5k2m - Revision history

OCA at 09:47, 15 November 2023

OCA — Wed, 15 Nov 2023 09:47:44 GMT

←Older revision		Revision as of 09:47, 15 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5k2m]] is a 14 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K2M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K2M FirstGlance]. <br>		<table><tr><td colspan='2'>[[5k2m]] is a 14 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K2M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K2M 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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=R0K:(2~{S})-2-[[(4~{S})-4-azanyl-5-oxidanyl-5-oxidanylidene-pentanoyl]amino]hexanedioic+acid'>R0K</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UN1:2-AMINOHEXANEDIOIC+ACID'>UN1</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.18Å</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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=R0K:(2~{S})-2-[[(4~{S})-4-azanyl-5-oxidanyl-5-oxidanylidene-pentanoyl]amino]hexanedioic+acid'>R0K</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UN1:2-AMINOHEXANEDIOIC+ACID'>UN1</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5k2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k2m OCA], [https://pdbe.org/5k2m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k2m RCSB], [https://www.ebi.ac.uk/pdbsum/5k2m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k2m 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=5k2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k2m OCA], [https://pdbe.org/5k2m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k2m RCSB], [https://www.ebi.ac.uk/pdbsum/5k2m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k2m ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:34, 7 April 2023

OCA — Fri, 07 Apr 2023 06:34:19 GMT

←Older revision		Revision as of 06:34, 7 April 2023
Line 1:		Line 1:

	==Bifunctional LysX/ArgX from Thermococcus kodakarensis with LysW-gamma-AAA==		==Bifunctional LysX/ArgX from Thermococcus kodakarensis with LysW-gamma-AAA==
-	<StructureSection load='5k2m' size='340' side='right' caption='[[5k2m]], [[Resolution\|resolution]] 2.18Å' scene=''>	+	<StructureSection load='5k2m' size='340' side='right'caption='[[5k2m]], [[Resolution\|resolution]] 2.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k2m]] is a 14 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K2M OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5K2M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k2m]] is a 14 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K2M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K2M 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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UN1:2-AMINOHEXANEDIOIC+ACID'>UN1</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=R0K:(2~{S})-2-[[(4~{S})-4-azanyl-5-oxidanyl-5-oxidanylidene-pentanoyl]amino]hexanedioic+acid'>R0K</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UN1:2-AMINOHEXANEDIOIC+ACID'>UN1</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vpb\|3vpb]], [[3vpc\|3vpc]], [[3vpd\|3vpd]]</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=5k2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k2m OCA], [https://pdbe.org/5k2m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k2m RCSB], [https://www.ebi.ac.uk/pdbsum/5k2m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k2m ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TK0278 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)]), TK0279 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)])</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=5k2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k2m OCA], [~~http~~://pdbe.org/5k2m PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5k2m RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5k2m PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5k2m ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q5JFW0_THEKO Q5JFW0_THEKO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Nishiyama, M~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Tomita, T~~]]	+	[[Category: Thermococcus kodakarensis KOD1]]
-	[[Category: ~~Yoshida, A~~]]	+	[[Category: Nishiyama M]]
-	[[Category: ~~Atp-dependent amine/thiol ligase family amino-group carrier protein lysine biosynthesis arginine biosynthesis~~]]	+	[[Category: Tomita T]]
-	[[Category: ~~Biosynthetic protein~~]]	+	[[Category: Yoshida A]]

