1set - Revision history

OCA at 08:30, 14 February 2024

2024-02-14T08:30:20Z

← Older revision		Revision as of 08:30, 14 February 2024
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	<StructureSection load='1set' size='340' side='right'caption='[[1set]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='1set' size='340' side='right'caption='[[1set]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1set]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971~~]. The April 2001 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aminoacyl-tRNA Synthetases'' by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2001_4 10.2210/rcsb_pdb/mom_2001_4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SET OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SET FirstGlance]. <br>		<table><tr><td colspan='2'>[[1set]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. The April 2001 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aminoacyl-tRNA Synthetases'' by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2001_4 10.2210/rcsb_pdb/mom_2001_4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SET OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SET FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SSA:5~~-~~O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE'>SSA</scene>~~</td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.55Å</td></tr>
	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks'>[https~~:~~//en.wikipedia.org/wiki/Serine~~--~~tRNA_ligase Serine~~--~~tRNA ligase], with EC number [https://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=6.1.1.11 6.1.1.11]~~ </~~span~~></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SSA:5-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE'>SSA</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1set FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1set OCA], [https://pdbe.org/1set PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1set RCSB], [https://www.ebi.ac.uk/pdbsum/1set PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1set 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=1set FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1set OCA], [https://pdbe.org/1set PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1set RCSB], [https://www.ebi.ac.uk/pdbsum/1set PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1set ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/SYS_THET2 SYS_THET2]] Catalyzes the attachment of serine to tRNA(Ser). Is also probably able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec).[HAMAP-Rule:MF_00176]		[https://www.uniprot.org/uniprot/SYS_THET2 SYS_THET2] Catalyzes the attachment of serine to tRNA(Ser). Is also probably able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec).[HAMAP-Rule:MF_00176]
	== 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=1set 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=1set ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Crystal structures of seryl-tRNA synthetase from Thermus thermophilus complexed with two different analogs of seryl adenylate have been determined at 2.5 A resolution. The first complex is between the enzyme and seryl-hydroxamate-AMP (adenosine monophosphate), produced enzymatically in the crystal from adenosine triphosphate (ATP) and serine hydroxamate, and the second is with a synthetic analog of seryl adenylate (5'-O-[N-(L-seryl)-sulfamoyl]adenosine), which is a strong inhibitor of the enzyme. Both molecules are bound in a similar fashion by a network of hydrogen bond interactions in a deep hydrophilic cleft formed by the antiparallel beta sheet and surrounding loops of the synthetase catalytic domain. Four regions in the primary sequence are involved in the interactions, including the motif 2 and 3 regions of class 2 synthetases. Apart from the specific recognition of the serine side chain, the interactions are likely to be similar in all class 2 synthetases.

	Crystal structures at 2.5 angstrom resolution of seryl-tRNA synthetase complexed with two analogs of seryl adenylate.,Belrhali H, Yaremchuk A, Tukalo M, Larsen K, Berthet-Colominas C, Leberman R, Beijer B, Sproat B, Als-Nielsen J, Grubel G, et al. Science. 1994 Mar 11;263(5152):1432-6. PMID:8128224<ref>PMID:8128224</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 1set" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[Aminoacyl tRNA synthetase 3D structures\|Aminoacyl tRNA synthetase 3D structures]]		*[[Aminoacyl tRNA synthetase 3D structures\|Aminoacyl tRNA synthetase 3D structures]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]~~
	[[Category: Aminoacyl-tRNA Synthetases]]		[[Category: Aminoacyl-tRNA Synthetases]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
	[[Category: ~~Serine--tRNA ligase~~]]		[[Category: Thermus thermophilus]]
	[[Category: Belrhali, H]]		[[Category: Belrhali H]]
	[[Category: Cusack, S]]		[[Category: Cusack S]]
	~~[[Category: Ligase]]~~
	~~[[Category: Synthetase~~]]

