3ctr - Revision history

OCA at 09:38, 21 February 2024

2024-02-21T09:38:25Z

← Older revision		Revision as of 09:38, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3ctr' size='340' side='right'caption='[[3ctr]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3ctr' size='340' side='right'caption='[[3ctr]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3ctr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CTR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CTR FirstGlance]. <br>		<table><tr><td colspan='2'>[[3ctr]] 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=3CTR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CTR FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MGP:7~~-~~METHYL-GUANOSINE-5-TRIPHOSPHATE'>MGP</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]] 2.1Å</td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>PARN, DAN ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=9606 HUMAN])</td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MGP:7-METHYL-GUANOSINE-5-TRIPHOSPHATE'>MGP</scene></td></tr>
	~~<tr id='activity'><td class~~="~~sblockLbl~~"><~~b>Activity:</b></td><td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/Poly(A)~~-~~specific_ribonuclease Poly(A)~~-~~specific ribonuclease], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=3ctr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ctr OCA], [https://pdbe.org/3ctr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ctr RCSB], [https://www.ebi.ac.uk/pdbsum/3ctr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ctr 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=3ctr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ctr OCA], [https://pdbe.org/3ctr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ctr RCSB], [https://www.ebi.ac.uk/pdbsum/3ctr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ctr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/PARN_HUMAN PARN_HUMAN]] 3'-exoribonuclease that has a preference for poly(A) tails of mRNAs, thereby efficiently degrading poly(A) tails. Exonucleolytic degradation of the poly(A) tail is often the first step in the decay of eukaryotic mRNAs and is also used to silence certain maternal mRNAs translationally during oocyte maturation and early embryonic development. Interacts with both the 3'-end poly(A) tail and the 5'-end cap structure during degradation, the interaction with the cap structure being required for an efficient degradation of poly(A) tails. Involved in nonsense-mediated mRNA decay, a critical process of selective degradation of mRNAs that contain premature stop codons. Also involved in degradation of inherently unstable mRNAs that contain AU-rich elements (AREs) in their 3'-UTR, possibly via its interaction with KHSRP. Probably mediates the removal of poly(A) tails of AREs mRNAs, which constitutes the first step of destabilization.<ref>PMID:9736620</ref> <ref>PMID:10882133</ref> <ref>PMID:11359775</ref> <ref>PMID:12748283</ref> <ref>PMID:15175153</ref>		[https://www.uniprot.org/uniprot/PARN_HUMAN PARN_HUMAN] 3'-exoribonuclease that has a preference for poly(A) tails of mRNAs, thereby efficiently degrading poly(A) tails. Exonucleolytic degradation of the poly(A) tail is often the first step in the decay of eukaryotic mRNAs and is also used to silence certain maternal mRNAs translationally during oocyte maturation and early embryonic development. Interacts with both the 3'-end poly(A) tail and the 5'-end cap structure during degradation, the interaction with the cap structure being required for an efficient degradation of poly(A) tails. Involved in nonsense-mediated mRNA decay, a critical process of selective degradation of mRNAs that contain premature stop codons. Also involved in degradation of inherently unstable mRNAs that contain AU-rich elements (AREs) in their 3'-UTR, possibly via its interaction with KHSRP. Probably mediates the removal of poly(A) tails of AREs mRNAs, which constitutes the first step of destabilization.<ref>PMID:9736620</ref> <ref>PMID:10882133</ref> <ref>PMID:11359775</ref> <ref>PMID:12748283</ref> <ref>PMID:15175153</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3ctr ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3ctr ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Poly(A)-specific ribonuclease (PARN) is a processive 3'-exoribonuclease involved in the decay of eukaryotic mRNAs. Interestingly, PARN interacts not only with the 3' end of the mRNA but also with its 5' end as PARN contains an RRM domain that specifically binds both the poly(A) tail and the 7-methylguanosine (m(7)G) cap. The interaction of PARN with the 5' cap of mRNAs stimulates the deadenylation activity and enhances the processivity of this reaction. We have determined the crystal structure of the PARN-RRM domain with a bound m(7)G triphosphate nucleotide, revealing a novel binding mode for the m(7)G cap. The structure of the m(7)G binding pocket is located outside of the canonical RNA-binding surface of the RRM domain and differs significantly from that of other m(7)G-cap-binding proteins. The crystal structure also shows a remarkable conformational flexibility of the RRM domain, leading to a perfect exchange of two alpha-helices with an adjacent protein molecule in the crystal lattice.

