5dv4 - Revision history

OCA at 09:10, 20 March 2024

OCA — Wed, 20 Mar 2024 09:10:28 GMT

←Older revision		Revision as of 09:10, 20 March 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/CNO6L_HUMAN CNO6L_HUMAN] Plays a role in the deadenylation of mRNAs in the cytoplasm. Has 3'-5' poly(A) exoribonuclease activity for synthetic poly(A) RNA substrate. May be involved in the deadenylation-dependent degradation of mRNAs through the 3'-UTR AU-rich element-mediated mechanism. Involved in deadenylation-dependent degradation of CDKN1B mRNA.<ref>PMID:17452450</ref>		[https://www.uniprot.org/uniprot/CNO6L_HUMAN CNO6L_HUMAN] Plays a role in the deadenylation of mRNAs in the cytoplasm. Has 3'-5' poly(A) exoribonuclease activity for synthetic poly(A) RNA substrate. May be involved in the deadenylation-dependent degradation of mRNAs through the 3'-UTR AU-rich element-mediated mechanism. Involved in deadenylation-dependent degradation of CDKN1B mRNA.<ref>PMID:17452450</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Human CNOT6L/CCR4, a member of the endonuclease-exonuclease-phosphatase (EEP) family enzymes, is one of the two deadenylase enzymes in the conserved CCR4-NOT complex. Here, we report inhibitor-bound crystal structures of the human CNOT6L nuclease domain in complex with the nucleotide CMP and the aminoglycoside neomycin. Deadenylase activity assays show that nucleotides are effective inhibitors of both CNOT6L and CNOT7, with AMP more effective than other nucleotides, and that neomycin is a weak deadenylase inhibitor. Structural analysis shows that all inhibitors occupy the substrate and magnesium-binding sites of CNOT6L, suggesting that inhibitors compete with both substrate and divalent magnesium ions for overlapping binding sites.
-
-	Structural basis for inhibition of the deadenylase activity of human CNOT6L.,Zhang Q, Yan D, Guo E, Ding B, Yang W, Liu R, Yamamoto T, Bartlam M FEBS Lett. 2016 Apr;590(8):1270-9. doi: 10.1002/1873-3468.12160. Epub 2016 Apr, 15. PMID:27013054<ref>PMID:27013054</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5dv4" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 22:01, 28 June 2023

OCA — Wed, 28 Jun 2023 22:01:18 GMT

←Older revision		Revision as of 22:01, 28 June 2023
Line 3:		Line 3:
	<StructureSection load='5dv4' size='340' side='right'caption='[[5dv4]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='5dv4' size='340' side='right'caption='[[5dv4]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dv4]] is a 1 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=5DV4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5DV4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dv4]] 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=5DV4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DV4 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=NMY:NEOMYCIN'>NMY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.8Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Related_structure~~\|~~Related:]]</b></td><td class="sblockDat">[[5dv2\|5dv2~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NMY:NEOMYCIN'>NMY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>CNOT6L, CCR4B ([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=5dv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dv4 OCA], [https://pdbe.org/5dv4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dv4 RCSB], [https://www.ebi.ac.uk/pdbsum/5dv4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dv4 ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Poly(A)-specific_ribonuclease Poly(A)-specific ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.13.4 3.1.13.4]~~ </~~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=5dv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dv4 OCA], [~~http~~://pdbe.org/5dv4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5dv4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5dv4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5dv4 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CNO6L_HUMAN CNO6L_HUMAN]] Plays a role in the deadenylation of mRNAs in the cytoplasm. Has 3'-5' poly(A) exoribonuclease activity for synthetic poly(A) RNA substrate. May be involved in the deadenylation-dependent degradation of mRNAs through the 3'-UTR AU-rich element-mediated mechanism. Involved in deadenylation-dependent degradation of CDKN1B mRNA.<ref>PMID:17452450</ref>	+	[https://www.uniprot.org/uniprot/CNO6L_HUMAN CNO6L_HUMAN] Plays a role in the deadenylation of mRNAs in the cytoplasm. Has 3'-5' poly(A) exoribonuclease activity for synthetic poly(A) RNA substrate. May be involved in the deadenylation-dependent degradation of mRNAs through the 3'-UTR AU-rich element-mediated mechanism. Involved in deadenylation-dependent degradation of CDKN1B mRNA.<ref>PMID:17452450</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bartlam, M]]	+	[[Category: Bartlam M]]
-	[[Category: Zhang, Q]]	+	[[Category: Zhang Q]]
-	~~[[Category: Deadenylase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Nuclease domain~~]]	+

OCA at 07:12, 19 February 2020

OCA — Wed, 19 Feb 2020 07:12:27 GMT

←Older revision		Revision as of 07:12, 19 February 2020
Line 1:		Line 1:

	==Crystal structure of human CNOT6L in complex with neomycin==		==Crystal structure of human CNOT6L in complex with neomycin==
-	<StructureSection load='5dv4' size='340' side='right' caption='[[5dv4]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='5dv4' size='340' side='right'caption='[[5dv4]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dv4]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DV4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DV4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dv4]] is a 1 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=5DV4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DV4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NMY:NEOMYCIN'>NMY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NMY:NEOMYCIN'>NMY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dv2\|5dv2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dv2\|5dv2]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CNOT6L, CCR4B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Poly(A)-specific_ribonuclease Poly(A)-specific ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.13.4 3.1.13.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Poly(A)-specific_ribonuclease Poly(A)-specific ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.13.4 3.1.13.4] </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=5dv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dv4 OCA], [http://pdbe.org/5dv4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dv4 RCSB], [http://www.ebi.ac.uk/pdbsum/5dv4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dv4 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=5dv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dv4 OCA], [http://pdbe.org/5dv4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dv4 RCSB], [http://www.ebi.ac.uk/pdbsum/5dv4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dv4 ProSAT]</span></td></tr>
Line 24:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Bartlam, M]]		[[Category: Bartlam, M]]
	[[Category: Zhang, Q]]		[[Category: Zhang, Q]]

OCA at 18:37, 26 October 2016

OCA — Wed, 26 Oct 2016 18:37:29 GMT

←Older revision		Revision as of 18:37, 26 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5dv4 is ~~ON HOLD~~	+	==Crystal structure of human CNOT6L in complex with neomycin==
		+	<StructureSection load='5dv4' size='340' side='right' caption='[[5dv4]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5dv4]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DV4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DV4 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NMY:NEOMYCIN'>NMY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dv2\|5dv2]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Poly(A)-specific_ribonuclease Poly(A)-specific ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.13.4 3.1.13.4] </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=5dv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dv4 OCA], [http://pdbe.org/5dv4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dv4 RCSB], [http://www.ebi.ac.uk/pdbsum/5dv4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dv4 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CNO6L_HUMAN CNO6L_HUMAN]] Plays a role in the deadenylation of mRNAs in the cytoplasm. Has 3'-5' poly(A) exoribonuclease activity for synthetic poly(A) RNA substrate. May be involved in the deadenylation-dependent degradation of mRNAs through the 3'-UTR AU-rich element-mediated mechanism. Involved in deadenylation-dependent degradation of CDKN1B mRNA.<ref>PMID:17452450</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Human CNOT6L/CCR4, a member of the endonuclease-exonuclease-phosphatase (EEP) family enzymes, is one of the two deadenylase enzymes in the conserved CCR4-NOT complex. Here, we report inhibitor-bound crystal structures of the human CNOT6L nuclease domain in complex with the nucleotide CMP and the aminoglycoside neomycin. Deadenylase activity assays show that nucleotides are effective inhibitors of both CNOT6L and CNOT7, with AMP more effective than other nucleotides, and that neomycin is a weak deadenylase inhibitor. Structural analysis shows that all inhibitors occupy the substrate and magnesium-binding sites of CNOT6L, suggesting that inhibitors compete with both substrate and divalent magnesium ions for overlapping binding sites.

-	~~Authors~~:	+	Structural basis for inhibition of the deadenylase activity of human CNOT6L.,Zhang Q, Yan D, Guo E, Ding B, Yang W, Liu R, Yamamoto T, Bartlam M FEBS Lett. 2016 Apr;590(8):1270-9. doi: 10.1002/1873-3468.12160. Epub 2016 Apr, 15. PMID:27013054<ref>PMID:27013054</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5dv4" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bartlam, M]]
		+	[[Category: Zhang, Q]]
		+	[[Category: Deadenylase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Nuclease domain]]

OCA at 12:05, 15 May 2016

OCA — Sun, 15 May 2016 12:05:30 GMT

←Older revision		Revision as of 12:05, 15 May 2016
Line 3:		Line 3:
	The entry 5dv4 is ON HOLD		The entry 5dv4 is ON HOLD

-	Authors: ~~Zhang, Q., Bartlam, M.~~	+	Authors:

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Bartlam, M]]
-	[[Category: Zhang, Q]]

OCA: Protected "5dv4" [edit=sysop:move=sysop]

OCA — Wed, 30 Sep 2015 13:34:24 GMT

Protected "5dv4" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:34, 30 September 2015

OCA: New page: '''Unreleased structure''' The entry 5dv4 is ON HOLD Authors: Zhang, Q., Bartlam, M. Description: Category: Unreleased Structures Category: Bartlam, M Category: Zhang, Q

OCA — Wed, 30 Sep 2015 13:34:23 GMT

New page: '''Unreleased structure''' The entry 5dv4 is ON HOLD Authors: Zhang, Q., Bartlam, M. Description: Category: Unreleased Structures Category: Bartlam, M Category: Zhang, Q

New page

'''Unreleased structure'''

The entry 5dv4 is ON HOLD

Authors: Zhang, Q., Bartlam, M.

Description:
[[Category: Unreleased Structures]]
[[Category: Bartlam, M]]
[[Category: Zhang, Q]]