1uc9 - Revision history

OCA at 23:50, 27 December 2023

OCA — Wed, 27 Dec 2023 23:50:47 GMT

←Older revision		Revision as of 23:50, 27 December 2023
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	<StructureSection load='1uc9' size='340' side='right'caption='[[1uc9]], [[Resolution\|resolution]] 2.38Å' scene=''>		<StructureSection load='1uc9' size='340' side='right'caption='[[1uc9]], [[Resolution\|resolution]] 2.38Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1uc9]] 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~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UC9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UC9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1uc9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UC9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UC9 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ADP:ADENOSINE~~-~~5-DIPHOSPHATE'>ADP</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]] 2.38Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>~~[[~~Non-Standard_Residue~~\|~~NonStd Res:~~]]~~</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1uc8\|1uc8]]~~</~~div~~></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=1uc9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uc9 OCA], [https://pdbe.org/1uc9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uc9 RCSB], [https://www.ebi.ac.uk/pdbsum/1uc9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uc9 ProSAT], [https://www.topsan.org/Proteins/RSGI/1uc9 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=1uc9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uc9 OCA], [https://pdbe.org/1uc9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uc9 RCSB], [https://www.ebi.ac.uk/pdbsum/1uc9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uc9 ProSAT], [https://www.topsan.org/Proteins/RSGI/1uc9 TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/LYSX_THET8 LYSX_THET8]] Catalyzes the ATP-dependent formation of a covalent bond between the amino group of alpha-aminoadipate (AAA) and the gamma-carboxyl group of the C-terminal glutamate residue in LysW.<ref>PMID:19620981</ref>	+	[https://www.uniprot.org/uniprot/LYSX_THET8 LYSX_THET8] Catalyzes the ATP-dependent formation of a covalent bond between the amino group of alpha-aminoadipate (AAA) and the gamma-carboxyl group of the C-terminal glutamate residue in LysW.<ref>PMID:19620981</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Kuramitsu, S~~]]	+	[[Category: Thermus thermophilus]]
-	[[Category: ~~Matsuura, T~~]]	+	[[Category: Kuramitsu S]]
-	[[Category: ~~Nishiyama, M~~]]	+	[[Category: Matsuura T]]
-	[[Category: ~~Structural genomic~~]]	+	[[Category: Nishiyama M]]
-	[[Category: Sakai, H]]	+	[[Category: Sakai H]]
-	[[Category: Sekine, S]]	+	[[Category: Sekine S]]
-	[[Category: Shirouzu, M]]	+	[[Category: Shirouzu M]]
-	[[Category: Terada, T]]	+	[[Category: Terada T]]
-	[[Category: Vassylyev~~, D G~~]]	+	[[Category: Vassylyev DG]]
-	[[Category: Vassylyeva~~, M N~~]]	+	[[Category: Vassylyeva MN]]
-	[[Category: Yokoyama, S]]	+	[[Category: Yokoyama S]]
-	~~[[Category: Alpha-aminoadipate pathway]]~~	+
-	~~[[Category: Biosynthetic protein]]~~	+
-	~~[[Category: Lysine biosynthesis]]~~	+
-	~~[[Category: Rsgi~~]]	+

