3tv1 - Revision history

OCA at 13:40, 14 March 2024

OCA — Thu, 14 Mar 2024 13:40:06 GMT

←Older revision		Revision as of 13:40, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3tv1' size='340' side='right'caption='[[3tv1]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3tv1' size='340' side='right'caption='[[3tv1]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3tv1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TV1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TV1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3tv1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TV1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TV1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 1.9Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1qmh\|1qmh]], [[1qmi\|1qmi]], [[3kgd\|3kgd]], [[3tut\|3tut]], [[3tux\|3tux]], [[3tw3\|3tw3]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b4475, JW5688, rtcA, yhgJ, yhgK ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/RNA-3'-phosphate_cyclase RNA-3'-phosphate cyclase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.4 6.5.1.4] </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=3tv1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tv1 OCA], [https://pdbe.org/3tv1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tv1 RCSB], [https://www.ebi.ac.uk/pdbsum/3tv1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tv1 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=3tv1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tv1 OCA], [https://pdbe.org/3tv1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tv1 RCSB], [https://www.ebi.ac.uk/pdbsum/3tv1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tv1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RTCA_ECOLI RTCA_ECOLI]] Catalyzes the conversion of 3'-phosphate to a 2',3'-cyclic phosphodiester at the end of RNA. The mechanism of action of the enzyme occurs in 3 steps: (A) adenylation of the enzyme by ATP; (B) transfer of adenylate to an RNA-N3'P to produce RNA-N3'PP5'A; (C) and attack of the adjacent 2'-hydroxyl on the 3'-phosphorus in the diester linkage to produce the cyclic end product. The biological role of this enzyme is unknown but it is likely to function in some aspects of cellular RNA processing.<ref>PMID:9738023</ref>	+	[https://www.uniprot.org/uniprot/RTCA_ECOLI RTCA_ECOLI] Catalyzes the conversion of 3'-phosphate to a 2',3'-cyclic phosphodiester at the end of RNA. The mechanism of action of the enzyme occurs in 3 steps: (A) adenylation of the enzyme by ATP; (B) transfer of adenylate to an RNA-N3'P to produce RNA-N3'PP5'A; (C) and attack of the adjacent 2'-hydroxyl on the 3'-phosphorus in the diester linkage to produce the cyclic end product. The biological role of this enzyme is unknown but it is likely to function in some aspects of cellular RNA processing.<ref>PMID:9738023</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	RNA 3'-phosphate cyclase (RtcA) synthesizes RNA 2',3' cyclic phosphate ends via three steps: reaction with ATP to form a covalent RtcA-(histidinyl-Nepsilon)-AMP intermediate; transfer of adenylate to an RNA 3'-phosphate to form RNA(3')pp(5')A; and attack of the vicinal O2' on the 3'-phosphorus to form a 2',3' cyclic phosphate and release AMP. Here we report the crystal structures of RtcAATP, RtcAATPMn(2+), and RtcAATPCo(2+) substrate complexes and an RtcAAMP product complex. Together with the structures of RtcA apoenzyme and the covalent RtcA-AMP intermediate, they illuminate the mechanism of nucleotidyl transfer, especially the stereochemical transitions at the AMP phosphate, the critical role of the metal in orienting the PP(i) leaving group of ATP during step 1, and the protein conformational switches that accompany substrate binding and product release. The octahedral metal complex of RtcAATPMn(2+) includes nonbridging oxygens from each of the ATP phosphates, two waters, and Glu14 as the sole RtcA component. Whereas the RtcA adenylylation step is metal-catalyzed, the subsequent steps in the cyclization pathway are metal-independent.	+
-		+
-	Structures of RNA 3'-phosphate cyclase bound to ATP reveal the mechanism of nucleotidyl transfer and metal-assisted catalysis.,Chakravarty AK, Smith P, Shuman S Proc Natl Acad Sci U S A. 2011 Dec 13. PMID:22167800<ref>PMID:22167800</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3tv1" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: RNA-3'-phosphate cyclase]]~~	+	[[Category: Chakravarty AK]]
-	[[Category: Chakravarty~~, A K~~]]	+	[[Category: Shuman S]]
-	[[Category: Shuman, S]]	+	[[Category: Smith P]]
-	[[Category: Smith, P]]	+
-	~~[[Category: Cyclase family]]~~	+
-	~~[[Category: Cyclizing 3'-phosphate end]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 05:46, 13 July 2022

