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| - | [[Image:2riq.jpg|left|200px]]<br /><applet load="2riq" size="350" color="white" frame="true" align="right" spinBox="true" | |
| - | caption="2riq, resolution 1.70Å" /> | |
| - | '''Crystal Structure of the Third Zinc-binding domain of human PARP-1'''<br /> | |
| | | | |
| - | ==Overview== | + | ==Crystal Structure of the Third Zinc-binding domain of human PARP-1== |
| - | PARP-1 is a chromatin-associated enzyme with multiple cellular functions, including DNA repair, transcriptional regulation, and cell signaling., PARP-1 has a modular architecture with six independent domains comprising, the 113 kDa polypeptide. Two zinc-finger domains at the N-terminus of, PARP-1 bind to DNA and thereby activate the catalytic domain situated at, the C-terminus of the enzyme. The tight coupling of DNA binding and, catalytic activities is critical to the cellular regulation of PARP-1, function, however, the mechanism for coordinating these activities remains, an unsolved problem. Here, we demonstrate using spectroscopic and, crystallographic analysis that human PARP-1 has a third zinc-binding, domain. Biochemical mutagenesis and deletion analysis indicate that this, region mediates inter-domain contacts important for DNA-dependent enzyme, activation. The crystal structure of the third zinc-binding domain reveals, a zinc ribbon fold and suggests conserved residues that could form, inter-domain contacts. The new zinc-binding domain self-associates in the, crystal lattice to form a homodimer with a head-to-tail arrangement. The, structure of the homodimer provides a scaffold for assembling the, activated state of PARP-1 and suggests a mechanism for coupling the DNA, binding and catalytic functions of PARP-1.
| + | <StructureSection load='2riq' size='340' side='right'caption='[[2riq]], [[Resolution|resolution]] 1.70Å' scene=''> |
| | + | == Structural highlights == |
| | + | <table><tr><td colspan='2'>[[2riq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RIQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RIQ FirstGlance]. <br> |
| | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7Å</td></tr> |
| | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EOH:ETHANOL'>EOH</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2riq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2riq OCA], [https://pdbe.org/2riq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2riq RCSB], [https://www.ebi.ac.uk/pdbsum/2riq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2riq ProSAT]</span></td></tr> |
| | + | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/PARP1_HUMAN PARP1_HUMAN] Involved in the base excision repair (BER) pathway, by catalyzing the poly(ADP-ribosyl)ation of a limited number of acceptor proteins involved in chromatin architecture and in DNA metabolism. This modification follows DNA damages and appears as an obligatory step in a detection/signaling pathway leading to the reparation of DNA strand breaks. Mediates the poly(ADP-ribosyl)ation of APLF and CHFR. Positively regulates the transcription of MTUS1 and negatively regulates the transcription of MTUS2/TIP150. With EEF1A1 and TXK, forms a complex that acts as a T-helper 1 (Th1) cell-specific transcription factor and binds the promoter of IFN-gamma to directly regulate its transcription, and is thus involved importantly in Th1 cytokine production.<ref>PMID:17177976</ref> <ref>PMID:18172500</ref> <ref>PMID:19344625</ref> <ref>PMID:19661379</ref> |
| | + | == Evolutionary Conservation == |
| | + | [[Image:Consurf_key_small.gif|200px|right]] |
| | + | Check<jmol> |
| | + | <jmolCheckbox> |
| | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ri/2riq_consurf.spt"</scriptWhenChecked> |
| | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | + | <text>to colour the structure by Evolutionary Conservation</text> |
| | + | </jmolCheckbox> |
| | + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2riq ConSurf]. |
| | + | <div style="clear:both"></div> |
| | | | |
| - | ==About this Structure== | + | ==See Also== |
| - | 2RIQ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=ZN:'>ZN</scene>, <scene name='pdbligand=EOH:'>EOH</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/NAD(+)_ADP-ribosyltransferase NAD(+) ADP-ribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.30 2.4.2.30] Known structural/functional Sites: <scene name='pdbsite=AC1:Zn+Binding+Site+For+Residue+A+1'>AC1</scene>, <scene name='pdbsite=AC2:Eoh+Binding+Site+For+Residue+A+2'>AC2</scene>, <scene name='pdbsite=AC3:Gol+Binding+Site+For+Residue+A+3'>AC3</scene>, <scene name='pdbsite=AC4:Gol+Binding+Site+For+Residue+A+4'>AC4</scene> and <scene name='pdbsite=AC5:Gol+Binding+Site+For+Residue+A+5'>AC5</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RIQ OCA].