OCA at 07:30, 22 September 2021

2021-09-22T07:30:16Z

← Older revision		Revision as of 07:30, 22 September 2021
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	<StructureSection load='1set' size='340' side='right'caption='[[1set]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='1set' size='340' side='right'caption='[[1set]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1set]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. The April 2001 RCSB PDB [~~http~~://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aminoacyl-tRNA Synthetases'' by David S. Goodsell is [~~http~~://dx.doi.org/10.2210/rcsb_pdb/mom_2001_4 10.2210/rcsb_pdb/mom_2001_4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SET OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1SET FirstGlance]. <br>		<table><tr><td colspan='2'>[[1set]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. The April 2001 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aminoacyl-tRNA Synthetases'' by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2001_4 10.2210/rcsb_pdb/mom_2001_4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SET OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SET FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SSA:5-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE'>SSA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SSA:5-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE'>SSA</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Serine--tRNA_ligase Serine--tRNA ligase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.11 6.1.1.11] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Serine--tRNA_ligase Serine--tRNA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.11 6.1.1.11] </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=1set FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1set OCA], [~~http~~://pdbe.org/1set PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1set RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1set PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1set 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=1set FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1set OCA], [https://pdbe.org/1set PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1set RCSB], [https://www.ebi.ac.uk/pdbsum/1set PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1set ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/SYS_THET2 SYS_THET2]] Catalyzes the attachment of serine to tRNA(Ser). Is also probably able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec).[HAMAP-Rule:MF_00176]		[[https://www.uniprot.org/uniprot/SYS_THET2 SYS_THET2]] Catalyzes the attachment of serine to tRNA(Ser). Is also probably able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec).[HAMAP-Rule:MF_00176]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 19:20, 11 December 2019

2019-12-11T19:20:40Z

← Older revision		Revision as of 19:20, 11 December 2019
Line 1:		Line 1:

	==CRYSTAL STRUCTURES AT 2.5 ANGSTROMS RESOLUTION OF SERYL-TRNA SYNTHETASE COMPLEXED WITH TWO DIFFERENT ANALOGUES OF SERYL-ADENYLATE==		==CRYSTAL STRUCTURES AT 2.5 ANGSTROMS RESOLUTION OF SERYL-TRNA SYNTHETASE COMPLEXED WITH TWO DIFFERENT ANALOGUES OF SERYL-ADENYLATE==
	<StructureSection load='1set' size='340' side='right' caption='[[1set]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='1set' size='340' side='right'caption='[[1set]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1set]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. The April 2001 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aminoacyl-tRNA Synthetases'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2001_4 10.2210/rcsb_pdb/mom_2001_4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SET OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SET FirstGlance]. <br>		<table><tr><td colspan='2'>[[1set]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. The April 2001 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aminoacyl-tRNA Synthetases'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2001_4 10.2210/rcsb_pdb/mom_2001_4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SET OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SET FirstGlance]. <br>
Line 31:		Line 31:

	==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 38:		Line 38:
	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]		[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Aminoacyl-tRNA Synthetases]]		[[Category: Aminoacyl-tRNA Synthetases]]
			[[Category: Large Structures]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Serine--tRNA ligase]]		[[Category: Serine--tRNA ligase]]

OCA at 06:52, 8 March 2018

2018-03-08T06:52:00Z

← Older revision		Revision as of 06:52, 8 March 2018
Line 1:		Line 1:

	==CRYSTAL STRUCTURES AT 2.5 ANGSTROMS RESOLUTION OF SERYL-TRNA SYNTHETASE COMPLEXED WITH TWO DIFFERENT ANALOGUES OF SERYL-ADENYLATE==		==CRYSTAL STRUCTURES AT 2.5 ANGSTROMS RESOLUTION OF SERYL-TRNA SYNTHETASE COMPLEXED WITH TWO DIFFERENT ANALOGUES OF SERYL-ADENYLATE==
	<StructureSection load='1set' size='340' side='right' caption='[[1set]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='1set' size='340' side='right' caption='[[1set]], [[Resolution\|resolution]] 2.55Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SSA:5-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE'>SSA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SSA:5-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE'>SSA</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine--tRNA_ligase Serine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.11 6.1.1.11] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine--tRNA_ligase Serine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.11 6.1.1.11] </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=1set FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1set OCA], [http://pdbe.org/1set PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1set RCSB], [http://www.ebi.ac.uk/pdbsum/1set 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=1set FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1set OCA], [http://pdbe.org/1set PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1set RCSB], [http://www.ebi.ac.uk/pdbsum/1set PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1set ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/se/1set_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/se/1set_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>
	</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=1set ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 17:34, 11 September 2015

