6mev - Revision history

OCA at 09:34, 1 April 2020

OCA — Wed, 01 Apr 2020 09:34:53 GMT

←Older revision		Revision as of 09:34, 1 April 2020
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/JMJD6_HUMAN JMJD6_HUMAN]] Dioxygenase that can both act as a histone arginine demethylase and a lysyl-hydroxylase. Acts as a lysyl-hydroxylase that catalyzes 5-hydroxylation on specific lysine residues of target proteins such as U2AF2/U2AF65 and LUC7L2. Acts as a regulator of RNA splicing by mediating 5-hydroxylation of U2AF2/U2AF65, affecting the pre-mRNA splicing activity of U2AF2/U2AF65. In addition to peptidyl-lysine 5-dioxygenase activity, may act as a RNA hydroxylase, as suggested by its ability to bind single strand RNA. Also acts as an arginine demethylase which demethylates histone H3 at 'Arg-2' (H3R2me) and histone H4 at 'Arg-3' (H4R3me), thereby playing a role in histone code. However, histone arginine demethylation may not constitute the primary activity in vivo. Has no histone lysine demethylase activity. Required for differentiation of multiple organs during embryogenesis. Acts as a key regulator of hematopoietic differentiation: required for angiogenic sprouting by regulating the pre-mRNA splicing activity of U2AF2/U2AF65. Seems to be necessary for the regulation of macrophage cytokine responses.<ref>PMID:17947579</ref> <ref>PMID:19574390</ref> <ref>PMID:21060799</ref> <ref>PMID:20684070</ref> <ref>PMID:20679243</ref>		[[http://www.uniprot.org/uniprot/JMJD6_HUMAN JMJD6_HUMAN]] Dioxygenase that can both act as a histone arginine demethylase and a lysyl-hydroxylase. Acts as a lysyl-hydroxylase that catalyzes 5-hydroxylation on specific lysine residues of target proteins such as U2AF2/U2AF65 and LUC7L2. Acts as a regulator of RNA splicing by mediating 5-hydroxylation of U2AF2/U2AF65, affecting the pre-mRNA splicing activity of U2AF2/U2AF65. In addition to peptidyl-lysine 5-dioxygenase activity, may act as a RNA hydroxylase, as suggested by its ability to bind single strand RNA. Also acts as an arginine demethylase which demethylates histone H3 at 'Arg-2' (H3R2me) and histone H4 at 'Arg-3' (H4R3me), thereby playing a role in histone code. However, histone arginine demethylation may not constitute the primary activity in vivo. Has no histone lysine demethylase activity. Required for differentiation of multiple organs during embryogenesis. Acts as a key regulator of hematopoietic differentiation: required for angiogenic sprouting by regulating the pre-mRNA splicing activity of U2AF2/U2AF65. Seems to be necessary for the regulation of macrophage cytokine responses.<ref>PMID:17947579</ref> <ref>PMID:19574390</ref> <ref>PMID:21060799</ref> <ref>PMID:20684070</ref> <ref>PMID:20679243</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	More than 30% of genes in higher eukaryotes are regulated by promoter-proximal pausing of RNA polymerase II (Pol II). Phosphorylation of Pol II CTD by positive transcription elongation factor b (P-TEFb) is a necessary precursor event that enables productive transcription elongation. The exact mechanism on how the sequestered P-TEFb is released from the 7SK snRNP complex and recruited to Pol II CTD remains unknown. In this report, we utilize mouse and human models to reveal methylphosphate capping enzyme (MePCE), a core component of the 7SK snRNP complex, as the cognate substrate for Jumonji domain-containing 6 (JMJD6)'s novel proteolytic function. Our evidences consist of a crystal structure of JMJD6 bound to methyl-arginine, enzymatic assays of JMJD6 cleaving MePCE in vivo and in vitro, binding assays, and downstream effects of Jmjd6 knockout and overexpression on Pol II CTD phosphorylation. We propose that JMJD6 assists bromodomain containing 4 (BRD4) to recruit P-TEFb to Pol II CTD by disrupting the 7SK snRNP complex.
		+
		+	JMJD6 cleaves MePCE to release positive transcription elongation factor b (P-TEFb) in higher eukaryotes.,Lee S, Liu H, Hill R, Chen C, Hong X, Crawford F, Kingsley M, Zhang Q, Liu X, Chen Z, Lengeling A, Bernt KM, Marrack P, Kappler J, Zhou Q, Li CY, Xue Y, Hansen K, Zhang G Elife. 2020 Feb 12;9. pii: 53930. doi: 10.7554/eLife.53930. PMID:32048991<ref>PMID:32048991</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6mev" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:54, 18 December 2019

