Human Poly(ADP-Ribose) Polymerase15

Target ID:

PARP15A

Aliases:

BAL3FLJ40196FLJ40597MGC126750MGC126752PARP15

Deposition Date:

Tuesday 11th December 2007

Families:

Poly ADP-ribose polymerase

Related Diseases:

Cancer

Structure type:

apo

Download Coordinates:

3BLJ

Authors:

T.KARLBERG,L.LEHTIO,C.H.ARROWSMITH,H.BERGLUND,R.D.BUSAM,R.COLLINS,L.G.DAHLGREN,A.EDWARDS,S.FLODIN,A.FLORES,S.GRASLUND,M.HAMMARSTROM,I.JOHANSSON,A.KALLAS,T.KOTENYOVA,M.MOCHE,M.E.NILSSON,P.NORDLUND,T.NYMAN,C.PERSSON,J.SAGEMARK,L.SVENSSON,A.G.THORSELL,L.TRESAUGUES,S.VAN DEN BERG,M.WELIN,J.WEIGELT

Site:

Stockholm

ICM Datapack:

ICM Datapack

3BLJ

tabs

Structure Details

Poly(ADP-ribose) polymerases (PARPs) are enzymes that use NAD+ as a substrate to add poly(ADP)ribose (PAR) to other proteins or themselves, leading to a changed three-dimensional and electrostatic surface of the modified proteins. The PARP family consists of 17 members that all contain a catalytic PARP domain and additional specificity domains. PAR has been shown to be linked to transcriptional regulation, genome organization and DNA-repair. The founding member, PARP-1 is triggered by DNA breaks and its activation results in the recruitment of the DNA repair machinery thus initiating a cellular response to DNA-damage. Several PARP-specific inhibitors have been developed that target the NAD-binding site and inhibit the activity of PARP-1 (and/or PARP-2) and are effective against inflammation, neurodegenerative and vascular diseases. More importantly, several PARP-inhibitors that are in clinical trials are shown to enhance the activity of anti-proliferative agents in cancer therapy and are specifically shown to be efficient in killing tumor cells that lack the tumor suppressor BRCA2.

PARP-15 or BAL-3 (B-aggressive lymphoma) belongs to the sub-class of MACRO-PARPs. In addition to a catalytic PARP domain these proteins have one to three MACRO-domains in their N-terminal part. MACRO-PARPs are thought to be transcription cofactors. Here, the crystal structure of the catalytic PARP domain is presented at 2.2 Å resolution. In PARP-15 the catalytic domain is smaller than in other PARPs e.g. PARP-1 and -3 and an α-helical regulatory domain is missing in the presented structure. However, in PARP-15 the catalytic glutamate has been replaced by a leucine. The protein's fold is comprised of two central β-sheets consisting of five and four strands. The β-sheets are surrounded by α-helices and loops.

Materials and Methods

PARP15

PDB:3BLJ

Revision

Revision Type:created
Revised by:created
Revision Date:created
Entry Clone Accession:BC101701
Entry Clone Source:Mammalian Gene Collection
SGC Clone Accession:
Tag:N-terminal hexahistidine tag with integrated TEV protease cleavage site: mhhhhhhssgvdlgtenlyfq*sm
Host:E.coli BL21(DE3) R3 pRARE, where R3 denotes a derivative of BL21(DE3) resistant to a strain of T1 bacteriophage (SGC Oxford) and the pRARE plasmid originating from the Rosetta strain (Novagen) supplies tRNAs for rare codons.

Construct

Prelude:
Sequence:mhhhhhhssgvdlgtenlyfq*smNLPEHWTDMNHQLFCMVQLEPGQSEYNTIKDKFTRTCSSYAIEKIERIQNAFLWQSYQVKKRQMDIKNDHKNNERLLFHGTDADSVPYVNQHGFNRSCAGKNAVSYGKGTYFAVDASYSAKDTYSKPDSNGRKHMYVVRVLTGVFTKGRAGLVTPPPKNPHNPTDLFDSVTNNTRSPKLFVVFFDNQAYPEYLITFTA
Vector:pNIC-Bsa4