OCA at 09:39, 29 September 2021

OCA — Wed, 29 Sep 2021 09:39:52 GMT

←Older revision		Revision as of 09:39, 29 September 2021
Line 3:		Line 3:
	<StructureSection load='1uc9' size='340' side='right'caption='[[1uc9]], [[Resolution\|resolution]] 2.38Å' scene=''>		<StructureSection load='1uc9' size='340' side='right'caption='[[1uc9]], [[Resolution\|resolution]] 2.38Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1uc9]] 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]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UC9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1UC9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1uc9]] 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]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UC9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UC9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1uc8\|1uc8]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1uc8\|1uc8]]</div></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=1uc9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uc9 OCA], [~~http~~://pdbe.org/1uc9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1uc9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1uc9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1uc9 ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/1uc9 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=1uc9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uc9 OCA], [https://pdbe.org/1uc9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uc9 RCSB], [https://www.ebi.ac.uk/pdbsum/1uc9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uc9 ProSAT], [https://www.topsan.org/Proteins/RSGI/1uc9 TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/LYSX_THET8 LYSX_THET8]] Catalyzes the ATP-dependent formation of a covalent bond between the amino group of alpha-aminoadipate (AAA) and the gamma-carboxyl group of the C-terminal glutamate residue in LysW.<ref>PMID:19620981</ref>	+	[[https://www.uniprot.org/uniprot/LYSX_THET8 LYSX_THET8]] Catalyzes the ATP-dependent formation of a covalent bond between the amino group of alpha-aminoadipate (AAA) and the gamma-carboxyl group of the C-terminal glutamate residue in LysW.<ref>PMID:19620981</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 14:12, 25 December 2019

OCA — Wed, 25 Dec 2019 14:12:48 GMT

←Older revision		Revision as of 14:12, 25 December 2019
Line 1:		Line 1:

	==Crystal structure of a lysine biosynthesis enzyme, Lysx, from thermus thermophilus HB8==		==Crystal structure of a lysine biosynthesis enzyme, Lysx, from thermus thermophilus HB8==
-	<StructureSection load='1uc9' size='340' side='right' caption='[[1uc9]], [[Resolution\|resolution]] 2.38Å' scene=''>	+	<StructureSection load='1uc9' size='340' side='right'caption='[[1uc9]], [[Resolution\|resolution]] 2.38Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1uc9]] 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]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UC9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UC9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1uc9]] 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]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UC9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UC9 FirstGlance]. <br>
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]		[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
		+	[[Category: Large Structures]]
	[[Category: Kuramitsu, S]]		[[Category: Kuramitsu, S]]
	[[Category: Matsuura, T]]		[[Category: Matsuura, T]]

OCA at 09:01, 21 March 2018

OCA — Wed, 21 Mar 2018 09:01:06 GMT

←Older revision		Revision as of 09:01, 21 March 2018
Line 1:		Line 1:
		+
	==Crystal structure of a lysine biosynthesis enzyme, Lysx, from thermus thermophilus HB8==		==Crystal structure of a lysine biosynthesis enzyme, Lysx, from thermus thermophilus HB8==
	<StructureSection load='1uc9' size='340' side='right' caption='[[1uc9]], [[Resolution\|resolution]] 2.38Å' scene=''>		<StructureSection load='1uc9' size='340' side='right' caption='[[1uc9]], [[Resolution\|resolution]] 2.38Å' scene=''>
Line 6:		Line 7:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1uc8\|1uc8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1uc8\|1uc8]]</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=1uc9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uc9 OCA], [http://pdbe.org/1uc9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1uc9 RCSB], [http://www.ebi.ac.uk/pdbsum/1uc9 PDBsum], [http://www.topsan.org/Proteins/RSGI/1uc9 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=1uc9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uc9 OCA], [http://pdbe.org/1uc9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1uc9 RCSB], [http://www.ebi.ac.uk/pdbsum/1uc9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1uc9 ProSAT], [http://www.topsan.org/Proteins/RSGI/1uc9 TOPSAN]</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/uc/1uc9_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/uc/1uc9_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=1uc9 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 14:52, 11 September 2015

OCA — Fri, 11 Sep 2015 14:52:53 GMT

←Older revision		Revision as of 14:52, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1uc9' size='340' side='right' caption='[[1uc9]], [[Resolution\|resolution]] 2.38Å' scene=''>		<StructureSection load='1uc9' size='340' side='right' caption='[[1uc9]], [[Resolution\|resolution]] 2.38Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1uc9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermus_thermophilus Thermus thermophilus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UC9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UC9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1uc9]] 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]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UC9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UC9 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1uc8\|1uc8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1uc8\|1uc8]]</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=1uc9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uc9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1uc9 RCSB], [http://www.ebi.ac.uk/pdbsum/1uc9 PDBsum], [http://www.topsan.org/Proteins/RSGI/1uc9 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=1uc9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uc9 OCA], [http://pdbe.org/1uc9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1uc9 RCSB], [http://www.ebi.ac.uk/pdbsum/1uc9 PDBsum], [http://www.topsan.org/Proteins/RSGI/1uc9 TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1uc9" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Thermus thermophilus~~]]	+	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Kuramitsu, S]]		[[Category: Kuramitsu, S]]
	[[Category: Matsuura, T]]		[[Category: Matsuura, T]]