	Crystal structure of the RRM domain of poly(A)-specific ribonuclease reveals a novel m(7)G-cap-binding mode.,Monecke T, Schell S, Dickmanns A, Ficner R J Mol Biol. 2008 Oct 17;382(4):827-34. Epub 2008 Jul 31. PMID:18694759<ref>PMID:18694759</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 3ctr" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
Line 37:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Human~~]]		[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Dickmanns, A]]		[[Category: Dickmanns A]]
	[[Category: Ficner, R]]		[[Category: Ficner R]]
	[[Category: Monecke, T]]		[[Category: Monecke T]]
	[[Category: Schell, S]]		[[Category: Schell S]]
	~~[[Category: Exonuclease]]~~
	~~[[Category: Hydrolase]]~~
	~~[[Category: M7g-cap]]~~
	~~[[Category: M7gtp]]~~
	~~[[Category: Magnesium]]~~
	~~[[Category: Metal-binding]]~~
	~~[[Category: Nonsense-mediated mrna decay]]~~
	~~[[Category: Nuclease]]~~
	~~[[Category: Nucleus]]~~
	~~[[Category: Parn]]~~
	~~[[Category: Phosphoprotein]]~~
	~~[[Category: Protein-rna-complex]]~~
	~~[[Category: Rna recognition motif]]~~
	~~[[Category: Rna-binding]]~~
	~~[[Category: Rrm~~]]

OCA at 07:44, 2 February 2022

2022-02-02T07:44:36Z

← Older revision		Revision as of 07:44, 2 February 2022
Line 1:		Line 1:

	==Crystal structure of the RRM-domain of the poly(A)-specific ribonuclease PARN bound to m7GTP==		==Crystal structure of the RRM-domain of the poly(A)-specific ribonuclease PARN bound to m7GTP==
	<StructureSection load='3ctr' size='340' side='right' caption='[[3ctr]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3ctr' size='340' side='right'caption='[[3ctr]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3ctr]] 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=3CTR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3CTR FirstGlance]. <br>		<table><tr><td colspan='2'>[[3ctr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CTR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CTR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MGP:7-METHYL-GUANOSINE-5-TRIPHOSPHATE'>MGP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MGP:7-METHYL-GUANOSINE-5-TRIPHOSPHATE'>MGP</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PARN, DAN ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PARN, DAN ([https://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'>[https://en.wikipedia.org/wiki/Poly(A)-specific_ribonuclease Poly(A)-specific ribonuclease], with EC number [https://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=3ctr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ctr OCA], [~~http~~://pdbe.org/3ctr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3ctr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3ctr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3ctr 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=3ctr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ctr OCA], [https://pdbe.org/3ctr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ctr RCSB], [https://www.ebi.ac.uk/pdbsum/3ctr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ctr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/PARN_HUMAN PARN_HUMAN]] 3'-exoribonuclease that has a preference for poly(A) tails of mRNAs, thereby efficiently degrading poly(A) tails. Exonucleolytic degradation of the poly(A) tail is often the first step in the decay of eukaryotic mRNAs and is also used to silence certain maternal mRNAs translationally during oocyte maturation and early embryonic development. Interacts with both the 3'-end poly(A) tail and the 5'-end cap structure during degradation, the interaction with the cap structure being required for an efficient degradation of poly(A) tails. Involved in nonsense-mediated mRNA decay, a critical process of selective degradation of mRNAs that contain premature stop codons. Also involved in degradation of inherently unstable mRNAs that contain AU-rich elements (AREs) in their 3'-UTR, possibly via its interaction with KHSRP. Probably mediates the removal of poly(A) tails of AREs mRNAs, which constitutes the first step of destabilization.<ref>PMID:9736620</ref> <ref>PMID:10882133</ref> <ref>PMID:11359775</ref> <ref>PMID:12748283</ref> <ref>PMID:15175153</ref>		[[https://www.uniprot.org/uniprot/PARN_HUMAN PARN_HUMAN]] 3'-exoribonuclease that has a preference for poly(A) tails of mRNAs, thereby efficiently degrading poly(A) tails. Exonucleolytic degradation of the poly(A) tail is often the first step in the decay of eukaryotic mRNAs and is also used to silence certain maternal mRNAs translationally during oocyte maturation and early embryonic development. Interacts with both the 3'-end poly(A) tail and the 5'-end cap structure during degradation, the interaction with the cap structure being required for an efficient degradation of poly(A) tails. Involved in nonsense-mediated mRNA decay, a critical process of selective degradation of mRNAs that contain premature stop codons. Also involved in degradation of inherently unstable mRNAs that contain AU-rich elements (AREs) in their 3'-UTR, possibly via its interaction with KHSRP. Probably mediates the removal of poly(A) tails of AREs mRNAs, which constitutes the first step of destabilization.<ref>PMID:9736620</ref> <ref>PMID:10882133</ref> <ref>PMID:11359775</ref> <ref>PMID:12748283</ref> <ref>PMID:15175153</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ct/3ctr_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ct/3ctr_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 32:		Line 32:

