1yt3 - Revision history

OCA at 08:59, 14 February 2024

OCA — Wed, 14 Feb 2024 08:59:41 GMT

←Older revision		Revision as of 08:59, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='1yt3' size='340' side='right'caption='[[1yt3]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1yt3' size='340' side='right'caption='[[1yt3]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yt3]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YT3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1YT3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yt3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YT3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YT3 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>~~, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.6Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>RND ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Ribonuclease_III Ribonuclease III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.3 3.1.26.3]~~ </~~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=1yt3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yt3 OCA], [https://pdbe.org/1yt3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yt3 RCSB], [https://www.ebi.ac.uk/pdbsum/1yt3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yt3 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=1yt3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yt3 OCA], [~~http~~://pdbe.org/1yt3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1yt3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1yt3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1yt3 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RND_ECOLI RND_ECOLI]] Exonuclease involved in the 3' processing of various precursor tRNAs. Initiates hydrolysis at the 3'-terminus of an RNA molecule and releases 5'-mononucleotides.<ref>PMID:3041371</ref> <ref>PMID:6263886</ref>	+	[https://www.uniprot.org/uniprot/RND_ECOLI RND_ECOLI] Exonuclease involved in the 3' processing of various precursor tRNAs. Initiates hydrolysis at the 3'-terminus of an RNA molecule and releases 5'-mononucleotides.<ref>PMID:3041371</ref> <ref>PMID:6263886</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=1yt3 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=1yt3 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	RNase D (RND) is one of seven exoribonucleases identified in Escherichia coli. RNase D has homologs in many eubacteria and eukaryotes, and has been shown to contribute to the 3' maturation of several stable RNAs. Here, we report the 1.6 A resolution crystal structure of E. coli RNase D. The conserved DEDD residues of RNase D fold into an arrangement very similar to the Klenow fragment exonuclease domain. Besides the catalytic domain, RNase D also contains two structurally similar alpha-helical domains with no discernible sequence homology between them. These closely resemble the HRDC domain previously seen in RecQ-family helicases and several other proteins acting on nucleic acids. More interestingly, the DEDD catalytic domain and the two helical domains come together to form a ring-shaped structure. The ring-shaped architecture of E. coli RNase D and the HRDC domains likely play a major role in determining the substrate specificity of this exoribonuclease.
-
-	Crystal structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing.,Zuo Y, Wang Y, Malhotra A Structure. 2005 Jul;13(7):973-84. PMID:16004870<ref>PMID:16004870</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1yt3" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]		*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
-	*[[Temp\|Temp]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Ribonuclease III]]~~	+	[[Category: Malhotra A]]
-	[[Category: Malhotra, A]]	+	[[Category: Wang Y]]
-	[[Category: Wang, Y]]	+	[[Category: Zuo Y]]
-	[[Category: Zuo, Y]]	+
-	~~[[Category: Exonuclease]]~~	+
-	~~[[Category: Exoribonuclease]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Nuclease]]~~	+
-	~~[[Category: Ribonuclease]]~~	+
-	~~[[Category: Rnase]]~~	+
-	~~[[Category: Translation]]~~	+
-	~~[[Category: Trna processing~~]]	+

OCA at 08:52, 20 January 2021

OCA — Wed, 20 Jan 2021 08:52:07 GMT

←Older revision		Revision as of 08:52, 20 January 2021
Line 1:		Line 1:

	==Crystal Structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing==		==Crystal Structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing==
-	<StructureSection load='1yt3' size='340' side='right' caption='[[1yt3]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='1yt3' size='340' side='right'caption='[[1yt3]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yt3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YT3 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1YT3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yt3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YT3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1YT3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RND ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RND ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_III Ribonuclease III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.3 3.1.26.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_III Ribonuclease III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.3 3.1.26.3] </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=1yt3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yt3 OCA], [http://pdbe.org/1yt3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yt3 RCSB], [http://www.ebi.ac.uk/pdbsum/1yt3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yt3 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=1yt3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yt3 OCA], [http://pdbe.org/1yt3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yt3 RCSB], [http://www.ebi.ac.uk/pdbsum/1yt3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yt3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 32:		Line 32:

	==See Also==		==See Also==
-	*[[Ribonuclease\|Ribonuclease]]	+	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
	*[[Temp\|Temp]]		*[[Temp\|Temp]]
	== References ==		== References ==
Line 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Ribonuclease III]]		[[Category: Ribonuclease III]]
	[[Category: Malhotra, A]]		[[Category: Malhotra, A]]

OCA at 07:07, 25 April 2018

OCA — Wed, 25 Apr 2018 07:07:38 GMT

←Older revision		Revision as of 07:07, 25 April 2018
Line 1:		Line 1:
		+
	==Crystal Structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing==		==Crystal Structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing==
	<StructureSection load='1yt3' size='340' side='right' caption='[[1yt3]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1yt3' size='340' side='right' caption='[[1yt3]], [[Resolution\|resolution]] 1.60Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RND ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RND ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_III Ribonuclease III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.3 3.1.26.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_III Ribonuclease III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.3 3.1.26.3] </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=1yt3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yt3 OCA], [http://pdbe.org/1yt3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yt3 RCSB], [http://www.ebi.ac.uk/pdbsum/1yt3 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=1yt3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yt3 OCA], [http://pdbe.org/1yt3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yt3 RCSB], [http://www.ebi.ac.uk/pdbsum/1yt3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yt3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yt/1yt3_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yt/1yt3_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>

OCA at 19:40, 9 February 2016

OCA — Tue, 09 Feb 2016 19:40:52 GMT

←Older revision		Revision as of 19:40, 9 February 2016
Line 18:		Line 18:
	<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=1yt3 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 01:26, 11 September 2015

OCA — Fri, 11 Sep 2015 01:26:29 GMT

←Older revision		Revision as of 01:26, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1yt3' size='340' side='right' caption='[[1yt3]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1yt3' size='340' side='right' caption='[[1yt3]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yt3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YT3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YT3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yt3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YT3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YT3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RND ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RND ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_III Ribonuclease III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.3 3.1.26.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_III Ribonuclease III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.3 3.1.26.3] </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=1yt3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yt3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yt3 RCSB], [http://www.ebi.ac.uk/pdbsum/1yt3 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=1yt3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yt3 OCA], [http://pdbe.org/1yt3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yt3 RCSB], [http://www.ebi.ac.uk/pdbsum/1yt3 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	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 1yt3" 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: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Ribonuclease III]]		[[Category: Ribonuclease III]]
	[[Category: Malhotra, A]]		[[Category: Malhotra, A]]

OCA at 09:06, 25 December 2014

OCA — Thu, 25 Dec 2014 09:06:08 GMT

←Older revision		Revision as of 09:06, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1yt3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YT3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YT3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1yt3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YT3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YT3 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RND ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RND ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_III Ribonuclease III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.3 3.1.26.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_III Ribonuclease III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.3 3.1.26.3] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yt3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yt3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yt3 RCSB], [http://www.ebi.ac.uk/pdbsum/1yt3 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=1yt3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yt3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yt3 RCSB], [http://www.ebi.ac.uk/pdbsum/1yt3 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RND_ECOLI RND_ECOLI]] Exonuclease involved in the 3' processing of various precursor tRNAs. Initiates hydrolysis at the 3'-terminus of an RNA molecule and releases 5'-mononucleotides.<ref>PMID:3041371</ref> <ref>PMID:6263886</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 35:		Line 39:
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Ribonuclease III]]		[[Category: Ribonuclease III]]
-	[[Category: Malhotra, A.]]	+	[[Category: Malhotra, A]]
-	[[Category: Wang, Y.]]	+	[[Category: Wang, Y]]
-	[[Category: Zuo, Y.]]	+	[[Category: Zuo, Y]]
	[[Category: Exonuclease]]		[[Category: Exonuclease]]
	[[Category: Exoribonuclease]]		[[Category: Exoribonuclease]]

OCA at 22:08, 28 September 2014

OCA — Sun, 28 Sep 2014 22:08:36 GMT

←Older revision		Revision as of 22:08, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1yt3.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing==
		+	<StructureSection load='1yt3' size='340' side='right' caption='[[1yt3]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1yt3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YT3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YT3 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RND ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_III Ribonuclease III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.3 3.1.26.3] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yt3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yt3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yt3 RCSB], [http://www.ebi.ac.uk/pdbsum/1yt3 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/yt/1yt3_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 ==
		+	RNase D (RND) is one of seven exoribonucleases identified in Escherichia coli. RNase D has homologs in many eubacteria and eukaryotes, and has been shown to contribute to the 3' maturation of several stable RNAs. Here, we report the 1.6 A resolution crystal structure of E. coli RNase D. The conserved DEDD residues of RNase D fold into an arrangement very similar to the Klenow fragment exonuclease domain. Besides the catalytic domain, RNase D also contains two structurally similar alpha-helical domains with no discernible sequence homology between them. These closely resemble the HRDC domain previously seen in RecQ-family helicases and several other proteins acting on nucleic acids. More interestingly, the DEDD catalytic domain and the two helical domains come together to form a ring-shaped structure. The ring-shaped architecture of E. coli RNase D and the HRDC domains likely play a major role in determining the substrate specificity of this exoribonuclease.

-	~~{{STRUCTURE_1yt3\| PDB=1yt3 \| SCENE= }}~~	+	Crystal structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing.,Zuo Y, Wang Y, Malhotra A Structure. 2005 Jul;13(7):973-84. PMID:16004870<ref>PMID:16004870</ref>

-	~~===Crystal Structure of Escherichia coli RNase D~~, ~~an exoribonuclease involved in structured RNA processing===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16004870}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1yt3]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1YT3 OCA].~~	+

	==See Also==		==See Also==
	*[[Ribonuclease\|Ribonuclease]]		*[[Ribonuclease\|Ribonuclease]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:016004870<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Ribonuclease III]]		[[Category: Ribonuclease III]]

OCA at 14:55, 20 October 2012

OCA — Sat, 20 Oct 2012 14:55:21 GMT

←Older revision		Revision as of 14:55, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1yt3]] is a 1 chain structure ~~of [[Ribonuclease]]~~ with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YT3 OCA].	+	[[1yt3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YT3 OCA].

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

OCA: Protected "1yt3" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 16:41:54 GMT

Protected "1yt3" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:41, 26 July 2012

OCA at 16:41, 26 July 2012

OCA — Thu, 26 Jul 2012 16:41:52 GMT

←Older revision		Revision as of 16:41, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1yt3.png\|left\|200px]]		[[Image:1yt3.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1yt3", 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.
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	{{STRUCTURE_1yt3\| PDB=1yt3 \| SCENE= }}		{{STRUCTURE_1yt3\| PDB=1yt3 \| SCENE= }}

	===Crystal Structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing===		===Crystal Structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16004870}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16004870 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_16004870}}		{{ABSTRACT_PUBMED_16004870}}

	==About this Structure==		==About this Structure==
-	~~1YT3~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YT3 OCA].	+	[[1yt3]] is a 1 chain structure of [[Ribonuclease]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YT3 OCA].
		+
		+	==See Also==
		+	*[[Ribonuclease\|Ribonuclease]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16004870~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016004870</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Ribonuclease III]]		[[Category: Ribonuclease III]]
Line 35:		Line 26:
	[[Category: Ribonuclease]]		[[Category: Ribonuclease]]
	[[Category: Rnase]]		[[Category: Rnase]]
		+	[[Category: Translation]]
	[[Category: Trna processing]]		[[Category: Trna processing]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 12:15:54 2009''