OCA — Wed, 13 Jul 2022 05:46:36 GMT

←Older revision		Revision as of 05:46, 13 July 2022
Line 1:		Line 1:

	==Crystal structure of RtcA.AMP product complex==		==Crystal structure of RtcA.AMP product complex==
-	<StructureSection load='3tv1' size='340' side='right' caption='[[3tv1]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='3tv1' size='340' side='right'caption='[[3tv1]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3tv1]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TV1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3TV1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3tv1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TV1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TV1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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">[[1qmh\|1qmh]], [[1qmi\|1qmi]], [[3kgd\|3kgd]], [[3tut\|3tut]], [[3tux\|3tux]], [[3tw3\|3tw3]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1qmh\|1qmh]], [[1qmi\|1qmi]], [[3kgd\|3kgd]], [[3tut\|3tut]], [[3tux\|3tux]], [[3tw3\|3tw3]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b4475, JW5688, rtcA, yhgJ, yhgK ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b4475, JW5688, rtcA, yhgJ, yhgK ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/RNA-3'-phosphate_cyclase RNA-3'-phosphate cyclase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.4 6.5.1.4] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/RNA-3'-phosphate_cyclase RNA-3'-phosphate cyclase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.4 6.5.1.4] </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=3tv1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tv1 OCA], [~~http~~://pdbe.org/3tv1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3tv1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3tv1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3tv1 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=3tv1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tv1 OCA], [https://pdbe.org/3tv1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tv1 RCSB], [https://www.ebi.ac.uk/pdbsum/3tv1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tv1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RTCA_ECOLI RTCA_ECOLI]] Catalyzes the conversion of 3'-phosphate to a 2',3'-cyclic phosphodiester at the end of RNA. The mechanism of action of the enzyme occurs in 3 steps: (A) adenylation of the enzyme by ATP; (B) transfer of adenylate to an RNA-N3'P to produce RNA-N3'PP5'A; (C) and attack of the adjacent 2'-hydroxyl on the 3'-phosphorus in the diester linkage to produce the cyclic end product. The biological role of this enzyme is unknown but it is likely to function in some aspects of cellular RNA processing.<ref>PMID:9738023</ref>	+	[[https://www.uniprot.org/uniprot/RTCA_ECOLI RTCA_ECOLI]] Catalyzes the conversion of 3'-phosphate to a 2',3'-cyclic phosphodiester at the end of RNA. The mechanism of action of the enzyme occurs in 3 steps: (A) adenylation of the enzyme by ATP; (B) transfer of adenylate to an RNA-N3'P to produce RNA-N3'PP5'A; (C) and attack of the adjacent 2'-hydroxyl on the 3'-phosphorus in the diester linkage to produce the cyclic end product. The biological role of this enzyme is unknown but it is likely to function in some aspects of cellular RNA processing.<ref>PMID:9738023</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Ecoli]]		[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: RNA-3'-phosphate cyclase]]		[[Category: RNA-3'-phosphate cyclase]]
	[[Category: Chakravarty, A K]]		[[Category: Chakravarty, A K]]

OCA at 15:13, 4 August 2016

OCA — Thu, 04 Aug 2016 15:13:29 GMT

←Older revision		Revision as of 15:13, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of RtcA.AMP product complex==		==Crystal structure of RtcA.AMP product complex==
	<StructureSection load='3tv1' size='340' side='right' caption='[[3tv1]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3tv1' size='340' side='right' caption='[[3tv1]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3tv1]] is a 2 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=3TV1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TV1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3tv1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TV1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TV1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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">[[1qmh\|1qmh]], [[1qmi\|1qmi]], [[3kgd\|3kgd]], [[3tut\|3tut]], [[3tux\|3tux]], [[3tw3\|3tw3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qmh\|1qmh]], [[1qmi\|1qmi]], [[3kgd\|3kgd]], [[3tut\|3tut]], [[3tux\|3tux]], [[3tw3\|3tw3]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b4475, JW5688, rtcA, yhgJ, yhgK ([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">b4475, JW5688, rtcA, yhgJ, yhgK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA-3'-phosphate_cyclase RNA-3'-phosphate cyclase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.4 6.5.1.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA-3'-phosphate_cyclase RNA-3'-phosphate cyclase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.4 6.5.1.4] </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=3tv1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tv1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tv1 RCSB], [http://www.ebi.ac.uk/pdbsum/3tv1 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=3tv1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tv1 OCA], [http://pdbe.org/3tv1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3tv1 RCSB], [http://www.ebi.ac.uk/pdbsum/3tv1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3tv1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	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 3tv1" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia coli~~]]	+	[[Category: Ecoli]]
	[[Category: RNA-3'-phosphate cyclase]]		[[Category: RNA-3'-phosphate cyclase]]
	[[Category: Chakravarty, A K]]		[[Category: Chakravarty, A K]]

