1jsz - Revision history

OCA at 13:25, 13 March 2024

2024-03-13T13:25:03Z

←Older revision		Revision as of 13:25, 13 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1jsz]] 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=1JSZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JSZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1jsz]] 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=1JSZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JSZ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NDM:7,9~~-~~DIMETHYLGUANINE'>NDM</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]] 1.93Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1jte\|1jte]], [[1jtf\|1jtf]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NDM:7,9-DIMETHYLGUANINE'>NDM</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~~'>~~[https://en.wikipedia.org/wiki/Polynucleotide_adenylyltransferase Polynucleotide adenylyltransferase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=1jsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jsz OCA], [https://pdbe.org/1jsz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jsz RCSB], [https://www.ebi.ac.uk/pdbsum/1jsz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jsz 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=1jsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jsz OCA], [https://pdbe.org/1jsz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jsz RCSB], [https://www.ebi.ac.uk/pdbsum/1jsz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jsz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[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>	+	[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=1jsz 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=1jsz ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The N7-methylguanine portion of the mRNA cap structure interacts with cap-binding proteins via an unusual double-stacking arrangement in which the positively charged cap is sandwiched between two parallel-oriented aromatic protein side chains. Three-dimensional costructures of cap with two mRNA cap-binding proteins, namely, translational initiation factor eIF4E and VP39 (the vaccinia virus-encoded mRNA cap-specific 2'-O-methyltransferase), have heretofore been reported. Despite striking similarities between the two proteins in the double stack with the cap, the stack differs most notably in the species of stacked side chain donated by the protein. Whereas eIF4E employs two tryptophans, VP39 uses a tyrosine and a phenylalanine. Here, we have generated tryptophan substitutions in VP39. Tryptophan substitution was shown, crystallographically, not to disrupt the maintenance of a bona fide parallel stack. However, the single-tryptophan and double-tryptophan substitutions were associated with increased affinity for cap nucleoside by factors of 10 and 50, respectively. VP39 interacted more strongly with a true substrate (containing portions of RNA downstream of the cap in addition to the cap itself) than with isolated cap nucleoside, by several orders of magnitude. VP39 mutants with tryptophan substitution at position 180 exhibited apparent defects in substrate catalytic rate during the first turnover cycle, indicating the possibility of an exquisite sensitivity of the catalytic center to subtle changes in substrate position brought about by alterations in the cap-binding slot. The X-ray structure of VP39 with a genuine nucleobase analogue of N7-methylguanosine, namely, N7,9-dimethylguanine, indicated that the N7-methylguanosine rotational orientation within the stack is a property of the cap nucleobase itself.
-
-	The "cap-binding slot" of an mRNA cap-binding protein: quantitative effects of aromatic side chain choice in the double-stacking sandwich with cap.,Hu G, Oguro A, Li C, Gershon PD, Quiocho FA Biochemistry. 2002 Jun 18;41(24):7677-87. PMID:12056899<ref>PMID:12056899</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1jsz" 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: Hu, G]]	+	[[Category: Hu G]]
-	[[Category: Oguro, A]]	+	[[Category: Oguro A]]
-	[[Category: Quiocho~~, F A]]~~	+	[[Category: Quiocho FA]]
-	~~[[Category: Methyltransferase]]~~	+
-	~~[[Category: Mrna cap-binding protein]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Vp39~~]]	+

OCA at 07:21, 14 April 2021

2021-04-14T07:21:57Z

←Older revision		Revision as of 07:21, 14 April 2021
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	<StructureSection load='1jsz' size='340' side='right'caption='[[1jsz]], [[Resolution\|resolution]] 1.93Å' scene=''>		<StructureSection load='1jsz' size='340' side='right'caption='[[1jsz]], [[Resolution\|resolution]] 1.93Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1jsz]] 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=1JSZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1JSZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1jsz]] 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=1JSZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JSZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NDM:7,9-DIMETHYLGUANINE'>NDM</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=NDM:7,9-DIMETHYLGUANINE'>NDM</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jte\|1jte]], [[1jtf\|1jtf]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1jte\|1jte]], [[1jtf\|1jtf]]</div></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'>[https://en.wikipedia.org/wiki/Polynucleotide_adenylyltransferase Polynucleotide adenylyltransferase], with EC number [https://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=1jsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jsz OCA], [~~http~~://pdbe.org/1jsz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1jsz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1jsz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1jsz 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=1jsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jsz OCA], [https://pdbe.org/1jsz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jsz RCSB], [https://www.ebi.ac.uk/pdbsum/1jsz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jsz 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]]

