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5jh5

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Revision as of 07:48, 10 June 2020

Structural Basis for the Hierarchical Assembly of the Core of PRC1.1

Structural highlights

5jh5 is a 4 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
NonStd Res:
Gene:	KDM2B, CXXC2, FBL10, FBXL10, JHDM1B, PCCX2 (HUMAN), SKP1, EMC19, OCP2, SKP1A, TCEB1L (HUMAN), PCGF1, NSPC1, RNF68 (HUMAN), BCORL1 (HUMAN)
Activity:	[Histone_H3-lysine-36_demethylase [Histone H3]-lysine-36 demethylase], with EC number 1.14.11.27
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[BCORL_HUMAN] Transcriptional corepressor. May specifically inhibit gene expression when recruited to promoter regions by sequence specific DNA-binding proteins such as BCL6. This repression may be mediated at least in part by histone deacetylase activities which can associate with this corepressor.^[1] [KDM2B_HUMAN] Histone demethylase that demethylates 'Lys-4' and 'Lys-36' of histone H3, thereby playing a central role in histone code. Preferentially demethylates trimethylated H3 'Lys-4' and dimethylated H3 'Lys-36' residue while it has weak or no activity for mono- and tri-methylated H3 'Lys-36'. Preferentially binds the transcribed region of ribosomal RNA and represses the transcription of ribosomal RNA genes which inhibits cell growth and proliferation. May also serve as a substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex.^[2] ^[3] [PCGF1_HUMAN] Component of the Polycomb group (PcG) multiprotein BCOR complex, a complex required to maintain the transcriptionally repressive state of some genes, such as BCL6 and the cyclin-dependent kinase inhibitor, CDKN1A. Transcriptional repressor that may be targeted to the DNA by BCL6; this transcription repressor activity may be related to PKC signaling pathway. Represses CDKN1A expression by binding to its promoter, and this repression is dependent on the retinoic acid response element (RARE element). Promotes cell cycle progression and enhances cell proliferation as well. May have a positive role in tumor cell growth by down-regulating CDKN1A. Component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones; it mediates monoubiquitination of histone H2A 'Lys-119', rendering chromatin heritably changed in its expressibility.^[4] ^[5] ^[6] [SKP1_HUMAN] Essential component of the SCF (SKP1-CUL1-F-box protein) ubiquitin ligase complex, which mediates the ubiquitination of proteins involved in cell cycle progression, signal transduction and transcription. In the SCF complex, serves as an adapter that links the F-box protein to CUL1. SCF(BTRC) mediates the ubiquitination of NFKBIA at 'Lys-21' and 'Lys-22'; the degradation frees the associated NFKB1-RELA dimer to translocate into the nucleus and to activate transcription. SCF(Cyclin F) directs ubiquitination of CP110.^[7] ^[8]

Publication Abstract from PubMed

KDM2B recruits H2A-ubiquitinating activity of a non-canonical Polycomb Repression Complex 1 (PRC1.1) to CpG islands, facilitating gene repression. We investigated the molecular basis of recruitment using in vitro assembly assays to identify minimal components, subcomplexes, and domains required for recruitment. A minimal four-component PRC1.1 complex can be assembled by combining two separately isolated subcomplexes: the DNA-binding KDM2B/SKP1 heterodimer and the heterodimer of BCORL1 and PCGF1, a core component of PRC1.1. The crystal structure of the KDM2B/SKP1/BCORL1/PCGF1 complex illustrates the crucial role played by the PCGF1/BCORL1 heterodimer. The BCORL1 PUFD domain positions residues preceding the RAWUL domain of PCGF1 to create an extended interface for interaction with KDM2B, which is unique to the PCGF1-containing PRC1.1 complex. The structure also suggests how KDM2B might simultaneously function in PRC1.1 and an SCF ubiquitin ligase complex and the possible molecular consequences of BCOR PUFD internal tandem duplications found in pediatric kidney and brain tumors.