	==See Also==		==See Also==
	*[[Ribonuclease\|Ribonuclease]]		*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
	*[[Temp\|Temp]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
			[[Category: Large Structures]]
	[[Category: Dickmanns, A]]		[[Category: Dickmanns, A]]
	[[Category: Ficner, R]]		[[Category: Ficner, R]]

OCA at 22:55, 4 August 2016

2016-08-04T22:55:19Z

← Older revision		Revision as of 22:55, 4 August 2016
Line 1:		Line 1:

	==Crystal structure of the RRM-domain of the poly(A)-specific ribonuclease PARN bound to m7GTP==		==Crystal structure of the RRM-domain of the poly(A)-specific ribonuclease PARN bound to m7GTP==
	<StructureSection load='3ctr' size='340' side='right' caption='[[3ctr]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3ctr' size='340' side='right' caption='[[3ctr]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3ctr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CTR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CTR FirstGlance]. <br>		<table><tr><td colspan='2'>[[3ctr]] 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=3CTR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CTR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MGP:7-METHYL-GUANOSINE-5-TRIPHOSPHATE'>MGP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MGP:7-METHYL-GUANOSINE-5-TRIPHOSPHATE'>MGP</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PARN, DAN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PARN, DAN ([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=3ctr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ctr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ctr RCSB], [http://www.ebi.ac.uk/pdbsum/3ctr PDBsum]</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=3ctr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ctr OCA], [http://pdbe.org/3ctr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ctr RCSB], [http://www.ebi.ac.uk/pdbsum/3ctr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ctr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3ctr ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 29:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 3ctr" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Ribonuclease\|Ribonuclease]]		*[[Ribonuclease\|Ribonuclease]]
	*[[Temp\|Temp]]		*[[Temp\|Temp]]
	*[[User:Jaime.Prilusky/Test/tree\|User:Jaime.Prilusky/Test/tree]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Homo sapiens~~]]		[[Category: Human]]
	[[Category: Dickmanns, A]]		[[Category: Dickmanns, A]]
	[[Category: Ficner, R]]		[[Category: Ficner, R]]

