the bovine papillomavirus type 1 life cycle. J Virol 80, 3660-3665.
Wu, S. Y., Lee, A. Y., Hou, S. Y., Kemper, J. K., Erdjument-Bromage, H., Tempst, P., and Chiang, C. M. (2006). Brd4 links chromatin targeting to HPV transcriptional silencing. Genes Dev 20, 2383-2396.
You, J., Srinivasan, V., Denis, G. V., Harrington, W. J., Jr., Ballestas, M. E., Kaye, K. M., and Howley, P. M. (2006). Kaposi's sarcoma-associated herpesvirus latency-associated nuclear antigen interacts with bromodomain protein Brd4 on host mitotic chromosomes. J Virol 80, 8909-8919.
Zhou, Q., and Yik, J. H. (2006). The Yin and Yang of P-TEFb regulation: implications for human immunodeficiency virus gene expression and global control of cell growth and differentiation. Microbiol Mol Biol Rev 70, 646-659.