5f5i: Difference between revisions

Revision as of 19:40, 30 December 2015

Crystal Structure of human JMJD2A complexed with KDOOA011340

Structural highlights

5f5i is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	5V1, NI, SO4, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[KDM4A_HUMAN] Histone demethylase that specifically demethylates 'Lys-9' and 'Lys-36' residues of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27' nor H4 'Lys-20'. Demethylates trimethylated H3 'Lys-9' and H3 'Lys-36' residue, while it has no activity on mono- and dimethylated residues. Demethylation of Lys residue generates formaldehyde and succinate. Participates in transcriptional repression of ASCL2 and E2F-responsive promoters via the recruitment of histone deacetylases and NCOR1, respectively.^[1] ^[2] ^[3] Isoform 2: Crucial for muscle differentiation, promotes transcriptional activation of the Myog gene by directing the removal of repressive chromatin marks at its promoter. Lacks the N-terminal demethylase domain.^[4] ^[5] ^[6]

References

↑ Zhang D, Yoon HG, Wong J. JMJD2A is a novel N-CoR-interacting protein and is involved in repression of the human transcription factor achaete scute-like homologue 2 (ASCL2/Hash2). Mol Cell Biol. 2005 Aug;25(15):6404-14. PMID:16024779 doi:https://dx.doi.org/25/15/6404
↑ Whetstine JR, Nottke A, Lan F, Huarte M, Smolikov S, Chen Z, Spooner E, Li E, Zhang G, Colaiacovo M, Shi Y. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell. 2006 May 5;125(3):467-81. Epub 2006 Apr 6. PMID:16603238 doi:10.1016/j.cell.2006.03.028
↑ Verrier L, Escaffit F, Chailleux C, Trouche D, Vandromme M. A new isoform of the histone demethylase JMJD2A/KDM4A is required for skeletal muscle differentiation. PLoS Genet. 2011 Jun;7(6):e1001390. doi: 10.1371/journal.pgen.1001390. Epub 2011 , Jun 2. PMID:21694756 doi:https://dx.doi.org/10.1371/journal.pgen.1001390
↑ Zhang D, Yoon HG, Wong J. JMJD2A is a novel N-CoR-interacting protein and is involved in repression of the human transcription factor achaete scute-like homologue 2 (ASCL2/Hash2). Mol Cell Biol. 2005 Aug;25(15):6404-14. PMID:16024779 doi:https://dx.doi.org/25/15/6404
↑ Whetstine JR, Nottke A, Lan F, Huarte M, Smolikov S, Chen Z, Spooner E, Li E, Zhang G, Colaiacovo M, Shi Y. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell. 2006 May 5;125(3):467-81. Epub 2006 Apr 6. PMID:16603238 doi:10.1016/j.cell.2006.03.028
↑ Verrier L, Escaffit F, Chailleux C, Trouche D, Vandromme M. A new isoform of the histone demethylase JMJD2A/KDM4A is required for skeletal muscle differentiation. PLoS Genet. 2011 Jun;7(6):e1001390. doi: 10.1371/journal.pgen.1001390. Epub 2011 , Jun 2. PMID:21694756 doi:https://dx.doi.org/10.1371/journal.pgen.1001390

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OCA

[1] Zhang D, Yoon HG, Wong J. JMJD2A is a novel N-CoR-interacting protein and is involved in repression of the human transcription factor achaete scute-like homologue 2 (ASCL2/Hash2). Mol Cell Biol. 2005 Aug;25(15):6404-14. PMID:16024779 doi:https://dx.doi.org/25/15/6404

[2] Whetstine JR, Nottke A, Lan F, Huarte M, Smolikov S, Chen Z, Spooner E, Li E, Zhang G, Colaiacovo M, Shi Y. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell. 2006 May 5;125(3):467-81. Epub 2006 Apr 6. PMID:16603238 doi:10.1016/j.cell.2006.03.028

[3] Verrier L, Escaffit F, Chailleux C, Trouche D, Vandromme M. A new isoform of the histone demethylase JMJD2A/KDM4A is required for skeletal muscle differentiation. PLoS Genet. 2011 Jun;7(6):e1001390. doi: 10.1371/journal.pgen.1001390. Epub 2011 , Jun 2. PMID:21694756 doi:https://dx.doi.org/10.1371/journal.pgen.1001390

[4] Zhang D, Yoon HG, Wong J. JMJD2A is a novel N-CoR-interacting protein and is involved in repression of the human transcription factor achaete scute-like homologue 2 (ASCL2/Hash2). Mol Cell Biol. 2005 Aug;25(15):6404-14. PMID:16024779 doi:https://dx.doi.org/25/15/6404

