6aix - Revision history

OCA at 19:26, 29 May 2024

2024-05-29T19:26:17Z

←Older revision		Revision as of 19:26, 29 May 2024
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	<StructureSection load='6aix' size='340' side='right'caption='[[6aix]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='6aix' size='340' side='right'caption='[[6aix]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6aix]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AIX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6AIX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6aix]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AIX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6AIX FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=A3P:ADENOSINE~~-~~3-5-DIPHOSPHATE'>A3P</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~Dxo, Dom3z, Ng6 ([https~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=10090 LK3 transgenic mice])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A3P:ADENOSINE-3-5-DIPHOSPHATE'>A3P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=6aix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6aix OCA], [https://pdbe.org/6aix PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6aix RCSB], [https://www.ebi.ac.uk/pdbsum/6aix PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6aix ProSAT]</span></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=6aix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6aix OCA], [https://pdbe.org/6aix PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6aix RCSB], [https://www.ebi.ac.uk/pdbsum/6aix PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6aix ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DXO_MOUSE DXO_MOUSE]] Ribonuclease that specifically degrades pre-mRNAs with a defective 5' end cap and is part of a pre-mRNA capping quality control. Has decapping, pyrophosphohydrolase and 5'-3' exonuclease activities. Has decapping activity toward incomplete 5' end cap mRNAs such as unmethylated 5' end-capped RNA to release GpppN and 5' end monophosphate RNA. The 5' end monophosphate RNA is then degraded by the 5'-3' exoribonuclease activity, enabling this enzyme to decap and degrade incompletely capped mRNAs. Also possesses RNA 5'-pyrophosphohydrolase activity by hydrolyzing the 5' end triphosphate to release pyrophosphates.<ref>PMID:23523372</ref>	+	[https://www.uniprot.org/uniprot/DXO_MOUSE DXO_MOUSE] Ribonuclease that specifically degrades pre-mRNAs with a defective 5' end cap and is part of a pre-mRNA capping quality control. Has decapping, pyrophosphohydrolase and 5'-3' exonuclease activities. Has decapping activity toward incomplete 5' end cap mRNAs such as unmethylated 5' end-capped RNA to release GpppN and 5' end monophosphate RNA. The 5' end monophosphate RNA is then degraded by the 5'-3' exoribonuclease activity, enabling this enzyme to decap and degrade incompletely capped mRNAs. Also possesses RNA 5'-pyrophosphohydrolase activity by hydrolyzing the 5' end triphosphate to release pyrophosphates.<ref>PMID:23523372</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: Chang~~, J H~~]]	+	[[Category: Chang JH]]
-	[[Category: Tong, L]]	+	[[Category: Tong L]]
-	~~[[Category: Dxo]]~~	+
-	~~[[Category: Hydrolase-hydrolase inhibitor complex]]~~	+
-	~~[[Category: Nuclease inhibitor~~]]	+

OCA at 11:37, 23 March 2022

2022-03-23T11:37:26Z

←Older revision		Revision as of 11:37, 23 March 2022
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	<StructureSection load='6aix' size='340' side='right'caption='[[6aix]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='6aix' size='340' side='right'caption='[[6aix]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6aix]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AIX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6AIX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6aix]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AIX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6AIX FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A3P:ADENOSINE-3-5-DIPHOSPHATE'>A3P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A3P:ADENOSINE-3-5-DIPHOSPHATE'>A3P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6aix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6aix OCA], [~~http~~://pdbe.org/6aix PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6aix RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6aix PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6aix ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Dxo, Dom3z, Ng6 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=6aix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6aix OCA], [https://pdbe.org/6aix PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6aix RCSB], [https://www.ebi.ac.uk/pdbsum/6aix PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6aix ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DXO_MOUSE DXO_MOUSE]] Ribonuclease that specifically degrades pre-mRNAs with a defective 5' end cap and is part of a pre-mRNA capping quality control. Has decapping, pyrophosphohydrolase and 5'-3' exonuclease activities. Has decapping activity toward incomplete 5' end cap mRNAs such as unmethylated 5' end-capped RNA to release GpppN and 5' end monophosphate RNA. The 5' end monophosphate RNA is then degraded by the 5'-3' exoribonuclease activity, enabling this enzyme to decap and degrade incompletely capped mRNAs. Also possesses RNA 5'-pyrophosphohydrolase activity by hydrolyzing the 5' end triphosphate to release pyrophosphates.<ref>PMID:23523372</ref>	+	[[https://www.uniprot.org/uniprot/DXO_MOUSE DXO_MOUSE]] Ribonuclease that specifically degrades pre-mRNAs with a defective 5' end cap and is part of a pre-mRNA capping quality control. Has decapping, pyrophosphohydrolase and 5'-3' exonuclease activities. Has decapping activity toward incomplete 5' end cap mRNAs such as unmethylated 5' end-capped RNA to release GpppN and 5' end monophosphate RNA. The 5' end monophosphate RNA is then degraded by the 5'-3' exoribonuclease activity, enabling this enzyme to decap and degrade incompletely capped mRNAs. Also possesses RNA 5'-pyrophosphohydrolase activity by hydrolyzing the 5' end triphosphate to release pyrophosphates.<ref>PMID:23523372</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Chang, J H]]		[[Category: Chang, J H]]
	[[Category: Tong, L]]		[[Category: Tong, L]]

OCA at 21:28, 28 October 2020

2020-10-28T21:28:41Z

←Older revision		Revision as of 21:28, 28 October 2020
Line 1:		Line 1:

	==Crystal structure of DXO in complex with adenosine 3', 5' bisphosphate and two magnesium ions==		==Crystal structure of DXO in complex with adenosine 3', 5' bisphosphate and two magnesium ions==
-	<StructureSection load='6aix' size='340' side='right' caption='[[6aix]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='6aix' size='340' side='right'caption='[[6aix]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6aix]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AIX OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6AIX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6aix]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AIX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6AIX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A3P:ADENOSINE-3-5-DIPHOSPHATE'>A3P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A3P:ADENOSINE-3-5-DIPHOSPHATE'>A3P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=6aix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6aix OCA], [http://pdbe.org/6aix PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6aix RCSB], [http://www.ebi.ac.uk/pdbsum/6aix PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6aix ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6aix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6aix OCA], [http://pdbe.org/6aix PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6aix RCSB], [http://www.ebi.ac.uk/pdbsum/6aix PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6aix ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Chang, J H]]		[[Category: Chang, J H]]
	[[Category: Tong, L]]		[[Category: Tong, L]]

OCA at 07:53, 17 October 2018

2018-10-17T07:53:02Z

←Older revision		Revision as of 07:53, 17 October 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6aix is ~~ON HOLD~~	+	==Crystal structure of DXO in complex with adenosine 3', 5' bisphosphate and two magnesium ions==
		+	<StructureSection load='6aix' size='340' side='right' caption='[[6aix]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6aix]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AIX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AIX FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A3P:ADENOSINE-3-5-DIPHOSPHATE'>A3P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=6aix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6aix OCA], [http://pdbe.org/6aix PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6aix RCSB], [http://www.ebi.ac.uk/pdbsum/6aix PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6aix ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DXO_MOUSE DXO_MOUSE]] Ribonuclease that specifically degrades pre-mRNAs with a defective 5' end cap and is part of a pre-mRNA capping quality control. Has decapping, pyrophosphohydrolase and 5'-3' exonuclease activities. Has decapping activity toward incomplete 5' end cap mRNAs such as unmethylated 5' end-capped RNA to release GpppN and 5' end monophosphate RNA. The 5' end monophosphate RNA is then degraded by the 5'-3' exoribonuclease activity, enabling this enzyme to decap and degrade incompletely capped mRNAs. Also possesses RNA 5'-pyrophosphohydrolase activity by hydrolyzing the 5' end triphosphate to release pyrophosphates.<ref>PMID:23523372</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The decapping exoribonuclease DXO functions in pre-mRNA capping quality control, and shows multiple biochemical activities such as decapping, deNADding, pyrophosphohydrolase, and 5'-3' exoribonuclease activities. Previous studies revealed the molecular mechanisms of DXO based on the structures in complexes with a product, substrate mimic, cap analogue, and 3'-NADP(+). Despite several reports on the substrate-specific reaction mechanism, the inhibitory mechanism of DXO remains elusive. Here, we demonstrate that adenosine 3', 5'-bisphosphate (pAp), a known inhibitor of the 5'-3' exoribonuclease Xrn1, inhibits the nuclease activity of DXO based on the results of structural and biochemical experiments. We determined the crystal structure of the DXO-pAp-Mg(2+) complex at 1.8A resolution. In comparison with the DXO-RNA product complex, the position of pAp is well superimposed with the first nucleotide of the product RNA in the vicinity of two magnesium ions. Furthermore, biochemical assays showed that the inhibition by pAp is comparable between Xrn1 and DXO. Collectively, these structural and biochemical studies reveal that pAp inhibits the activities of DXO by occupying the active site to act as a competitive inhibitor.

-	~~Authors: Chang~~, ~~J.H~~., ~~Tong~~, L.	+	Molecular mechanism for the inhibition of DXO by adenosine 3',5'-bisphosphate.,Yun JS, Yoon JH, Choi YJ, Son YJ, Kim S, Tong L, Chang JH Biochem Biophys Res Commun. 2018 Sep 26;504(1):89-95. doi:, 10.1016/j.bbrc.2018.08.135. Epub 2018 Sep 1. PMID:30180947<ref>PMID:30180947</ref>

-	~~Description: Crystal structure of DXO in complex with adenosine 3'~~, ~~5' bisphosphate and two magnesium ions~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6aix" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Chang, J H]]
	[[Category: Tong, L]]		[[Category: Tong, L]]
-	[[Category: ~~Chang, J.H~~]]	+	[[Category: Dxo]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]
		+	[[Category: Nuclease inhibitor]]

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

2018-09-05T08:35:52Z

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

←Older revision

Revision as of 08:35, 5 September 2018

OCA: New page: '''Unreleased structure''' The entry 6aix is ON HOLD Authors: Chang, J.H., Tong, L. Description: Crystal structure of DXO in complex with adenosine 3', 5' bisphosphate and two magnesiu...

2018-09-05T08:35:51Z

New page: '''Unreleased structure''' The entry 6aix is ON HOLD Authors: Chang, J.H., Tong, L. Description: Crystal structure of DXO in complex with adenosine 3', 5' bisphosphate and two magnesiu...

New page

'''Unreleased structure'''

The entry 6aix is ON HOLD

Authors: Chang, J.H., Tong, L.

Description: Crystal structure of DXO in complex with adenosine 3', 5' bisphosphate and two magnesium ions
[[Category: Unreleased Structures]]
[[Category: Tong, L]]
[[Category: Chang, J.H]]