KDM2B Recruitment of the Polycomb Group Complex, PRC1.1, Requires Cooperation between PCGF1 and BCORL1.,Wong SJ, Gearhart MD, Taylor AB, Nanyes DR, Ha DJ, Robinson AK, Artigas JA, Lee OJ, Demeler B, Hart PJ, Bardwell VJ, Kim CA Structure. 2016 Aug 23. pii: S0969-2126(16)30222-2. doi:, 10.1016/j.str.2016.07.011. PMID:27568929^[9]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Pagan JK, Arnold J, Hanchard KJ, Kumar R, Bruno T, Jones MJ, Richard DJ, Forrest A, Spurdle A, Verdin E, Crossley M, Fanciulli M, Chenevix-Trench G, Young DB, Khanna KK. A novel corepressor, BCoR-L1, represses transcription through an interaction with CtBP. J Biol Chem. 2007 May 18;282(20):15248-57. Epub 2007 Mar 22. PMID:17379597 doi:10.1074/jbc.M700246200
↑ Tsukada Y, Fang J, Erdjument-Bromage H, Warren ME, Borchers CH, Tempst P, Zhang Y. Histone demethylation by a family of JmjC domain-containing proteins. Nature. 2006 Feb 16;439(7078):811-6. Epub 2005 Dec 18. PMID:16362057 doi:http://dx.doi.org/nature04433
↑ Frescas D, Guardavaccaro D, Bassermann F, Koyama-Nasu R, Pagano M. JHDM1B/FBXL10 is a nucleolar protein that represses transcription of ribosomal RNA genes. Nature. 2007 Nov 8;450(7167):309-13. PMID:17994099 doi:http://dx.doi.org/nature06255
↑ Gong Y, Wang X, Liu J, Shi L, Yin B, Peng X, Qiang B, Yuan J. NSPc1, a mainly nuclear localized protein of novel PcG family members, has a transcription repression activity related to its PKC phosphorylation site at S183. FEBS Lett. 2005 Jan 3;579(1):115-21. PMID:15620699 doi:10.1016/j.febslet.2004.11.056
↑ Gearhart MD, Corcoran CM, Wamstad JA, Bardwell VJ. Polycomb group and SCF ubiquitin ligases are found in a novel BCOR complex that is recruited to BCL6 targets. Mol Cell Biol. 2006 Sep;26(18):6880-9. PMID:16943429 doi:26/18/6880
↑ Gong Y, Yue J, Wu X, Wang X, Wen J, Lu L, Peng X, Qiang B, Yuan J. NSPc1 is a cell growth regulator that acts as a transcriptional repressor of p21Waf1/Cip1 via the RARE element. Nucleic Acids Res. 2006;34(21):6158-69. Epub 2006 Nov 6. PMID:17088287 doi:gkl834
↑ Hao B, Zheng N, Schulman BA, Wu G, Miller JJ, Pagano M, Pavletich NP. Structural basis of the Cks1-dependent recognition of p27(Kip1) by the SCF(Skp2) ubiquitin ligase. Mol Cell. 2005 Oct 7;20(1):9-19. PMID:16209941 doi:10.1016/j.molcel.2005.09.003
↑ Li Y, Hao B. Structural basis of dimerization-dependent ubiquitination by the SCF(Fbx4) ubiquitin ligase. J Biol Chem. 2010 Apr 30;285(18):13896-906. Epub 2010 Feb 24. PMID:20181953 doi:10.1074/jbc.M110.111518
↑ Wong SJ, Gearhart MD, Taylor AB, Nanyes DR, Ha DJ, Robinson AK, Artigas JA, Lee OJ, Demeler B, Hart PJ, Bardwell VJ, Kim CA. KDM2B Recruitment of the Polycomb Group Complex, PRC1.1, Requires Cooperation between PCGF1 and BCORL1. Structure. 2016 Aug 23. pii: S0969-2126(16)30222-2. doi:, 10.1016/j.str.2016.07.011. PMID:27568929 doi:http://dx.doi.org/10.1016/j.str.2016.07.011

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5jh5"

@@ Line 1: / Line 1: @@
 ==Structural Basis for the Hierarchical Assembly of the Core of PRC1.1==
-<StructureSection load='5jh5' size='340' side='right' caption='[[5jh5]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
+<StructureSection load='5jh5' size='340' side='right'caption='[[5jh5]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5jh5]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JH5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JH5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5jh5]] is a 4 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=5JH5 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5JH5 FirstGlance]. <br>
 </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">KDM2B, CXXC2, FBL10, FBXL10, JHDM1B, PCCX2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), SKP1, EMC19, OCP2, SKP1A, TCEB1L ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), PCGF1, NSPC1, RNF68 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), BCORL1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/[Histone_H3]-lysine-36_demethylase [Histone H3]-lysine-36 demethylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.27 1.14.11.27] </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=5jh5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jh5 OCA], [http://pdbe.org/5jh5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jh5 RCSB], [http://www.ebi.ac.uk/pdbsum/5jh5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jh5 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=5jh5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jh5 OCA], [http://pdbe.org/5jh5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jh5 RCSB], [http://www.ebi.ac.uk/pdbsum/5jh5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jh5 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 19: / Line 20: @@
 </div>
 <div class="pdbe-citations 5jh5" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Jumonji domain-containing protein 3D structures|Jumonji domain-containing protein 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Human]]
+[[Category: Large Structures]]
 [[Category: Hart, P J]]
 [[Category: Kim, C A]]

5jh5

From Proteopedia

Revision as of 07:48, 10 June 2020

Structural Basis for the Hierarchical Assembly of the Core of PRC1.1

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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