OCA at 17:59, 25 December 2014

OCA — Thu, 25 Dec 2014 17:59:43 GMT

←Older revision		Revision as of 17:59, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1uc9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UC9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UC9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1uc9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UC9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UC9 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1uc8\|1uc8]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1uc8\|1uc8]]</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=1uc9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uc9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1uc9 RCSB], [http://www.ebi.ac.uk/pdbsum/1uc9 PDBsum], [http://www.topsan.org/Proteins/RSGI/1uc9 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=1uc9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uc9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1uc9 RCSB], [http://www.ebi.ac.uk/pdbsum/1uc9 PDBsum], [http://www.topsan.org/Proteins/RSGI/1uc9 TOPSAN]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/LYSX_THET8 LYSX_THET8]] Catalyzes the ATP-dependent formation of a covalent bond between the amino group of alpha-aminoadipate (AAA) and the gamma-carboxyl group of the C-terminal glutamate residue in LysW.<ref>PMID:19620981</ref>
	== 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: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
-	[[Category: Kuramitsu, S.]]	+	[[Category: Kuramitsu, S]]
-	[[Category: Matsuura, T.]]	+	[[Category: Matsuura, T]]
-	[[Category: Nishiyama, M.]]	+	[[Category: Nishiyama, M]]
-	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Sakai, H.]]	+	[[Category: Sakai, H]]
-	[[Category: Sekine, S.]]	+	[[Category: Sekine, S]]
-	[[Category: Shirouzu, M.]]	+	[[Category: Shirouzu, M]]
-	[[Category: Terada, T.]]	+	[[Category: Terada, T]]
-	[[Category: Vassylyev, D G.]]	+	[[Category: Vassylyev, D G]]
-	[[Category: Vassylyeva, M N.]]	+	[[Category: Vassylyeva, M N]]
-	[[Category: Yokoyama, S.]]	+	[[Category: Yokoyama, S]]
	[[Category: Alpha-aminoadipate pathway]]		[[Category: Alpha-aminoadipate pathway]]
	[[Category: Biosynthetic protein]]		[[Category: Biosynthetic protein]]
	[[Category: Lysine biosynthesis]]		[[Category: Lysine biosynthesis]]
-	[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
-	[[Category: Structural genomic]]

OCA at 21:09, 29 September 2014

OCA — Mon, 29 Sep 2014 21:09:16 GMT

←Older revision		Revision as of 21:09, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1uc9.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of a lysine biosynthesis enzyme, Lysx, from thermus thermophilus HB8==
		+	<StructureSection load='1uc9' size='340' side='right' caption='[[1uc9]], [[Resolution\|resolution]] 2.38Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1uc9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UC9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UC9 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1uc8\|1uc8]]</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=1uc9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uc9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1uc9 RCSB], [http://www.ebi.ac.uk/pdbsum/1uc9 PDBsum], [http://www.topsan.org/Proteins/RSGI/1uc9 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/uc/1uc9_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The thermophilic bacterium Thermus thermophilus synthesizes lysine through the alpha-aminoadipate pathway, which uses alpha-aminoadipate as a biosynthetic intermediate of lysine. LysX is the essential enzyme in this pathway, and is believed to catalyze the acylation of alpha-aminoadipate. We have determined the crystal structures of LysX and its complex with ADP at 2.0A and 2.38A resolutions, respectively. LysX is composed of three alpha+beta domains, each composed of a four to five-stranded beta-sheet core flanked by alpha-helices. The C-terminal and central domains form an ATP-grasp fold, which is responsible for ATP binding. LysX has two flexible loop regions, which are expected to play an important role in substrate binding and protection. In spite of the low level of sequence identity, the overall fold of LysX is surprisingly similar to that of other ATP-grasp fold proteins, such as D-Ala:D-Ala ligase, PurT-encoded glycinamide ribonucleotide transformylase, glutathione synthetase, and synapsin I. In particular, they share a similar spatial arrangement of the amino acid residues around the ATP-binding site. This observation strongly suggests that LysX is an ATP-utilizing enzyme that shares a common evolutionary ancestor with other ATP-grasp fold proteins possessing a carboxylate-amine/thiol ligase activity.