[5] Whetstine JR, Nottke A, Lan F, Huarte M, Smolikov S, Chen Z, Spooner E, Li E, Zhang G, Colaiacovo M, Shi Y. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell. 2006 May 5;125(3):467-81. Epub 2006 Apr 6. PMID:16603238 doi:10.1016/j.cell.2006.03.028

[6] Verrier L, Escaffit F, Chailleux C, Trouche D, Vandromme M. A new isoform of the histone demethylase JMJD2A/KDM4A is required for skeletal muscle differentiation. PLoS Genet. 2011 Jun;7(6):e1001390. doi: 10.1371/journal.pgen.1001390. Epub 2011 , Jun 2. PMID:21694756 doi:https://dx.doi.org/10.1371/journal.pgen.1001390

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[2]

[3]

[4]

[5]

[6]

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
+==Crystal Structure of human JMJD2A complexed with KDOOA011340==
+<StructureSection load='5f5i' size='340' side='right' caption='[[5f5i]], [[Resolution|resolution]] 2.63&Aring;' scene=''>
-The entry 5f5i is ON HOLD
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5f5i]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F5I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5F5I FirstGlance]. <br>
-Authors: Krojer, T., Vollmar, M., Crawley, L., Szykowska, A., Gileadi, C., Johansson, C., England, K., Yang, H., Burgess-Brown, N., Brennan, P., Burley, S.K., Bountra, C., Arrowsmith, C.H., Edwards, A., Oppermann, U., von Delft, F., Structural Genomics Consortium (SGC)
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5V1:2-[[(PHENYLMETHYL)AMINO]METHYL]PYRIDINE-4-CARBOXYLIC+ACID'>5V1</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5f5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f5i OCA], [http://pdbe.org/5f5i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f5i RCSB], [http://www.ebi.ac.uk/pdbsum/5f5i PDBsum]</span></td></tr>
-Description: Crystal Structure of human JMJD2A complexed with KDOOA011340
+</table>
-[[Category: Unreleased Structures]]
+== Function ==
+[[http://www.uniprot.org/uniprot/KDM4A_HUMAN KDM4A_HUMAN]] Histone demethylase that specifically demethylates 'Lys-9' and 'Lys-36' residues of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27' nor H4 'Lys-20'. Demethylates trimethylated H3 'Lys-9' and H3 'Lys-36' residue, while it has no activity on mono- and dimethylated residues. Demethylation of Lys residue generates formaldehyde and succinate. Participates in transcriptional repression of ASCL2 and E2F-responsive promoters via the recruitment of histone deacetylases and NCOR1, respectively.<ref>PMID:16024779</ref> <ref>PMID:16603238</ref> <ref>PMID:21694756</ref>   Isoform 2: Crucial for muscle differentiation, promotes transcriptional activation of the Myog gene by directing the removal of repressive chromatin marks at its promoter. Lacks the N-terminal demethylase domain.<ref>PMID:16024779</ref> <ref>PMID:16603238</ref> <ref>PMID:21694756</ref>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Arrowsmith, C H]]
+[[Category: Bountra, C]]
+[[Category: Brennan, P]]
 [[Category: Burgess-Brown, N]]
-[[Category: Yang, H]]
+[[Category: Burley, S K]]
+[[Category: Crawley, L]]
+[[Category: Delft, F von]]
+[[Category: Edwards, A]]
+[[Category: England, K]]
+[[Category: Gileadi, C]]
+[[Category: Johansson, C]]
 [[Category: Krojer, T]]
-[[Category: Bountra, C]]
-[[Category: Vollmar, M]]
-[[Category: Burley, S.K]]
-[[Category: Arrowsmith, C.H]]
-[[Category: Gileadi, C]]
 [[Category: Oppermann, U]]
+[[Category: Structural genomic]]
 [[Category: Szykowska, A]]
-[[Category: Crawley, L]]
+[[Category: Vollmar, M]]
-[[Category: Von Delft, F]]
+[[Category: Yang, H]]
-[[Category: Johansson, C]]
+[[Category: Demethylase]]
-[[Category: Structural Genomics Consortium (Sgc)]]
+[[Category: Double-stranded beta helix]]
-[[Category: Edwards, A]]
+[[Category: Oxidoreductase]]
-[[Category: Brennan, P]]
+[[Category: Oxygenase]]
-[[Category: England, K]]
+[[Category: Sgc]]

5f5i: Difference between revisions

Revision as of 19:40, 30 December 2015

Crystal Structure of human JMJD2A complexed with KDOOA011340

Structural highlights

Function

References

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