OCA at 13:47, 25 December 2014

2014-12-25T13:47:07Z

← Older revision		Revision as of 13:47, 25 December 2014
Line 8:		Line 8:
	<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=3ctr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ctr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ctr RCSB], [http://www.ebi.ac.uk/pdbsum/3ctr PDBsum]</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=3ctr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ctr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ctr RCSB], [http://www.ebi.ac.uk/pdbsum/3ctr PDBsum]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/PARN_HUMAN PARN_HUMAN]] 3'-exoribonuclease that has a preference for poly(A) tails of mRNAs, thereby efficiently degrading poly(A) tails. Exonucleolytic degradation of the poly(A) tail is often the first step in the decay of eukaryotic mRNAs and is also used to silence certain maternal mRNAs translationally during oocyte maturation and early embryonic development. Interacts with both the 3'-end poly(A) tail and the 5'-end cap structure during degradation, the interaction with the cap structure being required for an efficient degradation of poly(A) tails. Involved in nonsense-mediated mRNA decay, a critical process of selective degradation of mRNAs that contain premature stop codons. Also involved in degradation of inherently unstable mRNAs that contain AU-rich elements (AREs) in their 3'-UTR, possibly via its interaction with KHSRP. Probably mediates the removal of poly(A) tails of AREs mRNAs, which constitutes the first step of destabilization.<ref>PMID:9736620</ref> <ref>PMID:10882133</ref> <ref>PMID:11359775</ref> <ref>PMID:12748283</ref> <ref>PMID:15175153</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 31:
	==See Also==		==See Also==
	*[[Ribonuclease\|Ribonuclease]]		*[[Ribonuclease\|Ribonuclease]]
			*[[Temp\|Temp]]
			*[[User:Jaime.Prilusky/Test/tree\|User:Jaime.Prilusky/Test/tree]]
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Dickmanns, A.]]		[[Category: Dickmanns, A]]
	[[Category: Ficner, R.]]		[[Category: Ficner, R]]
	[[Category: Monecke, T.]]		[[Category: Monecke, T]]
	[[Category: Schell, S.]]		[[Category: Schell, S]]
	[[Category: Exonuclease]]		[[Category: Exonuclease]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 06:28, 10 October 2014

2014-10-10T06:28:16Z

← Older revision		Revision as of 06:28, 10 October 2014
Line 1:		Line 1:
	~~{{STRUCTURE_3ctr\| PDB=3ctr \| SCENE= }}~~		==Crystal structure of the RRM-domain of the poly(A)-specific ribonuclease PARN bound to m7GTP==
	===Crystal structure of the RRM-domain of the poly(A)-specific ribonuclease PARN bound to m7GTP===		<StructureSection load='3ctr' size='340' side='right' caption='[[3ctr]], [[Resolution\|resolution]] 2.10Å' scene=''>
	~~{{ABSTRACT_PUBMED_18694759}}~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[3ctr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CTR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CTR FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MGP:7-METHYL-GUANOSINE-5-TRIPHOSPHATE'>MGP</scene></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PARN, DAN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=3ctr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ctr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ctr RCSB], [http://www.ebi.ac.uk/pdbsum/3ctr PDBsum]</span></td></tr>
			</table>
			== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
			Check<jmol>
			<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ct/3ctr_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Poly(A)-specific ribonuclease (PARN) is a processive 3'-exoribonuclease involved in the decay of eukaryotic mRNAs. Interestingly, PARN interacts not only with the 3' end of the mRNA but also with its 5' end as PARN contains an RRM domain that specifically binds both the poly(A) tail and the 7-methylguanosine (m(7)G) cap. The interaction of PARN with the 5' cap of mRNAs stimulates the deadenylation activity and enhances the processivity of this reaction. We have determined the crystal structure of the PARN-RRM domain with a bound m(7)G triphosphate nucleotide, revealing a novel binding mode for the m(7)G cap. The structure of the m(7)G binding pocket is located outside of the canonical RNA-binding surface of the RRM domain and differs significantly from that of other m(7)G-cap-binding proteins. The crystal structure also shows a remarkable conformational flexibility of the RRM domain, leading to a perfect exchange of two alpha-helices with an adjacent protein molecule in the crystal lattice.