OCA at 07:38, 6 December 2017

OCA — Wed, 06 Dec 2017 07:38:12 GMT

←Older revision		Revision as of 07:38, 6 December 2017
Line 3:		Line 3:
	<StructureSection load='5k2m' size='340' side='right' caption='[[5k2m]], [[Resolution\|resolution]] 2.18Å' scene=''>		<StructureSection load='5k2m' size='340' side='right' caption='[[5k2m]], [[Resolution\|resolution]] 2.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k2m]] is a 14 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K2M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K2M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k2m]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K2M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K2M 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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UN1:2-AMINOHEXANEDIOIC+ACID'>UN1</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UN1:2-AMINOHEXANEDIOIC+ACID'>UN1</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vpb\|3vpb]], [[3vpc\|3vpc]], [[3vpd\|3vpd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vpb\|3vpb]], [[3vpc\|3vpc]], [[3vpd\|3vpd]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TK0278 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)]), TK0279 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)])</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=5k2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k2m OCA], [http://pdbe.org/5k2m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k2m RCSB], [http://www.ebi.ac.uk/pdbsum/5k2m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k2m ProSAT]</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=5k2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k2m OCA], [http://pdbe.org/5k2m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k2m RCSB], [http://www.ebi.ac.uk/pdbsum/5k2m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k2m ProSAT]</span></td></tr>
	</table>		</table>

OCA at 21:10, 10 September 2016

OCA — Sat, 10 Sep 2016 21:10:37 GMT

←Older revision		Revision as of 21:10, 10 September 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5k2m is ~~ON HOLD until Paper~~ Publication	+	==Bifunctional LysX/ArgX from Thermococcus kodakarensis with LysW-gamma-AAA==
		+	<StructureSection load='5k2m' size='340' side='right' caption='[[5k2m]], [[Resolution\|resolution]] 2.18Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5k2m]] is a 14 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K2M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K2M 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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UN1:2-AMINOHEXANEDIOIC+ACID'>UN1</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vpb\|3vpb]], [[3vpc\|3vpc]], [[3vpd\|3vpd]]</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=5k2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k2m OCA], [http://pdbe.org/5k2m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k2m RCSB], [http://www.ebi.ac.uk/pdbsum/5k2m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k2m ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We recently discovered a biosynthetic system using a novel amino group carrier protein called LysW for lysine biosynthesis via alpha-aminoadipate (AAA), and revealed that this system is also utilized in the biosynthesis of arginine by Sulfolobus In the present study, we focused on the biosynthesis of lysine and ornithine in the hyperthermophilic archaeon, Thermococcus kodakarensis, and showed that their biosynthesis is accomplished by a single set of metabolic enzymes. We also determined the crystal structure of the LysX family protein from T. kodakarensis, which catalyzes the conjugation of LysW with either AAA or glutamate, in a complex with LysW-gamma-AAA. This crystal structure is the first example of how LysX recognizes AAA as a substrate and provides a structural basis for the bifunctionality of the LysX family protein from T. kodakarensis Based on comparisons with other LysX family proteins, we propose a mechanism for substrate recognition and its relationship with molecular evolution among LysX family proteins, which have different substrate specificities.

-	~~Authors~~:	+	Lysine Biosynthesis of Thermococcus kodakarensis with the Capacity to Function as an Ornithine Biosynthetic System.,Yoshida A, Tomita T, Atomi H, Kuzuyama T, Nishiyama M J Biol Chem. 2016 Aug 26. pii: jbc.M116.743021. PMID:27566549<ref>PMID:27566549</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5k2m" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Nishiyama, M]]
		+	[[Category: Tomita, T]]
		+	[[Category: Yoshida, A]]
		+	[[Category: Atp-dependent amine/thiol ligase family amino-group carrier protein lysine biosynthesis arginine biosynthesis]]
		+	[[Category: Biosynthetic protein]]

OCA at 13:22, 20 June 2016

OCA — Mon, 20 Jun 2016 13:22:30 GMT

←Older revision		Revision as of 13:22, 20 June 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5k2m is ON HOLD	+	The entry 5k2m is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5k2m" [edit=sysop:move=sysop]

OCA — Wed, 01 Jun 2016 14:14:14 GMT

Protected "5k2m" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:14, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5k2m is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 01 Jun 2016 14:14:13 GMT

New page: '''Unreleased structure''' The entry 5k2m is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5k2m is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]