3mag - Revision history

OCA at 10:24, 21 February 2024

OCA — Wed, 21 Feb 2024 10:24:40 GMT

←Older revision		Revision as of 10:24, 21 February 2024
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	<StructureSection load='3mag' size='340' side='right'caption='[[3mag]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='3mag' size='340' side='right'caption='[[3mag]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3mag]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Vaccinia_virus Vaccinia virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MAG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3MAG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3mag]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vaccinia_virus Vaccinia virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MAG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MAG FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=3MA:6~~-~~AMINO-3-METHYLPURINE'>3MA</scene>~~, ~~<scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</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]] 1.8Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[http:~~/~~/en.wikipedia.org/wiki/Polynucleotide_adenylyltransferase Polynucleotide adenylyltransferase]~~, ~~with EC number [http~~:~~//www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=2.7.7.19 2.7.7.19]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3MA:6-AMINO-3-METHYLPURINE'>3MA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></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=3mag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mag OCA], [~~http~~://pdbe.org/3mag PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3mag RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3mag PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3mag 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=3mag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mag OCA], [https://pdbe.org/3mag PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3mag RCSB], [https://www.ebi.ac.uk/pdbsum/3mag PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3mag ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/MCE_VACCW MCE_VACCW]] Displays methyltransferase, positive regulation of the poly(A) polymerase and transcription elongation activities. Involved in the modification of both mRNA ends and in intermediate and late gene positive transcription elongation. At the mRNAs 5' end, methylates the ribose 2' OH group of the first transcribed nucleotide, thereby producing a 2'-O-methylpurine cap. At the 3' end, functions as a processivity factor which stimulates the activity of the viral poly(A) polymerase VP55 that creates mRNA's poly(A) tail. In the presence of VP39, VP55 does not dissociate from the RNA allowing tail elongation to around 250 adenylates.<ref>PMID:1313572</ref> <ref>PMID:1670500</ref> <ref>PMID:12359447</ref>	+	[https://www.uniprot.org/uniprot/MCE_VACCW MCE_VACCW] Displays methyltransferase, positive regulation of the poly(A) polymerase and transcription elongation activities. Involved in the modification of both mRNA ends and in intermediate and late gene positive transcription elongation. At the mRNAs 5' end, methylates the ribose 2' OH group of the first transcribed nucleotide, thereby producing a 2'-O-methylpurine cap. At the 3' end, functions as a processivity factor which stimulates the activity of the viral poly(A) polymerase VP55 that creates mRNA's poly(A) tail. In the presence of VP39, VP55 does not dissociate from the RNA allowing tail elongation to around 250 adenylates.<ref>PMID:1313572</ref> <ref>PMID:1670500</ref> <ref>PMID:12359447</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=3mag 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=3mag ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	We have determined, by high resolution x-ray analysis, 10 structures comprising the mRNA cap-specific methyltransferase VP39 or specific mutants thereof in the presence of methylated nucleobase analogs (N1-methyladenine, N3-methyladenine, N1-methylcytosine, N3-methylcytosine) and their unmethylated counterparts, or nucleoside N7-methylguanosine. Together with solution affinity studies and previous crystallographic data for N7-methylguanosine and its phosphorylated derivatives, these data demonstrate that only methylated, positively charged bases are bound, indicating that their enhanced stacking with two aromatic side chains of VP39 (Tyr 22 and Phe 180) plays a dominant role in cap recognition. Four key features characterize this stacking interaction: (i) near perfect parallel alignment between the sandwiched methylated bases and aromatic side chains, (ii) substantial areas of overlap in the two-stacked rings, (iii) a 3.4-A interplanar spacing within the overlapping region, and (iv) positive charge in the heterocyclic nucleobase.
-
-	mRNA cap recognition: dominant role of enhanced stacking interactions between methylated bases and protein aromatic side chains.,Hu G, Gershon PD, Hodel AE, Quiocho FA Proc Natl Acad Sci U S A. 1999 Jun 22;96(13):7149-54. PMID:10377383<ref>PMID:10377383</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3mag" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
-	*[[Poly(A) ~~Polymerase~~\|Poly(A) ~~Polymerase~~]]	+	*[[Poly(A) polymerase 3D structures\|Poly(A) polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Polynucleotide adenylyltransferase]]
	[[Category: Vaccinia virus]]		[[Category: Vaccinia virus]]
-	[[Category: Gershon~~, P D~~]]	+	[[Category: Gershon PD]]
-	[[Category: Hodel~~, A E~~]]	+	[[Category: Hodel AE]]
-	[[Category: Hu, G]]	+	[[Category: Hu G]]
-	[[Category: Quiocho~~, F A]]~~	+	[[Category: Quiocho FA]]
-	~~[[Category: Methylated adenine]]~~	+
-	~~[[Category: Methyltransferase]]~~	+
-	~~[[Category: Mrna processing]]~~	+
-	~~[[Category: Rna cap analog]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Vaccinia~~]]	+