OCA at 16:14, 24 December 2014

OCA — Wed, 24 Dec 2014 16:14:31 GMT

←Older revision		Revision as of 16:14, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3tv1]] is a 2 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=3TV1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TV1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3tv1]] is a 2 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=3TV1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TV1 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qmh\|1qmh]], [[1qmi\|1qmi]], [[3kgd\|3kgd]], [[3tut\|3tut]], [[3tux\|3tux]], [[3tw3\|3tw3]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qmh\|1qmh]], [[1qmi\|1qmi]], [[3kgd\|3kgd]], [[3tut\|3tut]], [[3tux\|3tux]], [[3tw3\|3tw3]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b4475, JW5688, rtcA, yhgJ, yhgK ([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">b4475, JW5688, rtcA, yhgJ, yhgK ([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/RNA-3'-phosphate_cyclase RNA-3'-phosphate cyclase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.4 6.5.1.4] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA-3'-phosphate_cyclase RNA-3'-phosphate cyclase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.4 6.5.1.4] </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=3tv1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tv1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tv1 RCSB], [http://www.ebi.ac.uk/pdbsum/3tv1 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=3tv1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tv1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tv1 RCSB], [http://www.ebi.ac.uk/pdbsum/3tv1 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RTCA_ECOLI RTCA_ECOLI]] Catalyzes the conversion of 3'-phosphate to a 2',3'-cyclic phosphodiester at the end of RNA. The mechanism of action of the enzyme occurs in 3 steps: (A) adenylation of the enzyme by ATP; (B) transfer of adenylate to an RNA-N3'P to produce RNA-N3'PP5'A; (C) and attack of the adjacent 2'-hydroxyl on the 3'-phosphorus in the diester linkage to produce the cyclic end product. The biological role of this enzyme is unknown but it is likely to function in some aspects of cellular RNA processing.<ref>PMID:9738023</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 15:		Line 17:
	Structures of RNA 3'-phosphate cyclase bound to ATP reveal the mechanism of nucleotidyl transfer and metal-assisted catalysis.,Chakravarty AK, Smith P, Shuman S Proc Natl Acad Sci U S A. 2011 Dec 13. PMID:22167800<ref>PMID:22167800</ref>		Structures of RNA 3'-phosphate cyclase bound to ATP reveal the mechanism of nucleotidyl transfer and metal-assisted catalysis.,Chakravarty AK, Smith P, Shuman S Proc Natl Acad Sci U S A. 2011 Dec 13. PMID:22167800<ref>PMID:22167800</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==
Line 23:		Line 25:
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: RNA-3'-phosphate cyclase]]		[[Category: RNA-3'-phosphate cyclase]]
-	[[Category: Chakravarty, A K.]]	+	[[Category: Chakravarty, A K]]
-	[[Category: Shuman, S.]]	+	[[Category: Shuman, S]]
-	[[Category: Smith, P.]]	+	[[Category: Smith, P]]
	[[Category: Cyclase family]]		[[Category: Cyclase family]]
	[[Category: Cyclizing 3'-phosphate end]]		[[Category: Cyclizing 3'-phosphate end]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 06:26, 5 June 2014

OCA — Thu, 05 Jun 2014 06:26:22 GMT

←Older revision		Revision as of 06:26, 5 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3tv1.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of RtcA.AMP product complex==
		+	<StructureSection load='3tv1' size='340' side='right' caption='[[3tv1]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3tv1]] is a 2 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=3TV1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TV1 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qmh\|1qmh]], [[1qmi\|1qmi]], [[3kgd\|3kgd]], [[3tut\|3tut]], [[3tux\|3tux]], [[3tw3\|3tw3]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b4475, JW5688, rtcA, yhgJ, yhgK ([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/RNA-3'-phosphate_cyclase RNA-3'-phosphate cyclase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.4 6.5.1.4] </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=3tv1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tv1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tv1 RCSB], [http://www.ebi.ac.uk/pdbsum/3tv1 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	RNA 3'-phosphate cyclase (RtcA) synthesizes RNA 2',3' cyclic phosphate ends via three steps: reaction with ATP to form a covalent RtcA-(histidinyl-Nepsilon)-AMP intermediate; transfer of adenylate to an RNA 3'-phosphate to form RNA(3')pp(5')A; and attack of the vicinal O2' on the 3'-phosphorus to form a 2',3' cyclic phosphate and release AMP. Here we report the crystal structures of RtcAATP, RtcAATPMn(2+), and RtcAATPCo(2+) substrate complexes and an RtcAAMP product complex. Together with the structures of RtcA apoenzyme and the covalent RtcA-AMP intermediate, they illuminate the mechanism of nucleotidyl transfer, especially the stereochemical transitions at the AMP phosphate, the critical role of the metal in orienting the PP(i) leaving group of ATP during step 1, and the protein conformational switches that accompany substrate binding and product release. The octahedral metal complex of RtcAATPMn(2+) includes nonbridging oxygens from each of the ATP phosphates, two waters, and Glu14 as the sole RtcA component. Whereas the RtcA adenylylation step is metal-catalyzed, the subsequent steps in the cyclization pathway are metal-independent.

