3g8q - Revision history

OCA at 09:53, 21 February 2024

OCA — Wed, 21 Feb 2024 09:53:01 GMT

←Older revision		Revision as of 09:53, 21 February 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/CDAT8_METKA CDAT8_METKA] Catalyzes the deamimation of cytosine to uracil at position 8 of tRNA in 30 different tRNAs. This editing guarantees the proper folding and functionality of the tRNAs.<ref>PMID:19407206</ref>		[https://www.uniprot.org/uniprot/CDAT8_METKA CDAT8_METKA] Catalyzes the deamimation of cytosine to uracil at position 8 of tRNA in 30 different tRNAs. This editing guarantees the proper folding and functionality of the tRNAs.<ref>PMID:19407206</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	All canonical transfer RNAs (tRNAs) have a uridine at position 8, involved in maintaining tRNA tertiary structure. However, the hyperthermophilic archaeon Methanopyrus kandleri harbors 30 (out of 34) tRNA genes with cytidine at position 8. Here, we demonstrate C-to-U editing at this location in the tRNA's tertiary core, and present the crystal structure of a tRNA-specific cytidine deaminase, CDAT8, which has the cytidine deaminase domain linked to a tRNA-binding THUMP domain. CDAT8 is specific for C deamination at position 8, requires only the acceptor stem hairpin for activity, and belongs to a unique family within the "cytidine deaminase-like" superfamily. The presence of this C-to-U editing enzyme guarantees the proper folding and functionality of all M. kandleri tRNAs.
-
-	A cytidine deaminase edits C to U in transfer RNAs in Archaea.,Randau L, Stanley BJ, Kohlway A, Mechta S, Xiong Y, Soll D Science. 2009 May 1;324(5927):657-9. PMID:19407206<ref>PMID:19407206</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3g8q" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:40, 13 December 2023

OCA — Wed, 13 Dec 2023 16:40:54 GMT

←Older revision		Revision as of 16:40, 13 December 2023
Line 3:		Line 3:
	<StructureSection load='3g8q' size='340' side='right'caption='[[3g8q]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='3g8q' size='340' side='right'caption='[[3g8q]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3g8q]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Dsm_6324 Dsm 6324~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G8Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G8Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3g8q]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanopyrus_kandleri Methanopyrus kandleri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G8Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G8Q FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.4Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~MK0935 ([https~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=2320 DSM 6324])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=3g8q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g8q OCA], [https://pdbe.org/3g8q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g8q RCSB], [https://www.ebi.ac.uk/pdbsum/3g8q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g8q 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=3g8q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g8q OCA], [https://pdbe.org/3g8q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g8q RCSB], [https://www.ebi.ac.uk/pdbsum/3g8q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g8q ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/CDAT8_METKA CDAT8_METKA]] Catalyzes the deamimation of cytosine to uracil at position 8 of tRNA in 30 different tRNAs. This editing guarantees the proper folding and functionality of the tRNAs.<ref>PMID:19407206</ref>	+	[https://www.uniprot.org/uniprot/CDAT8_METKA CDAT8_METKA] Catalyzes the deamimation of cytosine to uracil at position 8 of tRNA in 30 different tRNAs. This editing guarantees the proper folding and functionality of the tRNAs.<ref>PMID:19407206</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Dsm 6324]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Stanley, B J~~]]	+	[[Category: Methanopyrus kandleri]]
-	[[Category: ~~Xiong, Y~~]]	+	[[Category: Stanley BJ]]
-	[[Category: ~~Cytidine deaminase]]~~	+	[[Category: Xiong Y]]
-	~~[[Category: Ferredoxin-like domain]]~~	+
-	~~[[Category: Rna binding protein]]~~	+
-	~~[[Category: Thump~~]]	+

OCA at 07:58, 9 March 2022

OCA — Wed, 09 Mar 2022 07:58:32 GMT

←Older revision		Revision as of 07:58, 9 March 2022
Line 1:		Line 1:

	==A cytidine deaminase edits C-to-U in transfer RNAs in archaea==		==A cytidine deaminase edits C-to-U in transfer RNAs in archaea==
-	<StructureSection load='3g8q' size='340' side='right' caption='[[3g8q]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='3g8q' size='340' side='right'caption='[[3g8q]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3g8q]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Dsm_6324 Dsm 6324]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G8Q OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3G8Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3g8q]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Dsm_6324 Dsm 6324]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G8Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G8Q FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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=NA:SODIUM+ION'>NA</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">MK0935 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2320 DSM 6324])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MK0935 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2320 DSM 6324])</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=3g8q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g8q OCA], [~~http~~://pdbe.org/3g8q PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3g8q RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3g8q PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3g8q 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=3g8q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g8q OCA], [https://pdbe.org/3g8q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g8q RCSB], [https://www.ebi.ac.uk/pdbsum/3g8q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g8q ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/CDAT8_METKA CDAT8_METKA]] Catalyzes the deamimation of cytosine to uracil at position 8 of tRNA in 30 different tRNAs. This editing guarantees the proper folding and functionality of the tRNAs.<ref>PMID:19407206</ref>	+	[[https://www.uniprot.org/uniprot/CDAT8_METKA CDAT8_METKA]] Catalyzes the deamimation of cytosine to uracil at position 8 of tRNA in 30 different tRNAs. This editing guarantees the proper folding and functionality of the tRNAs.<ref>PMID:19407206</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Dsm 6324]]		[[Category: Dsm 6324]]
		+	[[Category: Large Structures]]
	[[Category: Stanley, B J]]		[[Category: Stanley, B J]]
	[[Category: Xiong, Y]]		[[Category: Xiong, Y]]

OCA at 05:18, 7 December 2018

OCA — Fri, 07 Dec 2018 05:18:59 GMT

←Older revision		Revision as of 05:18, 7 December 2018
Line 1:		Line 1:
		+
	==A cytidine deaminase edits C-to-U in transfer RNAs in archaea==		==A cytidine deaminase edits C-to-U in transfer RNAs in archaea==
	<StructureSection load='3g8q' size='340' side='right' caption='[[3g8q]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='3g8q' size='340' side='right' caption='[[3g8q]], [[Resolution\|resolution]] 2.40Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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=NA:SODIUM+ION'>NA</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">MK0935 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2320 DSM 6324])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MK0935 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2320 DSM 6324])</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=3g8q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g8q OCA], [http://pdbe.org/3g8q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3g8q RCSB], [http://www.ebi.ac.uk/pdbsum/3g8q 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=3g8q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g8q OCA], [http://pdbe.org/3g8q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3g8q RCSB], [http://www.ebi.ac.uk/pdbsum/3g8q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3g8q ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 19:06, 30 November 2015

OCA — Mon, 30 Nov 2015 19:06:44 GMT

←Older revision		Revision as of 19:06, 30 November 2015
Line 2:		Line 2:
	<StructureSection load='3g8q' size='340' side='right' caption='[[3g8q]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='3g8q' size='340' side='right' caption='[[3g8q]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3g8q]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Methanopyrus_kandleri Methanopyrus kandleri~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G8Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G8Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3g8q]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Dsm_6324 Dsm 6324]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G8Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G8Q FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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=NA:SODIUM+ION'>NA</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">MK0935 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2320 ~~Methanopyrus kandleri~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MK0935 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2320 DSM 6324])</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=3g8q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g8q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g8q RCSB], [http://www.ebi.ac.uk/pdbsum/3g8q 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=3g8q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g8q OCA], [http://pdbe.org/3g8q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3g8q RCSB], [http://www.ebi.ac.uk/pdbsum/3g8q PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~Q8TWU6_METKA Q8TWU6_METKA~~]] Catalyzes the deamimation of cytosine to uracil at position 8 of tRNA in 30 different tRNAs. This editing guarantees the proper folding and functionality of the tRNAs.<ref>PMID:19407206</ref>	+	[[http://www.uniprot.org/uniprot/CDAT8_METKA CDAT8_METKA]] Catalyzes the deamimation of cytosine to uracil at position 8 of tRNA in 30 different tRNAs. This editing guarantees the proper folding and functionality of the tRNAs.<ref>PMID:19407206</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		Line 17:
	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 3g8q" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Methanopyrus kandleri~~]]	+	[[Category: Dsm 6324]]
	[[Category: Stanley, B J]]		[[Category: Stanley, B J]]
	[[Category: Xiong, Y]]		[[Category: Xiong, Y]]

OCA at 06:22, 25 December 2014

OCA — Thu, 25 Dec 2014 06:22:35 GMT

←Older revision		Revision as of 06:22, 25 December 2014
Line 7:		Line 7:
	<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=3g8q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g8q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g8q RCSB], [http://www.ebi.ac.uk/pdbsum/3g8q 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=3g8q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g8q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g8q RCSB], [http://www.ebi.ac.uk/pdbsum/3g8q PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Q8TWU6_METKA Q8TWU6_METKA]] Catalyzes the deamimation of cytosine to uracil at position 8 of tRNA in 30 different tRNAs. This editing guarantees the proper folding and functionality of the tRNAs.<ref>PMID:19407206</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 10:13, 3 December 2014

OCA — Wed, 03 Dec 2014 10:13:44 GMT

←Older revision		Revision as of 10:13, 3 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3g8q.~~png~~\|~~left~~\|~~200px~~]]	+	==A cytidine deaminase edits C-to-U in transfer RNAs in archaea==
		+	<StructureSection load='3g8q' size='340' side='right' caption='[[3g8q]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3g8q]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanopyrus_kandleri Methanopyrus kandleri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G8Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G8Q FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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">MK0935 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2320 Methanopyrus kandleri])</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=3g8q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g8q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g8q RCSB], [http://www.ebi.ac.uk/pdbsum/3g8q PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	All canonical transfer RNAs (tRNAs) have a uridine at position 8, involved in maintaining tRNA tertiary structure. However, the hyperthermophilic archaeon Methanopyrus kandleri harbors 30 (out of 34) tRNA genes with cytidine at position 8. Here, we demonstrate C-to-U editing at this location in the tRNA's tertiary core, and present the crystal structure of a tRNA-specific cytidine deaminase, CDAT8, which has the cytidine deaminase domain linked to a tRNA-binding THUMP domain. CDAT8 is specific for C deamination at position 8, requires only the acceptor stem hairpin for activity, and belongs to a unique family within the "cytidine deaminase-like" superfamily. The presence of this C-to-U editing enzyme guarantees the proper folding and functionality of all M. kandleri tRNAs.

-	~~{{STRUCTURE_3g8q\| PDB=3g8q \| SCENE= }}~~	+	A cytidine deaminase edits C to U in transfer RNAs in Archaea.,Randau L, Stanley BJ, Kohlway A, Mechta S, Xiong Y, Soll D Science. 2009 May 1;324(5927):657-9. PMID:19407206<ref>PMID:19407206</ref>

-	~~===A cytidine deaminase edits C-to-~~U ~~in transfer RNAs in archaea===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19407206}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3g8q]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Methanopyrus_kandleri Methanopyrus kandleri]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3G8Q OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:019407206<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Methanopyrus kandleri]]		[[Category: Methanopyrus kandleri]]
-	[[Category: Stanley, B J.]]	+	[[Category: Stanley, B J]]
-	[[Category: Xiong, Y.]]	+	[[Category: Xiong, Y]]
	[[Category: Cytidine deaminase]]		[[Category: Cytidine deaminase]]
	[[Category: Ferredoxin-like domain]]		[[Category: Ferredoxin-like domain]]
	[[Category: Rna binding protein]]		[[Category: Rna binding protein]]
	[[Category: Thump]]		[[Category: Thump]]

OCA: Protected "3g8q" [edit=sysop:move=sysop]

OCA — Wed, 20 Feb 2013 14:29:13 GMT

Protected "3g8q" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:29, 20 February 2013

OCA at 14:29, 20 February 2013

OCA — Wed, 20 Feb 2013 14:29:08 GMT

←Older revision		Revision as of 14:29, 20 February 2013
Line 1:		Line 1:
-	~~{{Seed}}~~	+	[[Image:3g8q.png\|left\|200px]]
-	[[Image:3g8q.~~jpg~~\|left\|200px]]	+

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3g8q", 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_3g8q\| PDB=3g8q \| SCENE= }}		{{STRUCTURE_3g8q\| PDB=3g8q \| SCENE= }}

	===A cytidine deaminase edits C-to-U in transfer RNAs in archaea===		===A cytidine deaminase edits C-to-U in transfer RNAs in archaea===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19407206}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19407206 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19407206}}		{{ABSTRACT_PUBMED_19407206}}

	==About this Structure==		==About this Structure==
-	~~3G8Q~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Methanopyrus_kandleri Methanopyrus kandleri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G8Q OCA].	+	[[3g8q]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanopyrus_kandleri Methanopyrus kandleri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G8Q OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19407206~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019407206</ref><references group="xtra"/>
	[[Category: Methanopyrus kandleri]]		[[Category: Methanopyrus kandleri]]
	[[Category: Stanley, B J.]]		[[Category: Stanley, B J.]]
Line 31:		Line 19:
	[[Category: Rna binding protein]]		[[Category: Rna binding protein]]
	[[Category: Thump]]		[[Category: Thump]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 27 15:22:25 2009''

OCA at 12:22, 27 May 2009

OCA — Wed, 27 May 2009 12:22:28 GMT

←Older revision		Revision as of 12:22, 27 May 2009
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3g8q.jpg\|left\|200px]]

-	The ~~entry 3g8q~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3g8q", 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_3g8q\| PDB=3g8q \| SCENE= }}

-	~~Authors: Xiong, Y., Stanley, B.J.~~	+	===A cytidine deaminase edits C-to-U in transfer RNAs in archaea===

-	Description: A cytidine deaminase edits C-to-U in transfer RNAs in archaea

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Mar 4 14~~:45:08 2009''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19407206}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19407206 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19407206}}
		+
		+	==About this Structure==
		+	3G8Q is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Methanopyrus_kandleri Methanopyrus kandleri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G8Q OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19407206</ref><references group="xtra"/>
		+	[[Category: Methanopyrus kandleri]]
		+	[[Category: Stanley, B J.]]
		+	[[Category: Xiong, Y.]]
		+	[[Category: Cytidine deaminase]]
		+	[[Category: Ferredoxin-like domain]]
		+	[[Category: Rna binding protein]]
		+	[[Category: Thump]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 27 15:22:25 2009''