OCA — Wed, 18 Dec 2019 10:54:44 GMT

←Older revision		Revision as of 10:54, 18 December 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6mev is ~~ON HOLD until Paper Publication~~	+	==Structure of JMJD6 bound to Mono-Methyl Arginine.==
-		+	<StructureSection load='6mev' size='340' side='right'caption='[[6mev]], [[Resolution\|resolution]] 2.60Å' scene=''>
-	~~Authors~~: ~~Lee~~, S., ~~Zhang~~, G.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6mev]] is a 8 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=6MEV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MEV FirstGlance]. <br>
-	~~Description~~: ~~Structure~~ of ~~JMJD6 bound~~ to ~~Mono~~-~~Methyl Arginine~~.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=NMM:(2S)-2-AMINO-5-[(N-METHYLCARBAMIMIDOYL)AMINO]PENTANOIC+ACID'>NMM</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">JMJD6, KIAA0585, PTDSR ([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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6mev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mev OCA], [http://pdbe.org/6mev PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mev RCSB], [http://www.ebi.ac.uk/pdbsum/6mev PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mev ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/JMJD6_HUMAN JMJD6_HUMAN]] Dioxygenase that can both act as a histone arginine demethylase and a lysyl-hydroxylase. Acts as a lysyl-hydroxylase that catalyzes 5-hydroxylation on specific lysine residues of target proteins such as U2AF2/U2AF65 and LUC7L2. Acts as a regulator of RNA splicing by mediating 5-hydroxylation of U2AF2/U2AF65, affecting the pre-mRNA splicing activity of U2AF2/U2AF65. In addition to peptidyl-lysine 5-dioxygenase activity, may act as a RNA hydroxylase, as suggested by its ability to bind single strand RNA. Also acts as an arginine demethylase which demethylates histone H3 at 'Arg-2' (H3R2me) and histone H4 at 'Arg-3' (H4R3me), thereby playing a role in histone code. However, histone arginine demethylation may not constitute the primary activity in vivo. Has no histone lysine demethylase activity. Required for differentiation of multiple organs during embryogenesis. Acts as a key regulator of hematopoietic differentiation: required for angiogenic sprouting by regulating the pre-mRNA splicing activity of U2AF2/U2AF65. Seems to be necessary for the regulation of macrophage cytokine responses.<ref>PMID:17947579</ref> <ref>PMID:19574390</ref> <ref>PMID:21060799</ref> <ref>PMID:20684070</ref> <ref>PMID:20679243</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Lee, S]]		[[Category: Lee, S]]
	[[Category: Zhang, G]]		[[Category: Zhang, G]]
		+	[[Category: Arginine]]
		+	[[Category: Endopeptidase]]
		+	[[Category: Exopeptidase]]
		+	[[Category: Jumonji]]
		+	[[Category: Methyl]]
		+	[[Category: Transcription]]

OCA at 06:27, 26 September 2018

OCA — Wed, 26 Sep 2018 06:27:52 GMT

←Older revision		Revision as of 06:27, 26 September 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6mev is ON HOLD	+	The entry 6mev is ON HOLD until Paper Publication

	Authors: Lee, S., Zhang, G.		Authors: Lee, S., Zhang, G.

OCA: Protected "6mev" [edit=sysop:move=sysop]

OCA — Wed, 19 Sep 2018 18:25:06 GMT

Protected "6mev" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:25, 19 September 2018

OCA: New page: '''Unreleased structure''' The entry 6mev is ON HOLD Authors: Lee, S., Zhang, G. Description: Structure of JMJD6 bound to Mono-Methyl Arginine. Category: Unreleased Structures [[Ca...

OCA — Wed, 19 Sep 2018 18:25:05 GMT

New page: '''Unreleased structure''' The entry 6mev is ON HOLD Authors: Lee, S., Zhang, G. Description: Structure of JMJD6 bound to Mono-Methyl Arginine. Category: Unreleased Structures [[Ca...

New page

'''Unreleased structure'''

The entry 6mev is ON HOLD

Authors: Lee, S., Zhang, G.

Description: Structure of JMJD6 bound to Mono-Methyl Arginine.
[[Category: Unreleased Structures]]
[[Category: Lee, S]]
[[Category: Zhang, G]]