| + | *[[Poly(ADP-ribose) polymerase 3D structures|Poly(ADP-ribose) polymerase 3D structures]] |
| - | | + | == References == |
| - | ==Reference==
| + | <references/> |
| - | A third zinc-binding domain of human PARP-1 coordinates DNA-dependent enzyme activation., Langelier MF, Servent KM, Rogers EE, Pascal JM, J Biol Chem. 2007 Nov 30;. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=18055453 18055453]
| + | __TOC__ |
| | + | </StructureSection> |
| | [[Category: Homo sapiens]] | | [[Category: Homo sapiens]] |
| - | [[Category: NAD(+) ADP-ribosyltransferase]] | + | [[Category: Large Structures]] |
| - | [[Category: Single protein]]
| + | [[Category: Langelier MF]] |
| - | [[Category: Langelier, M.F.]] | + | [[Category: Pascal JM]] |
| - | [[Category: Pascal, J.M.]] | + | [[Category: Servent KM]] |
| - | [[Category: Servent, K.M.]] | + | |
| - | [[Category: EOH]]
| + | |
| - | [[Category: GOL]]
| + | |
| - | [[Category: ZN]]
| + | |
| - | [[Category: adp-ribosylation]]
| + | |
| - | [[Category: dna damage]]
| + | |
| - | [[Category: dna repair]]
| + | |
| - | [[Category: dna-binding]]
| + | |
| - | [[Category: glycosyltransferase]]
| + | |
| - | [[Category: metal-binding]]
| + | |
| - | [[Category: nad]]
| + | |
| - | [[Category: nucleus]]
| + | |
| - | [[Category: phosphorylation]]
| + | |
| - | [[Category: polymorphism]]
| + | |
| - | [[Category: transferase]]
| + | |
| - | [[Category: zinc]]
| + | |
| - | [[Category: zinc-finger]]
| + | |
| - | [[Category: zn finger]]
| + | |
| - | [[Category: zn ribbon]]
| + | |
| - | [[Category: zn-binding domain]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 13 08:13:30 2008''
| + | |
| Structural highlights
Function
PARP1_HUMAN Involved in the base excision repair (BER) pathway, by catalyzing the poly(ADP-ribosyl)ation of a limited number of acceptor proteins involved in chromatin architecture and in DNA metabolism. This modification follows DNA damages and appears as an obligatory step in a detection/signaling pathway leading to the reparation of DNA strand breaks. Mediates the poly(ADP-ribosyl)ation of APLF and CHFR. Positively regulates the transcription of MTUS1 and negatively regulates the transcription of MTUS2/TIP150. With EEF1A1 and TXK, forms a complex that acts as a T-helper 1 (Th1) cell-specific transcription factor and binds the promoter of IFN-gamma to directly regulate its transcription, and is thus involved importantly in Th1 cytokine production.[1] [2] [3] [4]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
See Also
References
- ↑ Maruyama T, Nara K, Yoshikawa H, Suzuki N. Txk, a member of the non-receptor tyrosine kinase of the Tec family, forms a complex with poly(ADP-ribose) polymerase 1 and elongation factor 1alpha and regulates interferon-gamma gene transcription in Th1 cells. Clin Exp Immunol. 2007 Jan;147(1):164-75. PMID:17177976 doi:10.1111/j.1365-2249.2006.03249.x
- ↑ Ahel I, Ahel D, Matsusaka T, Clark AJ, Pines J, Boulton SJ, West SC. Poly(ADP-ribose)-binding zinc finger motifs in DNA repair/checkpoint proteins. Nature. 2008 Jan 3;451(7174):81-5. doi: 10.1038/nature06420. PMID:18172500 doi:10.1038/nature06420
- ↑ Reinemund J, Seidel K, Steckelings UM, Zaade D, Klare S, Rompe F, Katerbaum M, Schacherl J, Li Y, Menk M, Schefe JH, Goldin-Lang P, Szabo C, Olah G, Unger T, Funke-Kaiser H. Poly(ADP-ribose) polymerase-1 (PARP-1) transcriptionally regulates angiotensin AT2 receptor (AT2R) and AT2R binding protein (ATBP) genes. Biochem Pharmacol. 2009 Jun 15;77(12):1795-805. doi: 10.1016/j.bcp.2009.02.025., Epub 2009 Mar 19. PMID:19344625 doi:10.1016/j.bcp.2009.02.025
- ↑ Ahel D, Horejsi Z, Wiechens N, Polo SE, Garcia-Wilson E, Ahel I, Flynn H, Skehel M, West SC, Jackson SP, Owen-Hughes T, Boulton SJ. Poly(ADP-ribose)-dependent regulation of DNA repair by the chromatin remodeling enzyme ALC1. Science. 2009 Sep 4;325(5945):1240-3. doi: 10.1126/science.1177321. Epub 2009 Aug, 6. PMID:19661379 doi:10.1126/science.1177321
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