OCA at 06:57, 10 July 2019

2019-07-10T06:57:36Z

←Older revision		Revision as of 06:57, 10 July 2019
Line 1:		Line 1:

	==Crystal Structure Analysis of N7,9-dimethylguanine-VP39 complex==		==Crystal Structure Analysis of N7,9-dimethylguanine-VP39 complex==
-	<StructureSection load='1jsz' size='340' side='right' caption='[[1jsz]], [[Resolution\|resolution]] 1.93Å' scene=''>	+	<StructureSection load='1jsz' size='340' side='right'caption='[[1jsz]], [[Resolution\|resolution]] 1.93Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1jsz]] 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=1JSZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JSZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1jsz]] 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=1JSZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JSZ FirstGlance]. <br>
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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/js/1jsz_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/js/1jsz_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>
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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 09:48, 4 October 2017

2017-10-04T09:48:37Z

←Older revision		Revision as of 09:48, 4 October 2017
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		+
	==Crystal Structure Analysis of N7,9-dimethylguanine-VP39 complex==		==Crystal Structure Analysis of N7,9-dimethylguanine-VP39 complex==
	<StructureSection load='1jsz' size='340' side='right' caption='[[1jsz]], [[Resolution\|resolution]] 1.93Å' scene=''>		<StructureSection load='1jsz' size='340' side='right' caption='[[1jsz]], [[Resolution\|resolution]] 1.93Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jte\|1jte]], [[1jtf\|1jtf]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jte\|1jte]], [[1jtf\|1jtf]]</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=1jsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jsz OCA], [http://pdbe.org/1jsz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jsz RCSB], [http://www.ebi.ac.uk/pdbsum/1jsz 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=1jsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jsz OCA], [http://pdbe.org/1jsz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jsz RCSB], [http://www.ebi.ac.uk/pdbsum/1jsz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1jsz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	<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=1jsz ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:43, 11 September 2015

2015-09-11T23:43:17Z

←Older revision		Revision as of 23:43, 11 September 2015
Line 6:		Line 6:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jte\|1jte]], [[1jtf\|1jtf]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jte\|1jte]], [[1jtf\|1jtf]]</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=1jsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jsz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jsz RCSB], [http://www.ebi.ac.uk/pdbsum/1jsz 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=1jsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jsz OCA], [http://pdbe.org/1jsz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jsz RCSB], [http://www.ebi.ac.uk/pdbsum/1jsz PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 1jsz" style="background-color:#fffaf0;"></div>

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

OCA at 20:58, 25 December 2014

2014-12-25T20:58:16Z

←Older revision		Revision as of 20:58, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1jsz]] 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=1JSZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JSZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1jsz]] 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=1JSZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JSZ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NDM:7,9-DIMETHYLGUANINE'>NDM</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=NDM:7,9-DIMETHYLGUANINE'>NDM</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jte\|1jte]], [[1jtf\|1jtf]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jte\|1jte]], [[1jtf\|1jtf]]</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=1jsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jsz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jsz RCSB], [http://www.ebi.ac.uk/pdbsum/1jsz 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=1jsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jsz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jsz RCSB], [http://www.ebi.ac.uk/pdbsum/1jsz PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== 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>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: Polynucleotide adenylyltransferase]]		[[Category: Polynucleotide adenylyltransferase]]
	[[Category: Vaccinia virus]]		[[Category: Vaccinia virus]]
-	[[Category: Gershon, P D.]]	+	[[Category: Gershon, P D]]
-	[[Category: Hu, G.]]	+	[[Category: Hu, G]]
-	[[Category: Oguro, A.]]	+	[[Category: Oguro, A]]
-	[[Category: Quiocho, F A.]]	+	[[Category: Quiocho, F A]]
	[[Category: Methyltransferase]]		[[Category: Methyltransferase]]
	[[Category: Mrna cap-binding protein]]		[[Category: Mrna cap-binding protein]]
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Vp39]]		[[Category: Vp39]]

