3a4n - Revision history

OCA at 13:59, 13 March 2024

OCA — Wed, 13 Mar 2024 13:59:41 GMT

←Older revision		Revision as of 13:59, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='3a4n' size='340' side='right'caption='[[3a4n]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='3a4n' size='340' side='right'caption='[[3a4n]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3a4n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_43067 Atcc 43067~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A4N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A4N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3a4n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A4N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A4N FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=EDO:1~~,2~~-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.5Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[3a4l\|3a4l]], [[3a4m\|3a4m]]~~</~~div~~><~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">MJ1538 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])~~</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=3a4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a4n OCA], [https://pdbe.org/3a4n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a4n RCSB], [https://www.ebi.ac.uk/pdbsum/3a4n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a4n 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=3a4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a4n OCA], [https://pdbe.org/3a4n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a4n RCSB], [https://www.ebi.ac.uk/pdbsum/3a4n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a4n ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PSTK_METJA PSTK_METJA]] Specifically phosphorylates seryl-tRNA(Sec) to O-phosphoseryl-tRNA(Sec), an activated intermediate for selenocysteine biosynthesis.	+	[https://www.uniprot.org/uniprot/PSTK_METJA PSTK_METJA] Specifically phosphorylates seryl-tRNA(Sec) to O-phosphoseryl-tRNA(Sec), an activated intermediate for selenocysteine biosynthesis.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 20:
	</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=3a4n 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=3a4n ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Compared to bacteria, archaea and eukaryotes employ an additional enzyme for the biosynthesis of selenocysteine (Sec), the 21(st) natural amino acid (aa). An essential RNA-dependent kinase, O-phosphoseryl-tRNA(Sec) kinase (PSTK), converts seryl-tRNA(Sec) to O-phosphoseryl-tRNA(Sec), the immediate precursor of selenocysteinyl-tRNA(Sec). The sequence of Methanocaldococcus jannaschii PSTK (MjPSTK) suggests an N-terminal kinase domain (177 aa) followed by a presumed tRNA binding region (75 aa). The structures of MjPSTK complexed with ADP and AMPPNP revealed that this enzyme belongs to the P-loop kinase class, and that the kinase domain is closely related to gluconate kinase and adenylate kinase. ATP is bound by the P-loop domain (residues 11-18). Formed by antiparallel dimerization of two PSTK monomers, the enzyme structure shows a deep groove with positive electrostatic potential. Located in this groove is the enzyme's active site, which biochemical and genetic data suggest is composed of Asp-41, Arg-44, Glu-55, Tyr-82, Tyr-83, Met-86, and Met-132. Based on structural comparison with Escherichia coli adenylate kinase a docking model was generated that assigns these amino acids to the recognition of the terminal A76-Ser moieties of Ser-tRNA(Sec). The geometry and electrostatic environment of the groove in MjPSTK are perfectly complementary to the unusually long acceptor helix of tRNA(Sec).
-
-	Structure of a tRNA-dependent kinase essential for selenocysteine decoding.,Araiso Y, Sherrer RL, Ishitani R, Ho JM, Soll D, Nureki O Proc Natl Acad Sci U S A. 2009 Sep 22;106(38):16215-20. Epub 2009 Sep 10. PMID:19805283<ref>PMID:19805283</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3a4n" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 43067]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Araiso, Y]]	+	[[Category: Methanocaldococcus jannaschii]]
-	[[Category: Ishitani, R]]	+	[[Category: Araiso Y]]
-	[[Category: Nureki, O]]	+	[[Category: Ishitani R]]
-	[[Category: Soll, D]]	+	[[Category: Nureki O]]
-	~~[[Category: Atp binding motif]]~~	+	[[Category: Soll D]]
-	~~[[Category: Atp-binding]]~~	+
-	~~[[Category: Kinase]]~~	+
-	~~[[Category: Nucleotide-binding]]~~	+
-	~~[[Category: P-loop motif]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Walker a motif~~]]	+

OCA at 16:16, 22 December 2021

OCA — Wed, 22 Dec 2021 16:16:53 GMT

←Older revision		Revision as of 16:16, 22 December 2021
Line 1:		Line 1:

	==Crystal structure of archaeal O-phosphoseryl-tRNA(Sec) kinase==		==Crystal structure of archaeal O-phosphoseryl-tRNA(Sec) kinase==
-	<StructureSection load='3a4n' size='340' side='right' caption='[[3a4n]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='3a4n' size='340' side='right'caption='[[3a4n]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3a4n]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A4N OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3A4N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3a4n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A4N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A4N FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3a4l\|3a4l]], [[3a4m\|3a4m]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3a4l\|3a4l]], [[3a4m\|3a4m]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MJ1538 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MJ1538 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</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=3a4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a4n OCA], [~~http~~://pdbe.org/3a4n PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3a4n RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3a4n PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3a4n 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=3a4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a4n OCA], [https://pdbe.org/3a4n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a4n RCSB], [https://www.ebi.ac.uk/pdbsum/3a4n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a4n ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PSTK_METJA PSTK_METJA]] Specifically phosphorylates seryl-tRNA(Sec) to O-phosphoseryl-tRNA(Sec), an activated intermediate for selenocysteine biosynthesis.	+	[[https://www.uniprot.org/uniprot/PSTK_METJA PSTK_METJA]] Specifically phosphorylates seryl-tRNA(Sec) to O-phosphoseryl-tRNA(Sec), an activated intermediate for selenocysteine biosynthesis.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 43067]]		[[Category: Atcc 43067]]
		+	[[Category: Large Structures]]
	[[Category: Araiso, Y]]		[[Category: Araiso, Y]]
	[[Category: Ishitani, R]]		[[Category: Ishitani, R]]

OCA at 08:19, 24 October 2018

OCA — Wed, 24 Oct 2018 08:19:59 GMT

←Older revision		Revision as of 08:19, 24 October 2018
Line 1:		Line 1:
		+
	==Crystal structure of archaeal O-phosphoseryl-tRNA(Sec) kinase==		==Crystal structure of archaeal O-phosphoseryl-tRNA(Sec) kinase==
	<StructureSection load='3a4n' size='340' side='right' caption='[[3a4n]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='3a4n' size='340' side='right' caption='[[3a4n]], [[Resolution\|resolution]] 2.50Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3a4l\|3a4l]], [[3a4m\|3a4m]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3a4l\|3a4l]], [[3a4m\|3a4m]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MJ1538 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MJ1538 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</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=3a4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a4n OCA], [http://pdbe.org/3a4n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3a4n RCSB], [http://www.ebi.ac.uk/pdbsum/3a4n 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=3a4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a4n OCA], [http://pdbe.org/3a4n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3a4n RCSB], [http://www.ebi.ac.uk/pdbsum/3a4n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3a4n ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a4/3a4n_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a4/3a4n_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 05:24, 9 February 2016

OCA — Tue, 09 Feb 2016 05:24:34 GMT

←Older revision		Revision as of 05:24, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='3a4n' size='340' side='right' caption='[[3a4n]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='3a4n' size='340' side='right' caption='[[3a4n]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3a4n]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Methanocaldococcus_jannaschii Methanocaldococcus jannaschii~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A4N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3A4N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3a4n]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A4N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3A4N FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3a4l\|3a4l]], [[3a4m\|3a4m]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3a4l\|3a4l]], [[3a4m\|3a4m]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MJ1538 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ~~Methanocaldococcus jannaschii~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MJ1538 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</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=3a4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a4n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3a4n RCSB], [http://www.ebi.ac.uk/pdbsum/3a4n 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=3a4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a4n OCA], [http://pdbe.org/3a4n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3a4n RCSB], [http://www.ebi.ac.uk/pdbsum/3a4n PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 18:
	<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=3a4n ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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 3a4n" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Methanocaldococcus jannaschii~~]]	+	[[Category: Atcc 43067]]
	[[Category: Araiso, Y]]		[[Category: Araiso, Y]]
	[[Category: Ishitani, R]]		[[Category: Ishitani, R]]