	~~==Function==~~		Crystal structure of the RRM domain of poly(A)-specific ribonuclease reveals a novel m(7)G-cap-binding mode.,Monecke T, Schell S, Dickmanns A, Ficner R J Mol Biol. 2008 Oct 17;382(4):827-34. Epub 2008 Jul 31. PMID:18694759<ref>PMID:18694759</ref>
	~~[[http://www.uniprot.org/uniprot/PARN_HUMAN PARN_HUMAN]] 3'-exoribonuclease that has a preference for poly(A) tails~~ of ~~mRNAs, thereby efficiently degrading poly(A) tails. Exonucleolytic degradation~~ of ~~the~~ poly(A) tail is often the first step in the decay of eukaryotic mRNAs and is also used to silence certain maternal mRNAs translationally during oocyte maturation and early embryonic development. Interacts with both the 3'-~~end poly~~(A) ~~tail and the 5'~~-~~end~~ cap ~~structure during degradation~~, ~~the interaction with the cap structure being required for an efficient degradation of poly(~~A~~) tails. Involved in nonsense-mediated mRNA decay~~, ~~a critical process of selective degradation of mRNAs that contain premature stop codons~~. ~~Also involved in degradation of inherently unstable mRNAs that contain AU-rich elements~~ (~~AREs~~) ~~in their 3'~~-~~UTR, possibly via its interaction with KHSRP~~. ~~Probably mediates the removal of poly(A) tails of AREs mRNAs, which constitutes the first step of destabilization~~.~~<ref>PMID:9736620</ref> <ref>PMID:10882133</ref> <ref>PMID:11359775</ref> <ref>~~PMID:~~12748283</ref>~~ <ref>PMID:~~15175153~~</ref>

	~~==About this Structure==~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	~~[[3ctr]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http:/~~/~~oca.weizmann.ac.il/oca-bin/ocashort?id=3CTR OCA].~~		</div>

	==See Also==		==See Also==
	*[[Ribonuclease\|Ribonuclease]]		*[[Ribonuclease\|Ribonuclease]]
			== References ==
	==~~Reference~~==		<references/>
	~~<ref group="xtra">PMID:018694759</ref>~~<references ~~group="xtra"~~/><~~references~~/>		__TOC__
			</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Dickmanns, A.]]		[[Category: Dickmanns, A.]]

OCA at 06:27, 6 November 2013

2013-11-06T06:27:25Z

← Older revision		Revision as of 06:27, 6 November 2013
Line 1:		Line 1:
	~~[[Image:3ctr.png\|left\|200px]]~~

	{{STRUCTURE_3ctr\| PDB=3ctr \| SCENE= }}		{{STRUCTURE_3ctr\| PDB=3ctr \| SCENE= }}

	===Crystal structure of the RRM-domain of the poly(A)-specific ribonuclease PARN bound to m7GTP===		===Crystal structure of the RRM-domain of the poly(A)-specific ribonuclease PARN bound to m7GTP===
			{{ABSTRACT_PUBMED_18694759}}

	~~{{ABSTRACT_PUBMED_18694759}}~~		==Function==
			[[http://www.uniprot.org/uniprot/PARN_HUMAN PARN_HUMAN]] 3'-exoribonuclease that has a preference for poly(A) tails of mRNAs, thereby efficiently degrading poly(A) tails. Exonucleolytic degradation of the poly(A) tail is often the first step in the decay of eukaryotic mRNAs and is also used to silence certain maternal mRNAs translationally during oocyte maturation and early embryonic development. Interacts with both the 3'-end poly(A) tail and the 5'-end cap structure during degradation, the interaction with the cap structure being required for an efficient degradation of poly(A) tails. Involved in nonsense-mediated mRNA decay, a critical process of selective degradation of mRNAs that contain premature stop codons. Also involved in degradation of inherently unstable mRNAs that contain AU-rich elements (AREs) in their 3'-UTR, possibly via its interaction with KHSRP. Probably mediates the removal of poly(A) tails of AREs mRNAs, which constitutes the first step of destabilization.<ref>PMID:9736620</ref> <ref>PMID:10882133</ref> <ref>PMID:11359775</ref> <ref>PMID:12748283</ref> <ref>PMID:15175153</ref>

