2zvf - Revision history

OCA at 17:38, 15 December 2021

OCA — Wed, 15 Dec 2021 17:38:47 GMT

←Older revision		Revision as of 17:38, 15 December 2021
Line 1:		Line 1:

	==Crystal structure of Archaeoglobus fulgidus alanyl-tRNA synthetase C-terminal dimerization domain==		==Crystal structure of Archaeoglobus fulgidus alanyl-tRNA synthetase C-terminal dimerization domain==
-	<StructureSection load='2zvf' size='340' side='right' caption='[[2zvf]], [[Resolution\|resolution]] 3.20Å' scene=''>	+	<StructureSection load='2zvf' size='340' side='right'caption='[[2zvf]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zvf]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZVF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2ZVF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zvf]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZVF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZVF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ztg\|2ztg]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ztg\|2ztg]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF_2255, alaS ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 ARCFL])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF_2255, alaS ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 ARCFL])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Alanine--tRNA_ligase Alanine--tRNA ligase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.7 6.1.1.7] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Alanine--tRNA_ligase Alanine--tRNA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.7 6.1.1.7] </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=2zvf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zvf OCA], [~~http~~://pdbe.org/2zvf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2zvf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2zvf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2zvf ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/2zvf TOPSAN]</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=2zvf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zvf OCA], [https://pdbe.org/2zvf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zvf RCSB], [https://www.ebi.ac.uk/pdbsum/2zvf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zvf ProSAT], [https://www.topsan.org/Proteins/RSGI/2zvf TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/SYA_ARCFU SYA_ARCFU]] Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction: alanine is first activated by ATP to form Ala-AMP and then transferred to the acceptor end of tRNA(Ala). Incorrectly charged aminoacyl-tRNA(Ala) is also edited in situ by the editing domain.<ref>PMID:19423669</ref>	+	[[https://www.uniprot.org/uniprot/SYA_ARCFU SYA_ARCFU]] Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction: alanine is first activated by ATP to form Ala-AMP and then transferred to the acceptor end of tRNA(Ala). Incorrectly charged aminoacyl-tRNA(Ala) is also edited in situ by the editing domain.<ref>PMID:19423669</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:

	==See Also==		==See Also==
-	*[[Aminoacyl tRNA ~~Synthetase~~\|Aminoacyl tRNA ~~Synthetase~~]]	+	*[[Aminoacyl tRNA synthetase 3D structures\|Aminoacyl tRNA synthetase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 41:		Line 41:
	[[Category: Alanine--tRNA ligase]]		[[Category: Alanine--tRNA ligase]]
	[[Category: Arcfl]]		[[Category: Arcfl]]
		+	[[Category: Large Structures]]
	[[Category: Fukunaga, R]]		[[Category: Fukunaga, R]]
	[[Category: Naganuma, M]]		[[Category: Naganuma, M]]

OCA at 06:47, 18 October 2018

OCA — Thu, 18 Oct 2018 06:47:55 GMT

←Older revision		Revision as of 06:47, 18 October 2018
Line 17:		Line 17:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zv/2zvf_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zv/2zvf_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>
Line 43:		Line 43:
	[[Category: Fukunaga, R]]		[[Category: Fukunaga, R]]
	[[Category: Naganuma, M]]		[[Category: Naganuma, M]]
		+	[[Category: Structural genomic]]
	[[Category: Sekine, S]]		[[Category: Sekine, S]]
	[[Category: Yokoyama, S]]		[[Category: Yokoyama, S]]
Line 49:		Line 50:
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
	[[Category: C-terminal]]		[[Category: C-terminal]]
		+	[[Category: Cytoplasm]]
	[[Category: Ligase]]		[[Category: Ligase]]
	[[Category: National project on protein structural and functional analyse]]		[[Category: National project on protein structural and functional analyse]]
Line 55:		Line 57:
	[[Category: Oligomerization domain]]		[[Category: Oligomerization domain]]
	[[Category: Protein biosynthesis]]		[[Category: Protein biosynthesis]]
-	[[Category: Structural genomic]]
	[[Category: Rsgi]]		[[Category: Rsgi]]