2015-09-11T17:34:48Z

← Older revision		Revision as of 17:34, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1set' size='340' side='right' caption='[[1set]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='1set' size='340' side='right' caption='[[1set]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1set]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermus_thermophilus Thermus thermophilus~~]. The April 2001 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aminoacyl-tRNA Synthetases'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2001_4 10.2210/rcsb_pdb/mom_2001_4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SET OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SET FirstGlance]. <br>		<table><tr><td colspan='2'>[[1set]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. The April 2001 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aminoacyl-tRNA Synthetases'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2001_4 10.2210/rcsb_pdb/mom_2001_4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SET OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SET FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SSA:5-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE'>SSA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SSA:5-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE'>SSA</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine--tRNA_ligase Serine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.11 6.1.1.11] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine--tRNA_ligase Serine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.11 6.1.1.11] </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=1set FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1set OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1set RCSB], [http://www.ebi.ac.uk/pdbsum/1set 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=1set FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1set OCA], [http://pdbe.org/1set PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1set RCSB], [http://www.ebi.ac.uk/pdbsum/1set PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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 1set" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Aminoacyl-tRNA Synthetases]]		[[Category: Aminoacyl-tRNA Synthetases]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Serine--tRNA ligase]]		[[Category: Serine--tRNA ligase]]
	~~[[Category: Thermus thermophilus]]~~
	[[Category: Belrhali, H]]		[[Category: Belrhali, H]]
	[[Category: Cusack, S]]		[[Category: Cusack, S]]
	[[Category: Ligase]]		[[Category: Ligase]]
	[[Category: Synthetase]]		[[Category: Synthetase]]

OCA at 19:40, 25 December 2014

2014-12-25T19:40:37Z

← Older revision		Revision as of 19:40, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1set]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. The April 2001 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aminoacyl-tRNA Synthetases'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2001_4 10.2210/rcsb_pdb/mom_2001_4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SET OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SET FirstGlance]. <br>		<table><tr><td colspan='2'>[[1set]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. The April 2001 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aminoacyl-tRNA Synthetases'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2001_4 10.2210/rcsb_pdb/mom_2001_4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SET OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SET FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SSA:5-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE'>SSA</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SSA:5-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE'>SSA</scene></td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine--tRNA_ligase Serine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.11 6.1.1.11] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine--tRNA_ligase Serine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.11 6.1.1.11] </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=1set FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1set OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1set RCSB], [http://www.ebi.ac.uk/pdbsum/1set 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=1set FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1set OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1set RCSB], [http://www.ebi.ac.uk/pdbsum/1set PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/SYS_THET2 SYS_THET2]] Catalyzes the attachment of serine to tRNA(Ser). Is also probably able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec).[HAMAP-Rule:MF_00176]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	[[Category: Serine--tRNA ligase]]		[[Category: Serine--tRNA ligase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Belrhali, H.]]		[[Category: Belrhali, H]]
	[[Category: Cusack, S.]]		[[Category: Cusack, S]]
	[[Category: Ligase]]		[[Category: Ligase]]
	[[Category: Synthetase]]		[[Category: Synthetase]]

