5fys: Difference between revisions

Latest revision as of 13:32, 26 July 2023

Crystal structure of the catalytic domain of human JARID1B in complex with D-2-hydroxyglutarate

Structural highlights

5fys is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.89Å
Ligands:	2HG, CL, EDO, EPE, MN, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

KDM5B_HUMAN Histone demethylase that demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9' or H3 'Lys-27'. Demethylates trimethylated, dimethylated and monomethylated H3 'Lys-4'. Acts as a transcriptional corepressor for FOXG1B and PAX9. Favors the proliferation of breast cancer cells by repressing tumor suppressor genes such as BRCA1 and HOXA5. In contrast, may act as a tumor suppressor for melanoma.^[1] ^[2] ^[3] ^[4]

References

↑ Tan K, Shaw AL, Madsen B, Jensen K, Taylor-Papadimitriou J, Freemont PS. Human PLU-1 Has transcriptional repression properties and interacts with the developmental transcription factors BF-1 and PAX9. J Biol Chem. 2003 Jun 6;278(23):20507-13. Epub 2003 Mar 25. PMID:12657635 doi:https://dx.doi.org/10.1074/jbc.M301994200
↑ Roesch A, Becker B, Schneider-Brachert W, Hagen I, Landthaler M, Vogt T. Re-expression of the retinoblastoma-binding protein 2-homolog 1 reveals tumor-suppressive functions in highly metastatic melanoma cells. J Invest Dermatol. 2006 Aug;126(8):1850-9. Epub 2006 Apr 27. PMID:16645588 doi:https://dx.doi.org/10.1038/sj.jid.5700324
↑ 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
↑ Yamane K, Tateishi K, Klose RJ, Fang J, Fabrizio LA, Erdjument-Bromage H, Taylor-Papadimitriou J, Tempst P, Zhang Y. PLU-1 is an H3K4 demethylase involved in transcriptional repression and breast cancer cell proliferation. Mol Cell. 2007 Mar 23;25(6):801-12. Epub 2007 Mar 15. PMID:17363312 doi:https://dx.doi.org/S1097-2765(07)00146-3

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OCA

[1] Tan K, Shaw AL, Madsen B, Jensen K, Taylor-Papadimitriou J, Freemont PS. Human PLU-1 Has transcriptional repression properties and interacts with the developmental transcription factors BF-1 and PAX9. J Biol Chem. 2003 Jun 6;278(23):20507-13. Epub 2003 Mar 25. PMID:12657635 doi:https://dx.doi.org/10.1074/jbc.M301994200

[2] Roesch A, Becker B, Schneider-Brachert W, Hagen I, Landthaler M, Vogt T. Re-expression of the retinoblastoma-binding protein 2-homolog 1 reveals tumor-suppressive functions in highly metastatic melanoma cells. J Invest Dermatol. 2006 Aug;126(8):1850-9. Epub 2006 Apr 27. PMID:16645588 doi:https://dx.doi.org/10.1038/sj.jid.5700324

[3] 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

[4] Yamane K, Tateishi K, Klose RJ, Fang J, Fabrizio LA, Erdjument-Bromage H, Taylor-Papadimitriou J, Tempst P, Zhang Y. PLU-1 is an H3K4 demethylase involved in transcriptional repression and breast cancer cell proliferation. Mol Cell. 2007 Mar 23;25(6):801-12. Epub 2007 Mar 15. PMID:17363312 doi:https://dx.doi.org/S1097-2765(07)00146-3

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5fys is ON HOLD  until Paper Publication
+==Crystal structure of the catalytic domain of human JARID1B in complex with D-2-hydroxyglutarate==
+<StructureSection load='5fys' size='340' side='right'caption='[[5fys]], [[Resolution|resolution]] 1.89&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5fys]] 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=5FYS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FYS FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.89&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2HG:(2R)-2-HYDROXYPENTANEDIOIC+ACID'>2HG</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</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'>[https://proteopedia.org/fgij/fg.htm?mol=5fys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fys OCA], [https://pdbe.org/5fys PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fys RCSB], [https://www.ebi.ac.uk/pdbsum/5fys PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fys ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/KDM5B_HUMAN KDM5B_HUMAN] Histone demethylase that demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9' or H3 'Lys-27'. Demethylates trimethylated, dimethylated and monomethylated H3 'Lys-4'. Acts as a transcriptional corepressor for FOXG1B and PAX9. Favors the proliferation of breast cancer cells by repressing tumor suppressor genes such as BRCA1 and HOXA5. In contrast, may act as a tumor suppressor for melanoma.<ref>PMID:12657635</ref> <ref>PMID:16645588</ref> <ref>PMID:17320161</ref> <ref>PMID:17363312</ref>
-Authors: Nowak, R., Kopec, J., Johansson, C., Gileadi, C., Kupinska, K., Strain-Damerell, C., Szykowska, A., Von Delft, F., Burgess-Brown, N.A., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Oppermann, U.
+==See Also==
+*[[Lysine-specific histone demethylase 3D structures|Lysine-specific histone demethylase 3D structures]]
-Description: Crystal structure of the catalytic domain of human JARID1B in complex with D-2-hydroxyglutarate
+== References ==
-[[Category: Unreleased Structures]]
+<references/>
-[[Category: Nowak, R]]
+__TOC__
-[[Category: Burgess-Brown, N.A]]
+</StructureSection>
-[[Category: Bountra, C]]
+[[Category: Homo sapiens]]
-[[Category: Kupinska, K]]
+[[Category: Large Structures]]
-[[Category: Arrowsmith, C.H]]
+[[Category: Arrowsmith CH]]
-[[Category: Gileadi, C]]
+[[Category: Bountra C]]
-[[Category: Oppermann, U]]
+[[Category: Burgess-Brown NA]]
-[[Category: Szykowska, A]]
+[[Category: Edwards AM]]
-[[Category: Kopec, J]]
+[[Category: Gileadi C]]
-[[Category: Von Delft, F]]
+[[Category: Johansson C]]
-[[Category: Edwards, A.M]]
+[[Category: Kopec J]]
-[[Category: Johansson, C]]
+[[Category: Kupinska K]]
-[[Category: Strain-Damerell, C]]
+[[Category: Nowak R]]
+[[Category: Oppermann U]]
+[[Category: Strain-Damerell C]]
+[[Category: Szykowska A]]
+[[Category: Von Delft F]]

5fys: Difference between revisions

Latest revision as of 13:32, 26 July 2023

Crystal structure of the catalytic domain of human JARID1B in complex with D-2-hydroxyglutarate

Structural highlights

Function

See Also

References

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