OCA at 04:44, 25 December 2014

OCA — Thu, 25 Dec 2014 04:44:00 GMT

←Older revision		Revision as of 04:44, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3a4n]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A4N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3A4N FirstGlance]. <br>		<table><tr><td colspan='2'>[[3a4n]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A4N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3A4N FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3a4l\|3a4l]], [[3a4m\|3a4m]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3a4l\|3a4l]], [[3a4m\|3a4m]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MJ1538 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 Methanocaldococcus jannaschii])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MJ1538 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 Methanocaldococcus jannaschii])</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=3a4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a4n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3a4n RCSB], [http://www.ebi.ac.uk/pdbsum/3a4n 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=3a4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a4n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3a4n RCSB], [http://www.ebi.ac.uk/pdbsum/3a4n PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PSTK_METJA PSTK_METJA]] Specifically phosphorylates seryl-tRNA(Sec) to O-phosphoseryl-tRNA(Sec), an activated intermediate for selenocysteine biosynthesis.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Methanocaldococcus jannaschii]]		[[Category: Methanocaldococcus jannaschii]]
-	[[Category: Araiso, Y.]]	+	[[Category: Araiso, Y]]
-	[[Category: Ishitani, R.]]	+	[[Category: Ishitani, R]]
-	[[Category: Nureki, O.]]	+	[[Category: Nureki, O]]
-	[[Category: Soll, D.]]	+	[[Category: Soll, D]]
	[[Category: Atp binding motif]]		[[Category: Atp binding motif]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]

OCA at 05:42, 2 October 2014

OCA — Thu, 02 Oct 2014 05:42:20 GMT

←Older revision		Revision as of 05:42, 2 October 2014
Line 1:		Line 1:
-	[[~~Image:~~3a4n.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of archaeal O-phosphoseryl-tRNA(Sec) kinase==
		+	<StructureSection load='3a4n' size='340' side='right' caption='[[3a4n]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3a4n]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A4N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3A4N FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3a4l\|3a4l]], [[3a4m\|3a4m]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MJ1538 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 Methanocaldococcus jannaschii])</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=3a4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a4n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3a4n RCSB], [http://www.ebi.ac.uk/pdbsum/3a4n 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/a4/3a4n_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 ==
		+	Compared to bacteria, archaea and eukaryotes employ an additional enzyme for the biosynthesis of selenocysteine (Sec), the 21(st) natural amino acid (aa). An essential RNA-dependent kinase, O-phosphoseryl-tRNA(Sec) kinase (PSTK), converts seryl-tRNA(Sec) to O-phosphoseryl-tRNA(Sec), the immediate precursor of selenocysteinyl-tRNA(Sec). The sequence of Methanocaldococcus jannaschii PSTK (MjPSTK) suggests an N-terminal kinase domain (177 aa) followed by a presumed tRNA binding region (75 aa). The structures of MjPSTK complexed with ADP and AMPPNP revealed that this enzyme belongs to the P-loop kinase class, and that the kinase domain is closely related to gluconate kinase and adenylate kinase. ATP is bound by the P-loop domain (residues 11-18). Formed by antiparallel dimerization of two PSTK monomers, the enzyme structure shows a deep groove with positive electrostatic potential. Located in this groove is the enzyme's active site, which biochemical and genetic data suggest is composed of Asp-41, Arg-44, Glu-55, Tyr-82, Tyr-83, Met-86, and Met-132. Based on structural comparison with Escherichia coli adenylate kinase a docking model was generated that assigns these amino acids to the recognition of the terminal A76-Ser moieties of Ser-tRNA(Sec). The geometry and electrostatic environment of the groove in MjPSTK are perfectly complementary to the unusually long acceptor helix of tRNA(Sec).