OCA at 12:56, 5 August 2016

OCA — Fri, 05 Aug 2016 12:56:12 GMT

←Older revision		Revision as of 12:56, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of Archaeoglobus fulgidus alanyl-tRNA synthetase C-terminal dimerization domain==		==Crystal structure of Archaeoglobus fulgidus alanyl-tRNA synthetase C-terminal dimerization domain==
	<StructureSection load='2zvf' size='340' side='right' caption='[[2zvf]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='2zvf' size='340' side='right' caption='[[2zvf]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zvf]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Archaeoglobus_fulgidus Archaeoglobus fulgidus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZVF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZVF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zvf]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZVF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZVF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ztg\|2ztg]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ztg\|2ztg]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF_2255, alaS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 ~~Archaeoglobus fulgidus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF_2255, alaS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 ARCFL])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alanine--tRNA_ligase Alanine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.7 6.1.1.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alanine--tRNA_ligase Alanine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.7 6.1.1.7] </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=2zvf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zvf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zvf RCSB], [http://www.ebi.ac.uk/pdbsum/2zvf PDBsum], [http://www.topsan.org/Proteins/RSGI/2zvf TOPSAN]</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=2zvf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zvf OCA], [http://pdbe.org/2zvf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zvf RCSB], [http://www.ebi.ac.uk/pdbsum/2zvf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2zvf ProSAT], [http://www.topsan.org/Proteins/RSGI/2zvf TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 20:		Line 21:
	<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=2zvf ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 30:		Line 31:
	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 2zvf" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 38:		Line 40:
	</StructureSection>		</StructureSection>
	[[Category: Alanine--tRNA ligase]]		[[Category: Alanine--tRNA ligase]]
-	[[Category: ~~Archaeoglobus fulgidus~~]]	+	[[Category: Arcfl]]
	[[Category: Fukunaga, R]]		[[Category: Fukunaga, R]]
	[[Category: Naganuma, M]]		[[Category: Naganuma, M]]

OCA at 19:01, 25 December 2014

OCA — Thu, 25 Dec 2014 19:01:23 GMT

←Older revision		Revision as of 19:01, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2zvf]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZVF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZVF FirstGlance]. <br>		<table><tr><td colspan='2'>[[2zvf]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZVF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZVF FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ztg\|2ztg]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ztg\|2ztg]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF_2255, alaS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 Archaeoglobus fulgidus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF_2255, alaS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 Archaeoglobus fulgidus])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alanine--tRNA_ligase Alanine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.7 6.1.1.7] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alanine--tRNA_ligase Alanine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.7 6.1.1.7] </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=2zvf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zvf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zvf RCSB], [http://www.ebi.ac.uk/pdbsum/2zvf PDBsum], [http://www.topsan.org/Proteins/RSGI/2zvf TOPSAN]</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=2zvf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zvf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zvf RCSB], [http://www.ebi.ac.uk/pdbsum/2zvf PDBsum], [http://www.topsan.org/Proteins/RSGI/2zvf TOPSAN]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SYA_ARCFU SYA_ARCFU]] Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction: alanine is first activated by ATP to form Ala-AMP and then transferred to the acceptor end of tRNA(Ala). Incorrectly charged aminoacyl-tRNA(Ala) is also edited in situ by the editing domain.<ref>PMID:19423669</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 39:
	[[Category: Alanine--tRNA ligase]]		[[Category: Alanine--tRNA ligase]]
	[[Category: Archaeoglobus fulgidus]]		[[Category: Archaeoglobus fulgidus]]
-	[[Category: Fukunaga, R.]]	+	[[Category: Fukunaga, R]]
-	[[Category: Naganuma, M.]]	+	[[Category: Naganuma, M]]
-	[[Category: Sekine, S.]]	+	[[Category: Sekine, S]]
-	[[Category: Yokoyama, S.]]	+	[[Category: Yokoyama, S]]
	[[Category: Alanyl-trna synthetase]]		[[Category: Alanyl-trna synthetase]]
	[[Category: Aminoacyl-trna synthetase]]		[[Category: Aminoacyl-trna synthetase]]
Line 51:		Line 53:
	[[Category: Oligomerization domain]]		[[Category: Oligomerization domain]]
	[[Category: Protein biosynthesis]]		[[Category: Protein biosynthesis]]
-	[[Category: Riken structural genomics/proteomics initiative]]
-	[[Category: Rsgi]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
		+	[[Category: Rsgi]]

