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| | ==Zinc fingers of KDM2B== | | ==Zinc fingers of KDM2B== |
| - | <StructureSection load='4o64' size='340' side='right' caption='[[4o64]], [[Resolution|resolution]] 2.13Å' scene=''> | + | <StructureSection load='4o64' size='340' side='right'caption='[[4o64]], [[Resolution|resolution]] 2.13Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4o64]] is a 3 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=4O64 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4O64 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4o64]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O64 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4O64 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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])</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=4o64 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o64 OCA], [https://pdbe.org/4o64 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4o64 RCSB], [https://www.ebi.ac.uk/pdbsum/4o64 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4o64 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=4o64 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o64 OCA], [http://pdbe.org/4o64 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4o64 RCSB], [http://www.ebi.ac.uk/pdbsum/4o64 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4o64 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/KDM2B_HUMAN 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.<ref>PMID:16362057</ref> <ref>PMID:17994099</ref> | + | [[https://www.uniprot.org/uniprot/KDM2B_HUMAN 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.<ref>PMID:16362057</ref> <ref>PMID:17994099</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 4o64" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 4o64" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Jumonji domain-containing protein 3D structures|Jumonji domain-containing protein 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Human]] | + | [[Category: Large Structures]] |
| | [[Category: Arrowsmith, C H]] | | [[Category: Arrowsmith, C H]] |
| | [[Category: Bountra, C]] | | [[Category: Bountra, C]] |
| Structural highlights
Function
[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.[1] [2]
Publication Abstract from PubMed
The CXXC domain, first identified as the reader of unmodified CpG dinucleotide, plays important roles in epigenetic regulation by targeting various activities to CpG islands. Here we systematically measured and compared the DNA-binding selectivities of all known human CXXC domains by different binding assays, and complemented the existing function-based classification of human CXXC domains with a classification based on their DNA selectivities. Through a series of crystal structures of CXXC domains with DNA ligands, we unravel the molecular mechanisms of how these CXXC domains, including single CXXC domains and tandem CXXC-PHD domains, recognize distinct DNA ligands, which further supports our classification of human CXXC domains and also provides insights into selective recruitment of chromatin modifiers to their respective targets via CXXC domains recognizing different genomic DNA sequences. Our study facilitates the understanding of the relationship between the DNA-binding specificities of the CXXC proteins and their biological functions.
DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants.,Xu C, Liu K, Lei M, Yang A, Li Y, Hughes TR, Min J Structure. 2017 Dec 16. pii: S0969-2126(17)30396-9. doi:, 10.1016/j.str.2017.11.022. PMID:29276034[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ 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
- ↑ Xu C, Liu K, Lei M, Yang A, Li Y, Hughes TR, Min J. DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants. Structure. 2017 Dec 16. pii: S0969-2126(17)30396-9. doi:, 10.1016/j.str.2017.11.022. PMID:29276034 doi:http://dx.doi.org/10.1016/j.str.2017.11.022
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