-	~~{{STRUCTURE_1uc9\| PDB=1uc9 \| SCENE= }}~~	+	Crystal structure of a lysine biosynthesis enzyme, LysX, from Thermus thermophilus HB8.,Sakai H, Vassylyeva MN, Matsuura T, Sekine S, Gotoh K, Nishiyama M, Terada T, Shirouzu M, Kuramitsu S, Vassylyev DG, Yokoyama S J Mol Biol. 2003 Sep 19;332(3):729-40. PMID:12963379<ref>PMID:12963379</ref>

-	~~===Crystal structure of a lysine biosynthesis enzyme~~, ~~Lysx, from thermus thermophilus HB8===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12963379}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1uc9]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Thermus_thermophilus Thermus thermophilus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1UC9 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:012963379<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Kuramitsu, S.]]		[[Category: Kuramitsu, S.]]

OCA: Protected "1uc9" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 12:12:35 GMT

Protected "1uc9" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:12, 5 January 2013

OCA at 12:12, 5 January 2013

OCA — Sat, 05 Jan 2013 12:12:32 GMT

←Older revision		Revision as of 12:12, 5 January 2013
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-	{{Seed}}
	[[Image:1uc9.png\|left\|200px]]		[[Image:1uc9.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1uc9", 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_1uc9\| PDB=1uc9 \| SCENE= }}		{{STRUCTURE_1uc9\| PDB=1uc9 \| SCENE= }}

	===Crystal structure of a lysine biosynthesis enzyme, Lysx, from thermus thermophilus HB8===		===Crystal structure of a lysine biosynthesis enzyme, Lysx, from thermus thermophilus HB8===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12963379}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12963379 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12963379}}		{{ABSTRACT_PUBMED_12963379}}

	==About this Structure==		==About this Structure==
-	~~1UC9~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UC9 OCA].	+	[[1uc9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UC9 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12963379~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012963379</ref><references group="xtra"/>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Kuramitsu, S.]]		[[Category: Kuramitsu, S.]]
Line 37:		Line 25:
	[[Category: Yokoyama, S.]]		[[Category: Yokoyama, S.]]
	[[Category: Alpha-aminoadipate pathway]]		[[Category: Alpha-aminoadipate pathway]]
		+	[[Category: Biosynthetic protein]]
	[[Category: Lysine biosynthesis]]		[[Category: Lysine biosynthesis]]
	[[Category: Riken structural genomics/proteomics initiative]]		[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 00:53:43 2009''

OCA at 22:53, 17 February 2009

OCA — Tue, 17 Feb 2009 22:53:43 GMT

←Older revision		Revision as of 22:53, 17 February 2009
Line 23:		Line 23:

	==Reference==		==Reference==
-	Crystal structure of a lysine biosynthesis enzyme, LysX, from Thermus thermophilus HB8., Sakai H, Vassylyeva MN, Matsuura T, Sekine S, Gotoh K, Nishiyama M, Terada T, Shirouzu M, Kuramitsu S, Vassylyev DG, Yokoyama S, J Mol Biol. 2003 Sep 19;332(3):729-40. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/12963379 12963379]~~	+	<ref group="xtra">PMID:12963379</ref><references group="xtra"/>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Kuramitsu, S.]]		[[Category: Kuramitsu, S.]]
Line 42:		Line 42:
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Nov 16 16~~:42:~~37 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 00:53:43 2009''