OCA at 06:12, 29 September 2014

OCA — Mon, 29 Sep 2014 06:12:36 GMT

←Older revision		Revision as of 06:12, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2zvf.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of Archaeoglobus fulgidus alanyl-tRNA synthetase C-terminal dimerization domain==
		+	<StructureSection load='2zvf' size='340' side='right' caption='[[2zvf]], [[Resolution\|resolution]] 3.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2zvf]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZVF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZVF FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ztg\|2ztg]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF_2255, alaS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 Archaeoglobus fulgidus])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alanine--tRNA_ligase Alanine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.7 6.1.1.7] </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=2zvf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zvf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zvf RCSB], [http://www.ebi.ac.uk/pdbsum/2zvf PDBsum], [http://www.topsan.org/Proteins/RSGI/2zvf TOPSAN]</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/zv/2zvf_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 ==
		+	Alanyl-tRNA synthetase (AlaRS) specifically recognizes the major identity determinant, the G3:U70 base pair, in the acceptor stem of tRNA(Ala) by both the tRNA-recognition and editing domains. In this study, we solved the crystal structures of 2 halves of Archaeoglobus fulgidus AlaRS: AlaRS-DeltaC, comprising the aminoacylation, tRNA-recognition, and editing domains, and AlaRS-C, comprising the dimerization domain. The aminoacylation/tRNA-recognition domains contain an insertion incompatible with the class-specific tRNA-binding mode. The editing domain is fixed tightly via hydrophobic interactions to the aminoacylation/tRNA-recognition domains, on the side opposite from that in threonyl-tRNA synthetase. A groove formed between the aminoacylation/tRNA-recognition domains and the editing domain appears to be an alternative tRNA-binding site, which might be used for the aminoacylation and/or editing reactions. Actually, the amino acid residues required for the G3:U70 recognition are mapped in this groove. The dimerization domain consists of helical and globular subdomains. The helical subdomain mediates dimerization by forming a helix-loop-helix zipper. The globular subdomain, which is important for the aminoacylation and editing activities, has a positively-charged face suitable for tRNA binding.

-	~~{{STRUCTURE_2zvf\| PDB=2zvf \| SCENE= }}~~	+	Unique protein architecture of alanyl-tRNA synthetase for aminoacylation, editing, and dimerization.,Naganuma M, Sekine S, Fukunaga R, Yokoyama S Proc Natl Acad Sci U S A. 2009 May 26;106(21):8489-94. Epub 2009 May 7. PMID:19423669<ref>PMID:19423669</ref>

-	~~===Crystal structure~~ of ~~Archaeoglobus fulgidus alanyl-tRNA synthetase C-terminal dimerization domain===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19423669}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2zvf]] is a 8 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2ZVF OCA].~~	+

	==See Also==		==See Also==
	*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]		*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019423669<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Alanine--tRNA ligase]]		[[Category: Alanine--tRNA ligase]]
	[[Category: Archaeoglobus fulgidus]]		[[Category: Archaeoglobus fulgidus]]

OCA at 20:18, 20 October 2012

OCA — Sat, 20 Oct 2012 20:18:15 GMT

←Older revision		Revision as of 20:18, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2zvf]] is a 8 chain structure ~~of [[Aminoacyl tRNA Synthetase]]~~ with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZVF OCA].	+	[[2zvf]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZVF OCA].