Growth

Medium:
Antibiotics:
Procedure:Cells from a glycerol stock were grown in 60 ml TB supplemented with 8 g/l glycerol, 100 µg/ml kanamycin and 34 µg/ml chloramphenicol at 30 ºC overnight. The overnight culture was used to inoculate 3 x 1.5 l TB supplemented with 8 g/l glycerol, 50 µg/ml kanamycin and approximately 200 µl PPG P2,000 81380 anti-foam solution (Fluka). The culture was grown in a LEX bioreactor system (Harbinger Biotechnology) at 37 ºC until OD600 reached ~2. The bottle was down-tempered to 18 ºC over a period of 1 hour before target expression was induced by addition of 0.5 mM IPTG. Expression was allowed to continue overnight and cells were harvested the following morning by centrifugation (4,000 x g, 10 min, 4 ºC). The resulting cell pellet (65.1 g wet cell weight) was resuspended in lysis buffer (3 ml/g cell pellet), supplemented with 6000 U Benzonase (Merck) and three tablets of Complete EDTA-free protease inhibitor (Roche Applied Science). The cell suspension was stored at -80 ºC.

Purification

Procedure

Columns
IMAC 1: Ni-charged 5 ml HisTrap HP (GE Healthcare)
Desalting column: HiPrep 26/10 desalting (GE Healthcare)
IMAC 2: Ni-charged 1 ml HiTrap Chelating HP (GE Healthcare)
Gel filtration column: HiLoad 16/60 Superdex 75 Prep Grade (GE Healthcare)

Procedure
Purification of the protein was performed as a four step process on an ÄKTAxpress system (GE Healthcare). Prior to purification, columns were equilibrated with IMAC wash1 buffer (IMAC columns) and gel filtration buffer (gel filtration and desalting column), respectively. The filtered lysate was loaded onto the Ni-charged HisTrap column and washed with IMAC wash1 buffer followed by IMAC wash3 buffer. Bound protein was eluted from the IMAC column with IMAC elution buffer and automatically loaded onto the desalting column. The next morning fractions containing the target protein were pooled and loaded onto the Ni-charged HiTrap Chelating column. The protein was washed with IMAC wash1 buffer followed by IMAC wash2 buffer. Bound protein was eluted from the IMAC column with IMAC elution buffer and automatically loaded onto the gel filtration column. Fractions containing the target protein were pooled and fresh TCEP was added to a final concentration of 2 mM. The protein was subsequently concentrated using an Amicon Ultra-15 centrifugal filter device, 10,000 NMWL (Millipore) to 32.45 mg/ml in a volume of 1.1 ml. The identity of the protein was confirmed by mass spectrometry.

Extraction

Procedure
The cell suspension was quickly thawed in water. Cells were disrupted by sonication (Vibra-Cell, Sonics) at 80% amplitude for 3 min effective time (pulsed 4s on, 4s off) and cell debris was removed by centrifugation (49,100 x g, 20 min, 4 ºC). The supernatant was decanted and filtered through a 0.45 µm flask filter.
Concentration:
Ligand
MassSpec:
Crystallization:Crystals were obtained by the sitting drop vapour diffusion method in a 96-well plate. 0.1 µl protein solution (32.4 mg/ml) was mixed with 0.2 µl of well solution consisting of 0.2 M ammonium chloride and 20% (w/v) PEG 3350. The plate was incubated at 20 ºC and long plate shaped crystals appeared within 14 days. The crystals were quickly transferred to a cryo solution consisting of well solution complemented with 20% glycerol and 0.3 M NaCl, and flash frozen in liquid nitrogen.
NMR Spectroscopy:
Data Collection:Diffraction data to 2.2 Å resolution was collected at MAX-lab beamline I911-3.
Data Processing:The structure was solved by molecular replacement using PARP-12 as template (PDB: 2PQF). The space group was P212121 with cell dimensions a=45.21 Å b=68.12 Å c=158.28 Å. Two monomers were located in the asymmetric unit. Automatic model building using Arp/warp was performed; Refmac5 was used for refinement and Coot for model building. Data in the interval 20.0-2.20 Å resolution was used and at the end of the refinement the R values were: R=18.25% and Rfree=24.34%. Coordinates for the crystal structure were deposited in the Protein Data Bank, accession code 3BLJ.

References

Schreiber, V. et al., (2006). Poly(ADP-ribose): novel functions for an old molecule. Nature Rev. Mol. Cell Biol. 7, 517-528.
Diefenbach, J. and Bürkle, A. (2005). Introduction to Poly(ADP-ribose) metabolism. Cell Mol. Life. Sci. 62, 721-730.