	==About this Structure==		==About this Structure==
Line 14:		Line 13:

	==Reference==		==Reference==
	<ref group="xtra">PMID:018694759</ref><references group="xtra"/>		<ref group="xtra">PMID:018694759</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Dickmanns, A.]]		[[Category: Dickmanns, A.]]

OCA at 17:25, 20 October 2012

2012-10-20T17:25:47Z

← Older revision		Revision as of 17:25, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
	[[3ctr]] is a 1 chain structure ~~of [[Ribonuclease]]~~ with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CTR OCA].		[[3ctr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CTR OCA].

	==See Also==		==See Also==

OCA: Protected "3ctr" [edit=sysop:move=sysop]

2012-07-27T00:51:44Z

Protected "3ctr" [edit=sysop:move=sysop]

← Older revision	Revision as of 00:51, 27 July 2012
(No difference)

OCA at 00:51, 27 July 2012

2012-07-27T00:51:43Z

← Older revision		Revision as of 00:51, 27 July 2012
Line 1:		Line 1:
	~~{{Seed}}~~
	[[Image:3ctr.png\|left\|200px]]		[[Image:3ctr.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_3ctr", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_3ctr\| PDB=3ctr \| SCENE= }}		{{STRUCTURE_3ctr\| PDB=3ctr \| SCENE= }}

	===Crystal structure of the RRM-domain of the poly(A)-specific ribonuclease PARN bound to m7GTP===		===Crystal structure of the RRM-domain of the poly(A)-specific ribonuclease PARN bound to m7GTP===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_18694759}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 18694759 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_18694759}}		{{ABSTRACT_PUBMED_18694759}}

	==About this Structure==		==About this Structure==
	~~3CTR~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CTR OCA].		[[3ctr]] is a 1 chain structure of [[Ribonuclease]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CTR OCA].

			==See Also==
			*[[Ribonuclease\|Ribonuclease]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~18694759~~</ref><references group="xtra"/>		<ref group="xtra">PMID:018694759</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Dickmanns, A.]]		[[Category: Dickmanns, A.]]
Line 29:		Line 20:
	[[Category: Monecke, T.]]		[[Category: Monecke, T.]]
	[[Category: Schell, S.]]		[[Category: Schell, S.]]
	~~[[Category: Cytoplasm]]~~
	[[Category: Exonuclease]]		[[Category: Exonuclease]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
Line 45:		Line 35:
	[[Category: Rna-binding]]		[[Category: Rna-binding]]
	[[Category: Rrm]]		[[Category: Rrm]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 17:49:48 2009''~~

OCA at 15:49, 17 February 2009

2009-02-17T15:49:50Z

← Older revision		Revision as of 15:49, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
	3CTR is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CTR OCA].		3CTR is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CTR OCA].

	==Reference==		==Reference==
	Crystal structure of the RRM domain of poly(A)-specific ribonuclease reveals a novel m(7)G-cap-binding mode., Monecke T, Schell S, Dickmanns A, Ficner R, J Mol Biol. 2008 Oct 17;382(4):827-34. Epub 2008 Jul 31. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18694759 18694759]~~		<ref group="xtra">PMID:18694759</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	~~[[Category: Single protein]]~~
	[[Category: Dickmanns, A.]]		[[Category: Dickmanns, A.]]
	[[Category: Ficner, R.]]		[[Category: Ficner, R.]]
Line 47:		Line 46:
	[[Category: Rrm]]		[[Category: Rrm]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Nov 12 20~~:43:~~36 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 17:49:48 2009''