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| | <StructureSection load='6ycs' size='340' side='right'caption='[[6ycs]], [[Resolution|resolution]] 3.05Å' scene=''> | | <StructureSection load='6ycs' size='340' side='right'caption='[[6ycs]], [[Resolution|resolution]] 3.05Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6ycs]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YCS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YCS FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6ycs]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YCS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YCS FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.05Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AS:2-DEOXY-ADENOSINE+-5-THIO-MONOPHOSPHATE'>AS</scene>, <scene name='pdbligand=GS:GUANOSINE-5-THIO-MONOPHOSPHATE'>GS</scene>, <scene name='pdbligand=OKN:'>OKN</scene>, <scene name='pdbligand=OKQ:'>OKQ</scene>, <scene name='pdbligand=OKT:'>OKT</scene>, <scene name='pdbligand=PST:THYMIDINE-5-THIOPHOSPHATE'>PST</scene>, <scene name='pdbligand=RFJ:'>RFJ</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AS:2-DEOXY-ADENOSINE+-5-THIO-MONOPHOSPHATE'>AS</scene>, <scene name='pdbligand=GS:GUANOSINE-5-THIO-MONOPHOSPHATE'>GS</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OKN:5-methyl-2-deoxycytidine-5-phosphorothioate'>OKN</scene>, <scene name='pdbligand=OKQ:2-O-methylcytidine-5-phosphorothioate'>OKQ</scene>, <scene name='pdbligand=OKT:2-O-methyluridine-5-phosphorothioate'>OKT</scene>, <scene name='pdbligand=PPS:3-PHOSPHATE-ADENOSINE-5-PHOSPHATE+SULFATE'>PPS</scene>, <scene name='pdbligand=PST:THYMIDINE-5-THIOPHOSPHATE'>PST</scene>, <scene name='pdbligand=RFJ:2-O-methyl-5-O-thiophosphonoguanosine'>RFJ</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PC4, SUB1, hCG_1781938 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=6ycs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ycs OCA], [https://pdbe.org/6ycs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ycs RCSB], [https://www.ebi.ac.uk/pdbsum/6ycs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ycs ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6ycs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ycs OCA], [http://pdbe.org/6ycs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ycs RCSB], [http://www.ebi.ac.uk/pdbsum/6ycs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ycs ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/TCP4_HUMAN TCP4_HUMAN] General coactivator that functions cooperatively with TAFs and mediates functional interactions between upstream activators and the general transcriptional machinery. May be involved in stabilizing the multiprotein transcription complex. Binds single-stranded DNA. Also binds, in vitro, non-specifically to double-stranded DNA (ds DNA).<ref>PMID:8062392</ref> <ref>PMID:8062391</ref> <ref>PMID:7628453</ref> <ref>PMID:9482861</ref> <ref>PMID:16689930</ref> <ref>PMID:9360603</ref> <ref>PMID:16605275</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Human]] | + | [[Category: Homo sapiens]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Anderson, B]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Crooke, S T]] | + | [[Category: Anderson B]] |
| - | [[Category: Hyjek-Skladanowska, M]] | + | [[Category: Crooke ST]] |
| - | [[Category: Liang, X]] | + | [[Category: Hyjek-Skladanowska M]] |
| - | [[Category: Napiorkowska, A]] | + | [[Category: Liang X]] |
| - | [[Category: Nowotny, M]] | + | [[Category: Napiorkowska A]] |
| - | [[Category: Seth, P P]] | + | [[Category: Nowotny M]] |
| - | [[Category: Tanowitz, M]] | + | [[Category: Seth PP]] |
| - | [[Category: Vickers, T A]] | + | [[Category: Tanowitz M]] |
| - | [[Category: 2'-o-methyl]]
| + | [[Category: Vickers TA]] |
| - | [[Category: Aso]]
| + | |
| - | [[Category: Dna binding]]
| + | |
| - | [[Category: Phosphorothioate dna]]
| + | |
| - | [[Category: Transcription]]
| + | |
| Structural highlights
6ycs is a 6 chain structure with sequence from Homo sapiens and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 3.05Å |
| Ligands: | , , , , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
TCP4_HUMAN General coactivator that functions cooperatively with TAFs and mediates functional interactions between upstream activators and the general transcriptional machinery. May be involved in stabilizing the multiprotein transcription complex. Binds single-stranded DNA. Also binds, in vitro, non-specifically to double-stranded DNA (ds DNA).[1] [2] [3] [4] [5] [6] [7]