-	~~{{STRUCTURE_3a4n\| PDB=3a4n \| SCENE= }}~~	+	Structure of a tRNA-dependent kinase essential for selenocysteine decoding.,Araiso Y, Sherrer RL, Ishitani R, Ho JM, Soll D, Nureki O Proc Natl Acad Sci U S A. 2009 Sep 22;106(38):16215-20. Epub 2009 Sep 10. PMID:19805283<ref>PMID:19805283</ref>

-	~~===Crystal structure~~ of ~~archaeal O-phosphoseryl-tRNA(Sec) kinase===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19805283}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3a4n]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3A4N OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:019805283<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Methanocaldococcus jannaschii]]		[[Category: Methanocaldococcus jannaschii]]
	[[Category: Araiso, Y.]]		[[Category: Araiso, Y.]]

OCA: Protected "3a4n" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 20:34:19 GMT

Protected "3a4n" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:34, 7 January 2013

OCA at 20:34, 7 January 2013

OCA — Mon, 07 Jan 2013 20:34:14 GMT

←Older revision		Revision as of 20:34, 7 January 2013
Line 1:		Line 1:
-	~~{{Seed}}~~	+	[[Image:3a4n.png\|left\|200px]]
-	[[Image:3a4n.~~jpg~~\|left\|200px]]	+

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3a4n", 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_3a4n\| PDB=3a4n \| SCENE= }}		{{STRUCTURE_3a4n\| PDB=3a4n \| SCENE= }}

	===Crystal structure of archaeal O-phosphoseryl-tRNA(Sec) kinase===		===Crystal structure of archaeal O-phosphoseryl-tRNA(Sec) kinase===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19805283}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19805283 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19805283}}		{{ABSTRACT_PUBMED_19805283}}

	==About this Structure==		==About this Structure==
-	~~3A4N~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A4N OCA].	+	[[3a4n]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A4N OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19805283~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019805283</ref><references group="xtra"/>
	[[Category: Methanocaldococcus jannaschii]]		[[Category: Methanocaldococcus jannaschii]]
	[[Category: Araiso, Y.]]		[[Category: Araiso, Y.]]
Line 36:		Line 24:
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Walker a motif]]		[[Category: Walker a motif]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 21 10:26:24 2009''

OCA at 08:26, 21 October 2009

OCA — Wed, 21 Oct 2009 08:26:26 GMT

←Older revision		Revision as of 08:26, 21 October 2009
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3a4n.jpg\|left\|200px]]

-	The ~~entry 3a4n~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3a4n", 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_3a4n\| PDB=3a4n \| SCENE= }}

-	~~Authors: Araiso, Y., Ishitani, R., Soll, D., Nureki,~~ O.	+	===Crystal structure of archaeal O-phosphoseryl-tRNA(Sec) kinase===

-	Description: Crystal structure of archaeal O-phosphoseryl-tRNA(Sec) kinase

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Aug 12 12~~:20:39 2009''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19805283}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19805283 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19805283}}
		+
		+	==About this Structure==
		+	3A4N is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A4N OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19805283</ref><references group="xtra"/>
		+	[[Category: Methanocaldococcus jannaschii]]
		+	[[Category: Araiso, Y.]]
		+	[[Category: Ishitani, R.]]
		+	[[Category: Nureki, O.]]
		+	[[Category: Soll, D.]]
		+	[[Category: Atp binding motif]]
		+	[[Category: Atp-binding]]
		+	[[Category: Kinase]]
		+	[[Category: Nucleotide-binding]]
		+	[[Category: P-loop motif]]
		+	[[Category: Transferase]]
		+	[[Category: Walker a motif]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 21 10:26:24 2009''

OCA at 09:20, 12 August 2009

OCA — Wed, 12 Aug 2009 09:20:39 GMT

←Older revision		Revision as of 09:20, 12 August 2009
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3a4n is ON HOLD	+	The entry 3a4n is ON HOLD until Paper Publication

-	Authors: Araiso, Y. , Ishitani, R. , Soll, D. , Nureki, O.	+	Authors: Araiso, Y., Ishitani, R., Soll, D., Nureki, O.

-	Description: Crystal structure of archaeal O-phosphoseryl-tRNA(Sec) kinase ~~(CASP Target)~~	+	Description: Crystal structure of archaeal O-phosphoseryl-tRNA(Sec) kinase

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jul 22 20~~:29:08 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 12 12:20:39 2009''