-	<!--	+	Structures of RNA 3'-phosphate cyclase bound to ATP reveal the mechanism of nucleotidyl transfer and metal-assisted catalysis.,Chakravarty AK, Smith P, Shuman S Proc Natl Acad Sci U S A. 2011 Dec 13. PMID:22167800<ref>PMID:22167800</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3tv1"~~, ~~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_3tv1\| PDB=3tv1 \| SCENE= }}~~	+

-	~~===Crystal structure~~ of ~~RtcA.AMP product complex===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_22167800}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 22167800 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_22167800}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3tv1]] is a 2 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=3TV1 OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:022167800<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: RNA-3'-phosphate cyclase]]		[[Category: RNA-3'-phosphate cyclase]]

OCA at 05:39, 11 January 2012

OCA — Wed, 11 Jan 2012 05:39:08 GMT

←Older revision		Revision as of 05:39, 11 January 2012
Line 1:		Line 1:
-	[[Image:3tv1.~~jpg~~\|left\|200px]]	+	[[Image:3tv1.png\|left\|200px]]

	<!--		<!--

OCA at 07:25, 28 December 2011

OCA — Wed, 28 Dec 2011 07:25:20 GMT

←Older revision		Revision as of 07:25, 28 December 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3tv1.jpg\|left\|200px]]

-	The ~~entry 3tv1~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3tv1", 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_3tv1\| PDB=3tv1 \| SCENE= }}

-	~~Authors: Chakravarty, A.K., Smith, P., Shuman, S~~.	+	===Crystal structure of RtcA.AMP product complex===

-	~~Description~~: ~~Crystal~~ structure ~~of RtcA~~.~~AMP product complex~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22167800}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22167800 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22167800}}
		+
		+	==About this Structure==
		+	[[3tv1]] is a 2 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=3TV1 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022167800</ref><references group="xtra"/>
		+	[[Category: Escherichia coli]]
		+	[[Category: RNA-3'-phosphate cyclase]]
		+	[[Category: Chakravarty, A K.]]
		+	[[Category: Shuman, S.]]
		+	[[Category: Smith, P.]]
		+	[[Category: Cyclase family]]
		+	[[Category: Cyclizing 3'-phosphate end]]
		+	[[Category: Transferase]]

OCA at 07:55, 2 November 2011

OCA — Wed, 02 Nov 2011 07:55:53 GMT

←Older revision		Revision as of 07:55, 2 November 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3tv1 is ON HOLD	+	The entry 3tv1 is ON HOLD until Paper Publication

	Authors: Chakravarty, A.K., Smith, P., Shuman, S.		Authors: Chakravarty, A.K., Smith, P., Shuman, S.

	Description: Crystal structure of RtcA.AMP product complex		Description: Crystal structure of RtcA.AMP product complex

OCA at 08:44, 30 October 2011

OCA — Sun, 30 Oct 2011 08:44:07 GMT

←Older revision		Revision as of 08:44, 30 October 2011
Line 3:		Line 3:
	The entry 3tv1 is ON HOLD		The entry 3tv1 is ON HOLD

-	Authors: Chakravarty, A. K., Smith, P., Shuman, S.	+	Authors: Chakravarty, A.K., Smith, P., Shuman, S.

	Description: Crystal structure of RtcA.AMP product complex		Description: Crystal structure of RtcA.AMP product complex

OCA: Protected "3tv1" [edit=sysop:move=sysop]

OCA — Wed, 28 Sep 2011 05:17:45 GMT

Protected "3tv1" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:17, 28 September 2011