OCA at 06:40, 14 October 2020

OCA — Wed, 14 Oct 2020 06:40:30 GMT

←Older revision		Revision as of 06:40, 14 October 2020
Line 1:		Line 1:

	==VACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M3ADE AND S-ADENOSYLHOMOCYSTEINE==		==VACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M3ADE AND S-ADENOSYLHOMOCYSTEINE==
-	<StructureSection load='3mag' size='340' side='right' caption='[[3mag]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='3mag' size='340' side='right'caption='[[3mag]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3mag]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Vaccinia_virus Vaccinia virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MAG OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3MAG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3mag]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Vaccinia_virus Vaccinia virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MAG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3MAG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3MA:6-AMINO-3-METHYLPURINE'>3MA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3MA:6-AMINO-3-METHYLPURINE'>3MA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Polynucleotide_adenylyltransferase Polynucleotide adenylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.19 2.7.7.19] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Polynucleotide_adenylyltransferase Polynucleotide adenylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.19 2.7.7.19] </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=3mag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mag OCA], [http://pdbe.org/3mag PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3mag RCSB], [http://www.ebi.ac.uk/pdbsum/3mag PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3mag 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=3mag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mag OCA], [http://pdbe.org/3mag PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3mag RCSB], [http://www.ebi.ac.uk/pdbsum/3mag PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3mag ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Polynucleotide adenylyltransferase]]		[[Category: Polynucleotide adenylyltransferase]]
	[[Category: Vaccinia virus]]		[[Category: Vaccinia virus]]

OCA at 07:41, 9 January 2019

OCA — Wed, 09 Jan 2019 07:41:30 GMT

←Older revision		Revision as of 07:41, 9 January 2019
Line 1:		Line 1:
		+
	==VACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M3ADE AND S-ADENOSYLHOMOCYSTEINE==		==VACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M3ADE AND S-ADENOSYLHOMOCYSTEINE==
	<StructureSection load='3mag' size='340' side='right' caption='[[3mag]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='3mag' size='340' side='right' caption='[[3mag]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3MA:6-AMINO-3-METHYLPURINE'>3MA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3MA:6-AMINO-3-METHYLPURINE'>3MA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Polynucleotide_adenylyltransferase Polynucleotide adenylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.19 2.7.7.19] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Polynucleotide_adenylyltransferase Polynucleotide adenylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.19 2.7.7.19] </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=3mag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mag OCA], [http://pdbe.org/3mag PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3mag RCSB], [http://www.ebi.ac.uk/pdbsum/3mag 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=3mag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mag OCA], [http://pdbe.org/3mag PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3mag RCSB], [http://www.ebi.ac.uk/pdbsum/3mag PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3mag 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/ma/3mag_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ma/3mag_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 10:14, 8 February 2016

OCA — Mon, 08 Feb 2016 10:14:35 GMT

←Older revision		Revision as of 10:14, 8 February 2016
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3MA:6-AMINO-3-METHYLPURINE'>3MA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3MA:6-AMINO-3-METHYLPURINE'>3MA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Polynucleotide_adenylyltransferase Polynucleotide adenylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.19 2.7.7.19] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Polynucleotide_adenylyltransferase Polynucleotide adenylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.19 2.7.7.19] </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=3mag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mag OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3mag RCSB], [http://www.ebi.ac.uk/pdbsum/3mag 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=3mag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mag OCA], [http://pdbe.org/3mag PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3mag RCSB], [http://www.ebi.ac.uk/pdbsum/3mag PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~PAP2_VACCV PAP2_VACCV~~]] Displays methyltransferase, positive regulation of the poly(A) polymerase and transcription elongation activities. Involved in the modification of both mRNA ends and in intermediate and late gene positive transcription elongation. At the mRNAs 5' end, methylates the ribose 2' OH group of the first transcribed nucleotide, thereby producing a 2'-O-methylpurine cap. At the 3' end, functions as a processivity factor which stimulates the activity of the viral poly(A) polymerase VP55 that creates mRNA's poly(A) tail. In the presence of VP39, VP55 does not dissociate from the RNA allowing tail elongation to around 250 adenylates.<ref>PMID:1313572</ref> <ref>PMID:1670500</ref> <ref>PMID:12359447</ref>	+	[[http://www.uniprot.org/uniprot/MCE_VACCW MCE_VACCW]] Displays methyltransferase, positive regulation of the poly(A) polymerase and transcription elongation activities. Involved in the modification of both mRNA ends and in intermediate and late gene positive transcription elongation. At the mRNAs 5' end, methylates the ribose 2' OH group of the first transcribed nucleotide, thereby producing a 2'-O-methylpurine cap. At the 3' end, functions as a processivity factor which stimulates the activity of the viral poly(A) polymerase VP55 that creates mRNA's poly(A) tail. In the presence of VP39, VP55 does not dissociate from the RNA allowing tail elongation to around 250 adenylates.<ref>PMID:1313572</ref> <ref>PMID:1670500</ref> <ref>PMID:12359447</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 17:		Line 17:
	<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=3mag ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		Line 27:
	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 3mag" style="background-color:#fffaf0;"></div>

