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| | ==Crystal structure of the BRD2-BD2 in complex with phenanthridinone== | | ==Crystal structure of the BRD2-BD2 in complex with phenanthridinone== |
| - | <StructureSection load='5xhk' size='340' side='right' caption='[[5xhk]], [[Resolution|resolution]] 1.28Å' scene=''> | + | <StructureSection load='5xhk' size='340' side='right'caption='[[5xhk]], [[Resolution|resolution]] 1.28Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5xhk]] is a 1 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=5XHK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XHK FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5xhk]] 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=5XHK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XHK FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2ME:METHOXYETHANE'>2ME</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LDR:PHENANTHRIDIN-6(5H)-ONE'>LDR</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]] 1.28Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5xhe|5xhe]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2ME:METHOXYETHANE'>2ME</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LDR:PHENANTHRIDIN-6(5H)-ONE'>LDR</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BRD2, KIAA9001, RING3 ([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=5xhk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xhk OCA], [https://pdbe.org/5xhk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xhk RCSB], [https://www.ebi.ac.uk/pdbsum/5xhk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xhk ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5xhk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xhk OCA], [http://pdbe.org/5xhk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xhk RCSB], [http://www.ebi.ac.uk/pdbsum/5xhk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xhk ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/BRD2_HUMAN BRD2_HUMAN]] May play a role in spermatogenesis or folliculogenesis (By similarity). Binds hyperacetylated chromatin and plays a role in the regulation of transcription, probably by chromatin remodeling. Regulates transcription of the CCND1 gene. Plays a role in nucleosome assembly.<ref>PMID:18406326</ref> | + | [https://www.uniprot.org/uniprot/BRD2_HUMAN BRD2_HUMAN] May play a role in spermatogenesis or folliculogenesis (By similarity). Binds hyperacetylated chromatin and plays a role in the regulation of transcription, probably by chromatin remodeling. Regulates transcription of the CCND1 gene. Plays a role in nucleosome assembly.<ref>PMID:18406326</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==See Also== | | ==See Also== |
| - | *[[Bromodomain-containing protein|Bromodomain-containing protein]] | + | *[[Bromodomain-containing protein 3D structures|Bromodomain-containing protein 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Human]] | + | [[Category: Homo sapiens]] |
| - | [[Category: Deshmukh, P]] | + | [[Category: Large Structures]] |
| - | [[Category: Mathur, S]] | + | [[Category: Deshmukh P]] |
| - | [[Category: Padmanabhan, B]] | + | [[Category: Mathur S]] |
| - | [[Category: Tripathi, S]] | + | [[Category: Padmanabhan B]] |
| - | [[Category: Bet family]]
| + | [[Category: Tripathi S]] |
| - | [[Category: Brd2]]
| + | |
| - | [[Category: Bromodomain]]
| + | |
| - | [[Category: Phenanthridinone]]
| + | |
| - | [[Category: Transcription]]
| + | |
| Structural highlights
Function
BRD2_HUMAN May play a role in spermatogenesis or folliculogenesis (By similarity). Binds hyperacetylated chromatin and plays a role in the regulation of transcription, probably by chromatin remodeling. Regulates transcription of the CCND1 gene. Plays a role in nucleosome assembly.[1]
Publication Abstract from PubMed
Bromodomain and extra-terminal family proteins recognize the acetylated histone code on chromatin and participate in downstream processes like DNA replication, modification, and repair. As part of epigenetic approaches, BRD2 and BRD4 were identified as putative targets, for the management of chronic diseases. We have recently reported the discovery of a new scaffold of the phenanthridinone-based inhibitor (L10) of the second bromodomain of BRD2 (BRD2-BD2). Here, we present the crystal structure of the BRD2-BD2, refined to 1.4 A resolution, in complex with beta-mercaptoethanol (a component of the protein buffer). The beta-mercaptoethanol covalently links to C425 of BD2 in the acetyl-lysine binding pocket, to form a modified cysteine mercaptoethanol (CME). The CME modification significantly hinders the entry of ligands into the BD2 binding pocket, suggesting that beta-mercaptoethanol should be removed during protein production process. Next, to confirm whether phenanthridionone scaffold is a new inhibitor family of BRD2-BD2, we have determined the crystal structure of BD2 in complex with 6(5H)-Phenanthridinone (a core moiety of L10), refined to 1.28 A resolution. It confirmed that the phenanthridinone molecule, unambiguously, binds to BD2. Moreover, we performed molecular docking and molecular dynamic studies on selected phenanthridinone analogs. The predicted L10 analogs are stable with essential hydrophobic and hydrophilic interactions with BD2 during molecular dynamic simulations. We propose that the predicted phenanthridinone analogs may be potential molecules for inhibiting the BD2 function of acetylated histone recognition.
Insights into the crystal structure of BRD2-BD2 - phenanthridinone complex and theoretical studies on phenanthridinone analogs.,Mathur S, Deshmukh P, Tripathi S, Marimuthu P, Padmanabhan B J Biomol Struct Dyn. 2017 Jul 31:1-19. doi: 10.1080/07391102.2017.1353441. PMID:28696179[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ LeRoy G, Rickards B, Flint SJ. The double bromodomain proteins Brd2 and Brd3 couple histone acetylation to transcription. Mol Cell. 2008 Apr 11;30(1):51-60. doi: 10.1016/j.molcel.2008.01.018. PMID:18406326 doi:10.1016/j.molcel.2008.01.018
- ↑ Mathur S, Deshmukh P, Tripathi S, Marimuthu P, Padmanabhan B. Insights into the crystal structure of BRD2-BD2 - phenanthridinone complex and theoretical studies on phenanthridinone analogs. J Biomol Struct Dyn. 2017 Jul 31:1-19. doi: 10.1080/07391102.2017.1353441. PMID:28696179 doi:http://dx.doi.org/10.1080/07391102.2017.1353441
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