OCA at 11:44, 28 September 2014

2014-09-28T11:44:57Z

←Older revision		Revision as of 11:44, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1jsz.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure Analysis of N7,9-dimethylguanine-VP39 complex==
		+	<StructureSection load='1jsz' size='340' side='right' caption='[[1jsz]], [[Resolution\|resolution]] 1.93Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1jsz]] 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=1JSZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JSZ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NDM:7,9-DIMETHYLGUANINE'>NDM</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jte\|1jte]], [[1jtf\|1jtf]]</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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1jsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jsz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jsz RCSB], [http://www.ebi.ac.uk/pdbsum/1jsz 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/js/1jsz_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 ==
		+	The N7-methylguanine portion of the mRNA cap structure interacts with cap-binding proteins via an unusual double-stacking arrangement in which the positively charged cap is sandwiched between two parallel-oriented aromatic protein side chains. Three-dimensional costructures of cap with two mRNA cap-binding proteins, namely, translational initiation factor eIF4E and VP39 (the vaccinia virus-encoded mRNA cap-specific 2'-O-methyltransferase), have heretofore been reported. Despite striking similarities between the two proteins in the double stack with the cap, the stack differs most notably in the species of stacked side chain donated by the protein. Whereas eIF4E employs two tryptophans, VP39 uses a tyrosine and a phenylalanine. Here, we have generated tryptophan substitutions in VP39. Tryptophan substitution was shown, crystallographically, not to disrupt the maintenance of a bona fide parallel stack. However, the single-tryptophan and double-tryptophan substitutions were associated with increased affinity for cap nucleoside by factors of 10 and 50, respectively. VP39 interacted more strongly with a true substrate (containing portions of RNA downstream of the cap in addition to the cap itself) than with isolated cap nucleoside, by several orders of magnitude. VP39 mutants with tryptophan substitution at position 180 exhibited apparent defects in substrate catalytic rate during the first turnover cycle, indicating the possibility of an exquisite sensitivity of the catalytic center to subtle changes in substrate position brought about by alterations in the cap-binding slot. The X-ray structure of VP39 with a genuine nucleobase analogue of N7-methylguanosine, namely, N7,9-dimethylguanine, indicated that the N7-methylguanosine rotational orientation within the stack is a property of the cap nucleobase itself.

-	~~{{STRUCTURE_1jsz\| PDB=1jsz \| SCENE= }}~~	+	The "cap-binding slot" of an mRNA cap-binding protein: quantitative effects of aromatic side chain choice in the double-stacking sandwich with cap.,Hu G, Oguro A, Li C, Gershon PD, Quiocho FA Biochemistry. 2002 Jun 18;41(24):7677-87. PMID:12056899<ref>PMID:12056899</ref>

-	~~===Crystal Structure Analysis of N7~~,~~9-dimethylguanine-VP39 complex===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12056899}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1jsz]] 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=1JSZ OCA].~~	+

	==See Also==		==See Also==
	*[[Poly(A) Polymerase\|Poly(A) Polymerase]]		*[[Poly(A) Polymerase\|Poly(A) Polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:012056899<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Polynucleotide adenylyltransferase]]		[[Category: Polynucleotide adenylyltransferase]]
	[[Category: Vaccinia virus]]		[[Category: Vaccinia virus]]

OCA at 21:34, 20 October 2012

2012-10-20T21:34:07Z

←Older revision		Revision as of 21:34, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1jsz]] 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=1JSZ OCA].	+	[[1jsz]] 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=1JSZ OCA].

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

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

2012-07-27T13:37:44Z

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

←Older revision

Revision as of 13:37, 27 July 2012

OCA at 13:37, 27 July 2012

2012-07-27T13:37:43Z

←Older revision		Revision as of 13:37, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1jsz.png\|left\|200px]]		[[Image:1jsz.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1jsz", 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_1jsz\| PDB=1jsz \| SCENE= }}		{{STRUCTURE_1jsz\| PDB=1jsz \| SCENE= }}

	===Crystal Structure Analysis of N7,9-dimethylguanine-VP39 complex===		===Crystal Structure Analysis of N7,9-dimethylguanine-VP39 complex===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12056899}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12056899 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12056899}}		{{ABSTRACT_PUBMED_12056899}}

	==About this Structure==		==About this Structure==
-	~~1JSZ~~ 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=1JSZ OCA].	+	[[1jsz]] 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=1JSZ OCA].
		+
		+	==See Also==
		+	*[[Poly(A) Polymerase\|Poly(A) Polymerase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12056899~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012056899</ref><references group="xtra"/>
	[[Category: Polynucleotide adenylyltransferase]]		[[Category: Polynucleotide adenylyltransferase]]
	[[Category: Vaccinia virus]]		[[Category: Vaccinia virus]]
Line 32:		Line 23:
	[[Category: Methyltransferase]]		[[Category: Methyltransferase]]
	[[Category: Mrna cap-binding protein]]		[[Category: Mrna cap-binding protein]]
		+	[[Category: Transferase]]
	[[Category: Vp39]]		[[Category: Vp39]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 07:01:30 2009''