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

OCA at 22:36, 24 December 2014

OCA — Wed, 24 Dec 2014 22:36:29 GMT

←Older revision		Revision as of 22:36, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3mag]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Vaccinia_virus Vaccinia virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MAG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3MAG FirstGlance]. <br>		<table><tr><td colspan='2'>[[3mag]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Vaccinia_virus Vaccinia virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MAG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3MAG FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3MA:6-AMINO-3-METHYLPURINE'>3MA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3MA:6-AMINO-3-METHYLPURINE'>3MA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Polynucleotide_adenylyltransferase Polynucleotide adenylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.19 2.7.7.19] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Polynucleotide_adenylyltransferase Polynucleotide adenylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.19 2.7.7.19] </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=3mag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mag OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3mag RCSB], [http://www.ebi.ac.uk/pdbsum/3mag 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=3mag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mag OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3mag RCSB], [http://www.ebi.ac.uk/pdbsum/3mag PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PAP2_VACCV PAP2_VACCV]] Displays methyltransferase, positive regulation of the poly(A) polymerase and transcription elongation activities. Involved in the modification of both mRNA ends and in intermediate and late gene positive transcription elongation. At the mRNAs 5' end, methylates the ribose 2' OH group of the first transcribed nucleotide, thereby producing a 2'-O-methylpurine cap. At the 3' end, functions as a processivity factor which stimulates the activity of the viral poly(A) polymerase VP55 that creates mRNA's poly(A) tail. In the presence of VP39, VP55 does not dissociate from the RNA allowing tail elongation to around 250 adenylates.<ref>PMID:1313572</ref> <ref>PMID:1670500</ref> <ref>PMID:12359447</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	[[Category: Polynucleotide adenylyltransferase]]		[[Category: Polynucleotide adenylyltransferase]]
	[[Category: Vaccinia virus]]		[[Category: Vaccinia virus]]
-	[[Category: Gershon, P D.]]	+	[[Category: Gershon, P D]]
-	[[Category: Hodel, A E.]]	+	[[Category: Hodel, A E]]
-	[[Category: Hu, G.]]	+	[[Category: Hu, G]]
-	[[Category: Quiocho, F A.]]	+	[[Category: Quiocho, F A]]
	[[Category: Methylated adenine]]		[[Category: Methylated adenine]]
	[[Category: Methyltransferase]]		[[Category: Methyltransferase]]

OCA at 11:19, 29 September 2014

OCA — Mon, 29 Sep 2014 11:19:20 GMT

←Older revision		Revision as of 11:19, 29 September 2014
Line 1:		Line 1:
-	[[~~Image~~:3mag.~~png\|left~~\|200px]]	+	==VACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M3ADE AND S-ADENOSYLHOMOCYSTEINE==
		+	<StructureSection load='3mag' size='340' side='right' caption='[[3mag]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3mag]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Vaccinia_virus Vaccinia virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MAG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3MAG FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3MA:6-AMINO-3-METHYLPURINE'>3MA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene><br>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Polynucleotide_adenylyltransferase Polynucleotide adenylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.19 2.7.7.19] </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=3mag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mag OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3mag RCSB], [http://www.ebi.ac.uk/pdbsum/3mag 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/ma/3mag_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 ==
		+	We have determined, by high resolution x-ray analysis, 10 structures comprising the mRNA cap-specific methyltransferase VP39 or specific mutants thereof in the presence of methylated nucleobase analogs (N1-methyladenine, N3-methyladenine, N1-methylcytosine, N3-methylcytosine) and their unmethylated counterparts, or nucleoside N7-methylguanosine. Together with solution affinity studies and previous crystallographic data for N7-methylguanosine and its phosphorylated derivatives, these data demonstrate that only methylated, positively charged bases are bound, indicating that their enhanced stacking with two aromatic side chains of VP39 (Tyr 22 and Phe 180) plays a dominant role in cap recognition. Four key features characterize this stacking interaction: (i) near perfect parallel alignment between the sandwiched methylated bases and aromatic side chains, (ii) substantial areas of overlap in the two-stacked rings, (iii) a 3.4-A interplanar spacing within the overlapping region, and (iv) positive charge in the heterocyclic nucleobase.