OCA at 20:17, 28 September 2014

2014-09-28T20:17:19Z

← Older revision		Revision as of 20:17, 28 September 2014
Line 1:		Line 1:
	[[Image:~~1set~~.~~png~~\|~~left~~\|~~200px~~]]		==CRYSTAL STRUCTURES AT 2.5 ANGSTROMS RESOLUTION OF SERYL-TRNA SYNTHETASE COMPLEXED WITH TWO DIFFERENT ANALOGUES OF SERYL-ADENYLATE==
			<StructureSection load='1set' size='340' side='right' caption='[[1set]], [[Resolution\|resolution]] 2.55Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[1set]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. The April 2001 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aminoacyl-tRNA Synthetases'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2001_4 10.2210/rcsb_pdb/mom_2001_4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SET OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SET FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SSA:5-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE'>SSA</scene><br>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine--tRNA_ligase Serine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.11 6.1.1.11] </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=1set FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1set OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1set RCSB], [http://www.ebi.ac.uk/pdbsum/1set 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/se/1set_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 ==
			Crystal structures of seryl-tRNA synthetase from Thermus thermophilus complexed with two different analogs of seryl adenylate have been determined at 2.5 A resolution. The first complex is between the enzyme and seryl-hydroxamate-AMP (adenosine monophosphate), produced enzymatically in the crystal from adenosine triphosphate (ATP) and serine hydroxamate, and the second is with a synthetic analog of seryl adenylate (5'-O-[N-(L-seryl)-sulfamoyl]adenosine), which is a strong inhibitor of the enzyme. Both molecules are bound in a similar fashion by a network of hydrogen bond interactions in a deep hydrophilic cleft formed by the antiparallel beta sheet and surrounding loops of the synthetase catalytic domain. Four regions in the primary sequence are involved in the interactions, including the motif 2 and 3 regions of class 2 synthetases. Apart from the specific recognition of the serine side chain, the interactions are likely to be similar in all class 2 synthetases.

	~~{{STRUCTURE_1set\| PDB=1set \| SCENE= }}~~		Crystal structures at 2.5 angstrom resolution of seryl-tRNA synthetase complexed with two analogs of seryl adenylate.,Belrhali H, Yaremchuk A, Tukalo M, Larsen K, Berthet-Colominas C, Leberman R, Beijer B, Sproat B, Als-Nielsen J, Grubel G, et al. Science. 1994 Mar 11;263(5152):1432-6. PMID:8128224<ref>PMID:8128224</ref>

	~~===CRYSTAL STRUCTURES AT 2.5 ANGSTROMS RESOLUTION OF SERYL-TRNA SYNTHETASE COMPLEXED WITH TWO DIFFERENT ANALOGUES OF SERYL-ADENYLATE===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_8128224}}~~

	~~==About this Structure==~~
	~~[[1set]] is~~ a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. The April 2001 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the ~~Month] feature on ''Aminoacyl-tRNA Synthetases'' by David~~ S. ~~Goodsell is [http://dx~~.~~doi.org/10.2210/rcsb_pdb/mom_2001_4 10.2210/rcsb_pdb/mom_2001_4]. Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1SET OCA].~~

	==See Also==		==See Also==
	*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]		*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:008128224<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Aminoacyl-tRNA Synthetases]]		[[Category: Aminoacyl-tRNA Synthetases]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]

OCA at 20:39, 20 October 2012

2012-10-20T20:39:37Z

← Older revision		Revision as of 20:39, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
	[[1set]] is a 2 chain structure ~~of [[Aminoacyl tRNA Synthetase]]~~ with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. The April 2001 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aminoacyl-tRNA Synthetases'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2001_4 10.2210/rcsb_pdb/mom_2001_4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SET OCA].		[[1set]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. The April 2001 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aminoacyl-tRNA Synthetases'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2001_4 10.2210/rcsb_pdb/mom_2001_4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SET OCA].

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

OCA at 11:12, 27 July 2012

2012-07-27T11:12:16Z

← Older revision		Revision as of 11:12, 27 July 2012
Line 1:		Line 1:
	[[Image:1set.png\|left\|200px]]		[[Image:1set.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_1set", 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_1set\| PDB=1set \| SCENE= }}		{{STRUCTURE_1set\| PDB=1set \| SCENE= }}

	===CRYSTAL STRUCTURES AT 2.5 ANGSTROMS RESOLUTION OF SERYL-TRNA SYNTHETASE COMPLEXED WITH TWO DIFFERENT ANALOGUES OF SERYL-ADENYLATE===		===CRYSTAL STRUCTURES AT 2.5 ANGSTROMS RESOLUTION OF SERYL-TRNA SYNTHETASE COMPLEXED WITH TWO DIFFERENT ANALOGUES OF SERYL-ADENYLATE===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_8128224}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 8128224 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_8128224}}		{{ABSTRACT_PUBMED_8128224}}

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	==See Also==		==See Also==
	*[[Aminoacyl tRNA Synthetase]]		*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]

	==Reference==		==Reference==

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

2012-02-29T07:57:32Z

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

← Older revision	Revision as of 07:57, 29 February 2012
(No difference)