Publication Abstract from PubMed
The phosphorothioate backbone modification (PS) is one of the most widely used chemical modifications for enhancing the drug-like properties of nucleic acid-based drugs, including antisense oligonucleotides (ASOs). PS-modified nucleic acid therapeutics show improved metabolic stability from nuclease-mediated degradation and exhibit enhanced interactions with plasma, cell-surface, and intracellular proteins, which facilitates their tissue distribution and cellular uptake in animals. However, little is known about the structural basis of the interactions of PS nucleic acids with proteins. Here, we report a crystal structure of the DNA-binding domain of a model ASO-binding protein PC4, in complex with a full PS 2'-OMe DNA gapmer ASO. To our knowledge this is the first structure of a complex between a protein and fully PS nucleic acid. Each PC4 dimer comprises two DNA-binding interfaces. In the structure one interface binds the 5'-terminal 2'-OMe PS flank of the ASO, while the other interface binds the regular PS DNA central part in the opposite polarity. As a result, the ASO forms a hairpin-like structure. ASO binding also induces the formation of a dimer of dimers of PC4, which is stabilized by base pairing between homologous regions of the ASOs bound by each dimer of PC4. The protein interacts with the PS nucleic acid through a network of electrostatic and hydrophobic interactions, which provides insights into the origins for the enhanced affinity of PS for proteins. The importance of these contacts was further confirmed in a NanoBRET binding assay using a Nano luciferase tagged PC4 acting as the BRET donor, to a fluorescently conjugated ASO acting as the BRET acceptor. Overall, our results provide insights into the molecular forces that govern the interactions of PS ASOs with cellular proteins and provide a potential model for how these interactions can template protein-protein interactions causative of cellular toxicity.
Origins of the Increased Affinity of Phosphorothioate-Modified Therapeutic Nucleic Acids for Proteins.,Hyjek-Skladanowska M, Vickers TA, Napiorkowska A, Anderson BA, Tanowitz M, Crooke ST, Liang XH, Seth PP, Nowotny M J Am Chem Soc. 2020 Apr 22;142(16):7456-7468. doi: 10.1021/jacs.9b13524. Epub, 2020 Apr 10. PMID:32202774[8]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Kretzschmar M, Kaiser K, Lottspeich F, Meisterernst M. A novel mediator of class II gene transcription with homology to viral immediate-early transcriptional regulators. Cell. 1994 Aug 12;78(3):525-34. PMID:8062392
- ↑ Ge H, Roeder RG. Purification, cloning, and characterization of a human coactivator, PC4, that mediates transcriptional activation of class II genes. Cell. 1994 Aug 12;78(3):513-23. PMID:8062391
- ↑ Kaiser K, Stelzer G, Meisterernst M. The coactivator p15 (PC4) initiates transcriptional activation during TFIIA-TFIID-promoter complex formation. EMBO J. 1995 Jul 17;14(14):3520-7. PMID:7628453
- ↑ Malik S, Guermah M, Roeder RG. A dynamic model for PC4 coactivator function in RNA polymerase II transcription. Proc Natl Acad Sci U S A. 1998 Mar 3;95(5):2192-7. PMID:9482861
- ↑ Jonker HR, Wechselberger RW, Pinkse M, Kaptein R, Folkers GE. Gradual phosphorylation regulates PC4 coactivator function. FEBS J. 2006 Apr;273(7):1430-44. PMID:16689930 doi:http://dx.doi.org/10.1111/j.1742-4658.2006.05165.x
- ↑ Brandsen J, Werten S, van der Vliet PC, Meisterernst M, Kroon J, Gros P. C-terminal domain of transcription cofactor PC4 reveals dimeric ssDNA binding site. Nat Struct Biol. 1997 Nov;4(11):900-3. PMID:9360603
- ↑ Jonker HR, Wechselberger RW, Boelens R, Kaptein R, Folkers GE. The intrinsically unstructured domain of PC4 modulates the activity of the structured core through inter- and intramolecular interactions. Biochemistry. 2006 Apr 18;45(15):5067-81. PMID:16605275 doi:http://dx.doi.org/10.1021/bi052531b
- ↑ Hyjek-Skladanowska M, Vickers TA, Napiorkowska A, Anderson BA, Tanowitz M, Crooke ST, Liang XH, Seth PP, Nowotny M. Origins of the Increased Affinity of Phosphorothioate-Modified Therapeutic Nucleic Acids for Proteins. J Am Chem Soc. 2020 Apr 22;142(16):7456-7468. doi: 10.1021/jacs.9b13524. Epub, 2020 Apr 10. PMID:32202774 doi:http://dx.doi.org/10.1021/jacs.9b13524
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