-	~~{{STRUCTURE_3mag\| PDB=3mag \| SCENE= }}~~	+	mRNA cap recognition: dominant role of enhanced stacking interactions between methylated bases and protein aromatic side chains.,Hu G, Gershon PD, Hodel AE, Quiocho FA Proc Natl Acad Sci U S A. 1999 Jun 22;96(13):7149-54. PMID:10377383<ref>PMID:10377383</ref>

-	~~===VACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M3ADE AND S-ADENOSYLHOMOCYSTEINE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10377383}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3mag]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Vaccinia_virus Vaccinia virus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3MAG OCA].~~	+

	==See Also==		==See Also==
	*[[Poly(A) Polymerase\|Poly(A) Polymerase]]		*[[Poly(A) Polymerase\|Poly(A) Polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:010377383<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Polynucleotide adenylyltransferase]]		[[Category: Polynucleotide adenylyltransferase]]
	[[Category: Vaccinia virus]]		[[Category: Vaccinia virus]]

OCA at 09:49, 20 October 2012

OCA — Sat, 20 Oct 2012 09:49:33 GMT

←Older revision		Revision as of 09:49, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3mag]] is a 1 chain structure ~~of [[Poly(A) Polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Vaccinia_virus Vaccinia virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MAG OCA].	+	[[3mag]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Vaccinia_virus Vaccinia virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MAG OCA].

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

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

OCA — Thu, 26 Jul 2012 00:04:24 GMT

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

←Older revision

Revision as of 00:04, 26 July 2012

OCA at 00:04, 26 July 2012

OCA — Thu, 26 Jul 2012 00:04:23 GMT

←Older revision		Revision as of 00:04, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3mag.png\|left\|200px]]		[[Image:3mag.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3mag", 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_3mag\| PDB=3mag \| SCENE= }}		{{STRUCTURE_3mag\| PDB=3mag \| SCENE= }}

	===VACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M3ADE AND S-ADENOSYLHOMOCYSTEINE===		===VACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M3ADE AND S-ADENOSYLHOMOCYSTEINE===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_10377383}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 10377383 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_10377383}}		{{ABSTRACT_PUBMED_10377383}}

	==About this Structure==		==About this Structure==
-	~~3MAG~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Vaccinia_virus Vaccinia virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MAG OCA].	+	[[3mag]] is a 1 chain structure of [[Poly(A) Polymerase]] with sequence from [http://en.wikipedia.org/wiki/Vaccinia_virus Vaccinia virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MAG OCA].
		+
		+	==See Also==
		+	*[[Poly(A) Polymerase\|Poly(A) Polymerase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~10377383~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:010377383</ref><references group="xtra"/>
	[[Category: Polynucleotide adenylyltransferase]]		[[Category: Polynucleotide adenylyltransferase]]
	[[Category: Vaccinia virus]]		[[Category: Vaccinia virus]]
Line 36:		Line 27:
	[[Category: Transcription]]		[[Category: Transcription]]
	[[Category: Vaccinia]]		[[Category: Vaccinia]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 21:15:21 2009''

OCA at 19:15, 16 February 2009

OCA — Mon, 16 Feb 2009 19:15:22 GMT

←Older revision		Revision as of 19:15, 16 February 2009
Line 20:		Line 20:

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

	==Reference==		==Reference==
-	mRNA cap recognition: dominant role of enhanced stacking interactions between methylated bases and protein aromatic side chains., Hu G, Gershon PD, Hodel AE, Quiocho FA, Proc Natl Acad Sci U S A. 1999 Jun 22;96(13):7149-54. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/10377383 10377383]~~	+	<ref group="xtra">PMID:10377383</ref><references group="xtra"/>
	[[Category: Polynucleotide adenylyltransferase]]		[[Category: Polynucleotide adenylyltransferase]]
-	[[Category: Single protein]]
	[[Category: Vaccinia virus]]		[[Category: Vaccinia virus]]
	[[Category: Gershon, P D.]]		[[Category: Gershon, P D.]]
Line 38:		Line 37:
	[[Category: Vaccinia]]		[[Category: Vaccinia]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Jul 3 12~~:54:~~52 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 21:15:21 2009''