This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

5fwj

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 20:31, 24 January 2018

Crystal structure of human JARID1C in complex with KDM5-C49

Structural highlights

5fwj is a 2 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

[KDM5C_HUMAN] Syndromic X-linked intellectual disability due to JARID1C mutation. The disease is caused by mutations affecting the gene represented in this entry.

Function

[KDM5C_HUMAN] Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-4'. Participates in transcriptional repression of neuronal genes by recruiting histone deacetylases and REST at neuron-restrictive silencer elements. Represses the CLOCK-ARNTL/BMAL1 heterodimer-mediated transcriptional activation of the core clock component PER2 (By similarity).[UniProtKB:P41230]^[1] ^[2] ^[3]

Publication Abstract from PubMed

Members of the KDM5 (also known as JARID1) family are 2-oxoglutarate- and Fe2+-dependent oxygenases that act as histone H3K4 demethylases, thereby regulating cell proliferation and stem cell self-renewal and differentiation. Here we report crystal structures of the catalytic core of the human KDM5B enzyme in complex with three inhibitor chemotypes. These scaffolds exploit several aspects of the KDM5 active site, and their selectivity profiles reflect their hybrid features with respect to the KDM4 and KDM6 families. Whereas GSK-J1, a previously identified KDM6 inhibitor, showed about sevenfold less inhibitory activity toward KDM5B than toward KDM6 proteins, KDM5-C49 displayed 25-100-fold selectivity between KDM5B and KDM6B. The cell-permeable derivative KDM5-C70 had an antiproliferative effect in myeloma cells, leading to genome-wide elevation of H3K4me3 levels. The selective inhibitor GSK467 exploited unique binding modes, but it lacked cellular potency in the myeloma system. Taken together, these structural leads deliver multiple starting points for further rational and selective inhibitor design.

Structural analysis of human KDM5B guides histone demethylase inhibitor development.,Johansson C, Velupillai S, Tumber A, Szykowska A, Hookway ES, Nowak RP, Strain-Damerell C, Gileadi C, Philpott M, Burgess-Brown N, Wu N, Kopec J, Nuzzi A, Steuber H, Egner U, Badock V, Munro S, LaThangue NB, Westaway S, Brown J, Athanasou N, Prinjha R, Brennan PE, Oppermann U Nat Chem Biol. 2016 May 23. doi: 10.1038/nchembio.2087. PMID:27214403^[4]

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

References

↑ Iwase S, Lan F, Bayliss P, de la Torre-Ubieta L, Huarte M, Qi HH, Whetstine JR, Bonni A, Roberts TM, Shi Y. The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases. Cell. 2007 Mar 23;128(6):1077-88. Epub 2007 Feb 22. PMID:17320160 doi:10.1016/j.cell.2007.02.017
↑ Christensen J, Agger K, Cloos PA, Pasini D, Rose S, Sennels L, Rappsilber J, Hansen KH, Salcini AE, Helin K. RBP2 belongs to a family of demethylases, specific for tri-and dimethylated lysine 4 on histone 3. Cell. 2007 Mar 23;128(6):1063-76. Epub 2007 Feb 22. PMID:17320161 doi:S0092-8674(07)00182-1
↑ Tahiliani M, Mei P, Fang R, Leonor T, Rutenberg M, Shimizu F, Li J, Rao A, Shi Y. The histone H3K4 demethylase SMCX links REST target genes to X-linked mental retardation. Nature. 2007 May 31;447(7144):601-5. Epub 2007 Apr 29. PMID:17468742 doi:nature05823
↑ Johansson C, Velupillai S, Tumber A, Szykowska A, Hookway ES, Nowak RP, Strain-Damerell C, Gileadi C, Philpott M, Burgess-Brown N, Wu N, Kopec J, Nuzzi A, Steuber H, Egner U, Badock V, Munro S, LaThangue NB, Westaway S, Brown J, Athanasou N, Prinjha R, Brennan PE, Oppermann U. Structural analysis of human KDM5B guides histone demethylase inhibitor development. Nat Chem Biol. 2016 May 23. doi: 10.1038/nchembio.2087. PMID:27214403 doi:http://dx.doi.org/10.1038/nchembio.2087

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 3: / Line 3: @@
 <StructureSection load='5fwj' size='340' side='right' caption='[[5fwj]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5fwj]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FWJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FWJ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5fwj]] is a 2 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=5FWJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FWJ FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MMK:2-{[(2-{[(E)-2-(DIMETHYLAMINO)ETHENYL](ETHYL)AMINO}-2-OXOETHYL)AMINO]METHYL}PYRIDINE-4-CARBOXYLIC+ACID'>MMK</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=5fwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fwj OCA], [http://pdbe.org/5fwj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fwj RCSB], [http://www.ebi.ac.uk/pdbsum/5fwj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fwj ProSAT]</span></td></tr>
@@ Line 24: / Line 24: @@
 __TOC__
 </StructureSection>
+[[Category: Human]]
 [[Category: Arrowsmith, C H]]
 [[Category: Bountra, C]]
 [[Category: Burgess-Brown, N A]]
+[[Category: Delft, F von]]
 [[Category: Dong, W]]
 [[Category: Edwards, A]]
@@ Line 40: / Line 42: @@
 [[Category: Strain-Damerell, C]]
 [[Category: Szykowska, A]]
-[[Category: VonDELFT, F]]
 [[Category: Lysine-specific]]
 [[Category: Lysine-specific demethylase 5c]]
 [[Category: Oxidoreductase]]

5fwj

From Proteopedia

Revision as of 20:31, 24 January 2018

Crystal structure of human JARID1C in complex with KDM5-C49

Structural highlights

Disease

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox