4isj - Revision history

OCA at 11:59, 1 March 2024

OCA — Fri, 01 Mar 2024 11:59:35 GMT

←Older revision		Revision as of 11:59, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4isj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ISJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ISJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[4isj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ISJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ISJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PRD_900003:sucrose'>PRD_900003</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.344Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PRD_900003:sucrose'>PRD_900003</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4isj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4isj OCA], [https://pdbe.org/4isj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4isj RCSB], [https://www.ebi.ac.uk/pdbsum/4isj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4isj 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=4isj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4isj OCA], [https://pdbe.org/4isj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4isj RCSB], [https://www.ebi.ac.uk/pdbsum/4isj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4isj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/RTCB_PYRHO RTCB_PYRHO] tRNA-splicing ligase that acts by directly joining spliced tRNA halves to mature-sized tRNAs by incorporating the precursor-derived splice junction phosphate into the mature tRNA as a canonical 3',5'-phosphodiester. May act as a RNA ligase with broad substrate specificity, and may function toward other RNAs (By similarity).		[https://www.uniprot.org/uniprot/RTCB_PYRHO RTCB_PYRHO] tRNA-splicing ligase that acts by directly joining spliced tRNA halves to mature-sized tRNAs by incorporating the precursor-derived splice junction phosphate into the mature tRNA as a canonical 3',5'-phosphodiester. May act as a RNA ligase with broad substrate specificity, and may function toward other RNAs (By similarity).
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	RtcB is an atypical RNA ligase that joins either 2',3'-cyclic phosphate or 3'-phosphate termini to 5'-hydroxyl termini. In contrast to typical RNA ligases, which rely on ATP and Mg(II), catalysis by RtcB is dependent on GTP and Mn(II) with ligation proceeding through a covalent RtcB-histidine-GMP intermediate. Here, we present three structures of Pyrococcus horikoshii RtcB complexes that capture snapshots along the entire guanylylation pathway. These structures show that prior to binding GTP, a single manganese ion (Mn1) is bound to RtcB. To capture the step immediately preceding RtcB guanylylation, we determined a structure of RtcB in complex with Mn(II) and the unreactive GTP analogue guanosine 5'-(alpha-thio)triphosphate (GTPalphaS). This structure shows that Mn1 is poised to stabilize the pentavalent transition state of guanylylation while a second manganese ion (Mn2) is coordinated to a nonbridging oxygen of the gamma-phosphoryl group. The pyrophosphate leaving group of GTPalphaS is oriented apically to His404 with the epsilon-nitrogen poised for in-line attack on the alpha-phosphorus atom. The structure of RtcB in complex with GTPalphaS also reveals the network of hydrogen bonds that recognize GTP and illuminates the significant conformational changes that accompany the binding of this cofactor. Finally, a structure of the enzymic histidine-GMP intermediate depicts the end of the guanylylation pathway. The ensuing molecular description of the RtcB guanylylation pathway shows that RtcB and classical ATP- and Mg(II)-dependent nucleic acid ligases have converged upon a similar two-metal mechanism for formation of the nucleotidylated enzyme intermediate.
-
-	Structures of the Noncanonical RNA Ligase RtcB Reveal the Mechanism of Histidine Guanylylation.,Desai KK, Bingman CA, Phillips GN Jr, Raines RT Biochemistry. 2013 Apr 16;52(15):2518-25. doi: 10.1021/bi4002375. Epub 2013 Apr, 5. PMID:23560983<ref>PMID:23560983</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4isj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[RNA ligase\|RNA ligase]]		*[[RNA ligase\|RNA ligase]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 21:07, 16 November 2022

OCA — Wed, 16 Nov 2022 21:07:30 GMT

←Older revision		Revision as of 21:07, 16 November 2022
Line 1:		Line 1:

	==RNA Ligase RtcB in complex with Mn(II)==		==RNA Ligase RtcB in complex with Mn(II)==
-	<StructureSection load='4isj' size='340' side='right' caption='[[4isj]], [[Resolution\|resolution]] 2.34Å' scene=''>	+	<StructureSection load='4isj' size='340' side='right'caption='[[4isj]], [[Resolution\|resolution]] 2.34Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4isj]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pyrococcus_horikoshii~~ Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ISJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4ISJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4isj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ISJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ISJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:~~MANGANESE+(II)+ION~~'>MN</scene>, <scene name='pdbligand=~~SO4~~:~~SULFATE+ION~~'>~~SO4~~</scene>, <scene name='pdbligand=~~SUC~~:~~SUCROSE~~'>~~SUC~~</scene><~~/td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PRD_900003:sucrose'>PRD_900003</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat">[[4isz\|4isz]]~~, ~~[[4it0\|4it0]]~~<~~/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=4isj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4isj OCA], [https://pdbe.org/4isj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4isj RCSB], [https://www.ebi.ac.uk/pdbsum/4isj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4isj ProSAT]</span></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">PH1602, rtcB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])~~</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=4isj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4isj OCA], [~~http~~://pdbe.org/4isj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4isj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4isj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4isj ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RTCB_PYRHO RTCB_PYRHO]] tRNA-splicing ligase that acts by directly joining spliced tRNA halves to mature-sized tRNAs by incorporating the precursor-derived splice junction phosphate into the mature tRNA as a canonical 3',5'-phosphodiester. May act as a RNA ligase with broad substrate specificity, and may function toward other RNAs (By similarity).	+	[https://www.uniprot.org/uniprot/RTCB_PYRHO RTCB_PYRHO] tRNA-splicing ligase that acts by directly joining spliced tRNA halves to mature-sized tRNAs by incorporating the precursor-derived splice junction phosphate into the mature tRNA as a canonical 3',5'-phosphodiester. May act as a RNA ligase with broad substrate specificity, and may function toward other RNAs (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pyrococcus horikoshii~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Bingman, C A~~]]	+	[[Category: Pyrococcus horikoshii OT3]]
-	[[Category: ~~Desai, K K~~]]	+	[[Category: Bingman CA]]
-	[[Category: ~~Phillips, G N~~]]	+	[[Category: Desai KK]]
-	[[Category: ~~Raines, R T~~]]	+	[[Category: Phillips Jr GN]]
-	[[Category: ~~Ligase]]~~	+	[[Category: Raines RT]]
-	~~[[Category: Rna ligase~~]]	+

OCA at 11:57, 7 October 2017

OCA — Sat, 07 Oct 2017 11:57:46 GMT

←Older revision		Revision as of 11:57, 7 October 2017
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 4isj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4isj" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[RNA ligase\|RNA ligase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:14, 18 October 2016

OCA — Tue, 18 Oct 2016 07:14:59 GMT

←Older revision		Revision as of 07:14, 18 October 2016
Line 3:		Line 3:
	<StructureSection load='4isj' size='340' side='right' caption='[[4isj]], [[Resolution\|resolution]] 2.34Å' scene=''>		<StructureSection load='4isj' size='340' side='right' caption='[[4isj]], [[Resolution\|resolution]] 2.34Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4isj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pyrho Pyrho~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ISJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ISJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4isj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ISJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ISJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4isz\|4isz]], [[4it0\|4it0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4isz\|4isz]], [[4it0\|4it0]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PH1602, rtcB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 ~~PYRHO~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PH1602, rtcB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</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=4isj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4isj OCA], [http://pdbe.org/4isj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4isj RCSB], [http://www.ebi.ac.uk/pdbsum/4isj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4isj ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4isj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4isj OCA], [http://pdbe.org/4isj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4isj RCSB], [http://www.ebi.ac.uk/pdbsum/4isj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4isj ProSAT]</span></td></tr>
	</table>		</table>
Line 24:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pyrho~~]]	+	[[Category: Pyrococcus horikoshii]]
	[[Category: Bingman, C A]]		[[Category: Bingman, C A]]
	[[Category: Desai, K K]]		[[Category: Desai, K K]]

OCA at 02:09, 5 August 2016

OCA — Fri, 05 Aug 2016 02:09:00 GMT

←Older revision		Revision as of 02:09, 5 August 2016
Line 1:		Line 1:
		+
	==RNA Ligase RtcB in complex with Mn(II)==		==RNA Ligase RtcB in complex with Mn(II)==
	<StructureSection load='4isj' size='340' side='right' caption='[[4isj]], [[Resolution\|resolution]] 2.34Å' scene=''>		<StructureSection load='4isj' size='340' side='right' caption='[[4isj]], [[Resolution\|resolution]] 2.34Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4isj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pyrococcus_horikoshii_ot3 Pyrococcus horikoshii ot3~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ISJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ISJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4isj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrho Pyrho]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ISJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ISJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4isz\|4isz]], [[4it0\|4it0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4isz\|4isz]], [[4it0\|4it0]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PH1602, rtcB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 ~~Pyrococcus horikoshii OT3~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PH1602, rtcB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 PYRHO])</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=4isj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4isj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4isj RCSB], [http://www.ebi.ac.uk/pdbsum/4isj 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=4isj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4isj OCA], [http://pdbe.org/4isj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4isj RCSB], [http://www.ebi.ac.uk/pdbsum/4isj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4isj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 4isj" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pyrococcus horikoshii ot3~~]]	+	[[Category: Pyrho]]
	[[Category: Bingman, C A]]		[[Category: Bingman, C A]]
	[[Category: Desai, K K]]		[[Category: Desai, K K]]

OCA at 14:57, 25 December 2014

OCA — Thu, 25 Dec 2014 14:57:06 GMT

←Older revision		Revision as of 14:57, 25 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4isj\| PDB=4isj \| SCENE= }}~~	+	==RNA Ligase RtcB in complex with Mn(II)==
-	===RNA Ligase RtcB in complex with Mn(II)===	+	<StructureSection load='4isj' size='340' side='right' caption='[[4isj]], [[Resolution\|resolution]] 2.34Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23560983}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4isj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii_ot3 Pyrococcus horikoshii ot3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ISJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ISJ FirstGlance]. <br>
-	==Function==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4isz\|4isz]], [[4it0\|4it0]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PH1602, rtcB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii OT3])</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=4isj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4isj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4isj RCSB], [http://www.ebi.ac.uk/pdbsum/4isj PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
	[[http://www.uniprot.org/uniprot/RTCB_PYRHO RTCB_PYRHO]] tRNA-splicing ligase that acts by directly joining spliced tRNA halves to mature-sized tRNAs by incorporating the precursor-derived splice junction phosphate into the mature tRNA as a canonical 3',5'-phosphodiester. May act as a RNA ligase with broad substrate specificity, and may function toward other RNAs (By similarity).		[[http://www.uniprot.org/uniprot/RTCB_PYRHO RTCB_PYRHO]] tRNA-splicing ligase that acts by directly joining spliced tRNA halves to mature-sized tRNAs by incorporating the precursor-derived splice junction phosphate into the mature tRNA as a canonical 3',5'-phosphodiester. May act as a RNA ligase with broad substrate specificity, and may function toward other RNAs (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	RtcB is an atypical RNA ligase that joins either 2',3'-cyclic phosphate or 3'-phosphate termini to 5'-hydroxyl termini. In contrast to typical RNA ligases, which rely on ATP and Mg(II), catalysis by RtcB is dependent on GTP and Mn(II) with ligation proceeding through a covalent RtcB-histidine-GMP intermediate. Here, we present three structures of Pyrococcus horikoshii RtcB complexes that capture snapshots along the entire guanylylation pathway. These structures show that prior to binding GTP, a single manganese ion (Mn1) is bound to RtcB. To capture the step immediately preceding RtcB guanylylation, we determined a structure of RtcB in complex with Mn(II) and the unreactive GTP analogue guanosine 5'-(alpha-thio)triphosphate (GTPalphaS). This structure shows that Mn1 is poised to stabilize the pentavalent transition state of guanylylation while a second manganese ion (Mn2) is coordinated to a nonbridging oxygen of the gamma-phosphoryl group. The pyrophosphate leaving group of GTPalphaS is oriented apically to His404 with the epsilon-nitrogen poised for in-line attack on the alpha-phosphorus atom. The structure of RtcB in complex with GTPalphaS also reveals the network of hydrogen bonds that recognize GTP and illuminates the significant conformational changes that accompany the binding of this cofactor. Finally, a structure of the enzymic histidine-GMP intermediate depicts the end of the guanylylation pathway. The ensuing molecular description of the RtcB guanylylation pathway shows that RtcB and classical ATP- and Mg(II)-dependent nucleic acid ligases have converged upon a similar two-metal mechanism for formation of the nucleotidylated enzyme intermediate.
		+
		+	Structures of the Noncanonical RNA Ligase RtcB Reveal the Mechanism of Histidine Guanylylation.,Desai KK, Bingman CA, Phillips GN Jr, Raines RT Biochemistry. 2013 Apr 16;52(15):2518-25. doi: 10.1021/bi4002375. Epub 2013 Apr, 5. PMID:23560983<ref>PMID:23560983</ref>

-	==~~About this Structure~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[4isj]] is a 2 chain structure with sequence from [http:~~//~~en.wikipedia.org/wiki/Pyrococcus_horikoshii_ot3 Pyrococcus horikoshii ot3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ISJ OCA].~~	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Pyrococcus horikoshii ot3]]		[[Category: Pyrococcus horikoshii ot3]]
-	[[Category: Bingman, C A.]]	+	[[Category: Bingman, C A]]
-	[[Category: Desai, K K.]]	+	[[Category: Desai, K K]]
-	[[Category: Phillips, G N.]]	+	[[Category: Phillips, G N]]
-	[[Category: Raines, R T.]]	+	[[Category: Raines, R T]]
	[[Category: Ligase]]		[[Category: Ligase]]
	[[Category: Rna ligase]]		[[Category: Rna ligase]]

OCA at 06:47, 2 May 2013

OCA — Thu, 02 May 2013 06:47:18 GMT

←Older revision		Revision as of 06:47, 2 May 2013
Line 1:		Line 1:
	{{STRUCTURE_4isj\| PDB=4isj \| SCENE= }}		{{STRUCTURE_4isj\| PDB=4isj \| SCENE= }}
	===RNA Ligase RtcB in complex with Mn(II)===		===RNA Ligase RtcB in complex with Mn(II)===
		+	{{ABSTRACT_PUBMED_23560983}}

	==Function==		==Function==

OCA at 07:53, 27 March 2013

OCA — Wed, 27 Mar 2013 07:53:48 GMT

←Older revision		Revision as of 07:53, 27 March 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4isj\| PDB=4isj \| SCENE= }}
		+	===RNA Ligase RtcB in complex with Mn(II)===

-	~~The entry 4isj is ON HOLD until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/RTCB_PYRHO RTCB_PYRHO]] tRNA-splicing ligase that acts by directly joining spliced tRNA halves to mature-sized tRNAs by incorporating the precursor-derived splice junction phosphate into the mature tRNA as a canonical 3',5'-phosphodiester. May act as a RNA ligase with broad substrate specificity, and may function toward other RNAs (By similarity).

-	~~Authors~~: ~~Desai, K~~.K., Bingman, C.A., ~~Phillips Jr~~., G.N.~~, Rains~~, R.T.	+	==About this Structure==
-		+	[[4isj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii_ot3 Pyrococcus horikoshii ot3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ISJ OCA].
-	~~Description~~: ~~RNA~~ Ligase ~~RtcB in complex with Mn(II)~~	+	[[Category: Pyrococcus horikoshii ot3]]
		+	[[Category: Bingman, C A.]]
		+	[[Category: Desai, K K.]]
		+	[[Category: Phillips, G N.]]
		+	[[Category: Raines, R T.]]
		+	[[Category: Ligase]]
		+	[[Category: Rna ligase]]

OCA at 09:54, 13 March 2013

OCA — Wed, 13 Mar 2013 09:54:32 GMT

←Older revision		Revision as of 09:54, 13 March 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4isj is ON HOLD	+	The entry 4isj is ON HOLD until Paper Publication

	Authors: Desai, K.K., Bingman, C.A., Phillips Jr., G.N., Rains, R.T.		Authors: Desai, K.K., Bingman, C.A., Phillips Jr., G.N., Rains, R.T.

	Description: RNA Ligase RtcB in complex with Mn(II)		Description: RNA Ligase RtcB in complex with Mn(II)

OCA at 12:27, 6 February 2013

OCA — Wed, 06 Feb 2013 12:27:58 GMT

←Older revision		Revision as of 12:27, 6 February 2013
Line 3:		Line 3:
	The entry 4isj is ON HOLD		The entry 4isj is ON HOLD

-	Authors: Desai, K.K., Bingman, C.A., Phillips, G.N. Jr, Rains, R.T.	+	Authors: Desai, K.K., Bingman, C.A., Phillips Jr., G.N., Rains, R.T.

	Description: RNA Ligase RtcB in complex with Mn(II)		Description: RNA Ligase RtcB in complex with Mn(II)