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

OCA: Protected "2zvf" [edit=sysop:move=sysop]

OCA — Fri, 27 Jul 2012 10:02:54 GMT

Protected "2zvf" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:02, 27 July 2012

OCA at 10:02, 27 July 2012

OCA — Fri, 27 Jul 2012 10:02:52 GMT

←Older revision		Revision as of 10:02, 27 July 2012
Line 1:		Line 1:
-	~~{{Seed}}~~	+	[[Image:2zvf.png\|left\|200px]]
-	[[Image:2zvf.~~jpg~~\|left\|200px]]	+

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2zvf", 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_2zvf\| PDB=2zvf \| SCENE= }}		{{STRUCTURE_2zvf\| PDB=2zvf \| SCENE= }}

	===Crystal structure of Archaeoglobus fulgidus alanyl-tRNA synthetase C-terminal dimerization domain===		===Crystal structure of Archaeoglobus fulgidus alanyl-tRNA synthetase C-terminal dimerization domain===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19423669}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19423669 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19423669}}		{{ABSTRACT_PUBMED_19423669}}

	==About this Structure==		==About this Structure==
-	~~2ZVF~~ is a 8 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZVF OCA].	+	[[2zvf]] is a 8 chain structure of [[Aminoacyl tRNA Synthetase]] with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZVF OCA].
		+
		+	==See Also==
		+	*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19423669~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019423669</ref><references group="xtra"/>
	[[Category: Alanine--tRNA ligase]]		[[Category: Alanine--tRNA ligase]]
	[[Category: Archaeoglobus fulgidus]]		[[Category: Archaeoglobus fulgidus]]
Line 34:		Line 25:
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
	[[Category: C-terminal]]		[[Category: C-terminal]]
-	[[Category: Cytoplasm]]
	[[Category: Ligase]]		[[Category: Ligase]]
	[[Category: National project on protein structural and functional analyse]]		[[Category: National project on protein structural and functional analyse]]
Line 44:		Line 34:
	[[Category: Rsgi]]		[[Category: Rsgi]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 1 09:06:07 2009''

OCA at 06:06, 1 July 2009

OCA — Wed, 01 Jul 2009 06:06:11 GMT

←Older revision		Revision as of 06:06, 1 July 2009
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:2zvf.jpg\|left\|200px]]

-	The ~~entry 2zvf~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_2zvf", 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_2zvf\| PDB=2zvf \| SCENE= }}

-	~~Authors: Naganuma, M., Sekine, S., Fukunaga, R., Yokoyama, S~~	+	===Crystal structure of Archaeoglobus fulgidus alanyl-tRNA synthetase C-terminal dimerization domain===

-	Description:

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Nov 20 07~~:36:~~32 2008~~''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19423669}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19423669 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19423669}}
		+
		+	==About this Structure==
		+	2ZVF is a 8 chains structure of sequences from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZVF OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19423669</ref><references group="xtra"/>
		+	[[Category: Alanine--tRNA ligase]]
		+	[[Category: Archaeoglobus fulgidus]]
		+	[[Category: Fukunaga, R.]]
		+	[[Category: Naganuma, M.]]
		+	[[Category: Sekine, S.]]
		+	[[Category: Yokoyama, S.]]
		+	[[Category: Alanyl-trna synthetase]]
		+	[[Category: Aminoacyl-trna synthetase]]
		+	[[Category: Atp-binding]]
		+	[[Category: C-terminal]]
		+	[[Category: Cytoplasm]]
		+	[[Category: Ligase]]
		+	[[Category: National project on protein structural and functional analyse]]
		+	[[Category: Nppsfa]]
		+	[[Category: Nucleotide-binding]]
		+	[[Category: Oligomerization domain]]
		+	[[Category: Protein biosynthesis]]
		+	[[Category: Riken structural genomics/proteomics initiative]]
		+	[[Category: Rsgi]]
		+	[[Category: Structural genomic]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 1 09:06:07 2009''

OCA: New page: '''Unreleased structure''' The entry 2zvf is ON HOLD until Paper Publication Authors: Naganuma, M., Sekine, S., Fukunaga, R., Yokoyama, S Description: ''Page seeded by [http://oca.we...

OCA — Thu, 20 Nov 2008 05:36:32 GMT

New page: '''Unreleased structure''' The entry 2zvf is ON HOLD until Paper Publication Authors: Naganuma, M., Sekine, S., Fukunaga, R., Yokoyama, S Description: ''Page seeded by [http://oca.we...

New page

'''Unreleased structure'''

The entry 2zvf is ON HOLD until Paper Publication

Authors: Naganuma, M., Sekine, S., Fukunaga, R., Yokoyama, S

Description:

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Nov 20 07:36:32 2008''