5k4g - Revision history

OCA at 09:51, 27 September 2023

OCA — Wed, 27 Sep 2023 09:51:41 GMT

←Older revision		Revision as of 09:51, 27 September 2023
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	<StructureSection load='5k4g' size='340' side='right'caption='[[5k4g]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='5k4g' size='340' side='right'caption='[[5k4g]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k4g]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Vibrio_succinogenes Vibrio~~ succinogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K4G OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5K4G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k4g]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Wolinella_succinogenes_DSM_1740 Wolinella succinogenes DSM 1740]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K4G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K4G FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</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]] 1.6Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k3o\|5k3o]]~~, [[~~5k45~~\|~~5k45]], [[5k4h\|5k4h~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>ansA, ansB, WS0660 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~273121 Vibrio succinogenes])</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=5k4g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k4g OCA], [https://pdbe.org/5k4g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k4g RCSB], [https://www.ebi.ac.uk/pdbsum/5k4g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k4g ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/Asparaginase Asparaginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.1 3.5.1.1]~~ </~~span~~></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5k4g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k4g OCA], [~~http~~://pdbe.org/5k4g PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5k4g RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5k4g PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5k4g ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/ASPG_WOLSU ASPG_WOLSU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Asparaginase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Vibrio~~ succinogenes]]	+	[[Category: Wolinella succinogenes DSM 1740]]
-	[[Category: Lave, A]]	+	[[Category: Lave A]]
-	[[Category: Nguyen~~, H A]]~~	+	[[Category: Nguyen HA]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: L-aspartic acid]]~~	+
-	~~[[Category: Open conformation]]~~	+
-	~~[[Category: S121~~]]	+

OCA at 09:17, 25 June 2020

OCA — Thu, 25 Jun 2020 09:17:58 GMT

←Older revision		Revision as of 09:17, 25 June 2020
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	==Wolinella succinogenes L-asparaginase S121 + L-aspartic acid, open conformation==		==Wolinella succinogenes L-asparaginase S121 + L-aspartic acid, open conformation==
-	<StructureSection load='5k4g' size='340' side='right' caption='[[5k4g]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='5k4g' size='340' side='right'caption='[[5k4g]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k4g]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K4G OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5K4G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k4g]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibrio_succinogenes Vibrio succinogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K4G OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5K4G FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k3o\|5k3o]], [[5k45\|5k45]], [[5k4h\|5k4h]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k3o\|5k3o]], [[5k45\|5k45]], [[5k4h\|5k4h]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ansA, ansB, WS0660 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273121 Vibrio succinogenes])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Asparaginase Asparaginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.1 3.5.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Asparaginase Asparaginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.1 3.5.1.1] </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=5k4g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k4g OCA], [http://pdbe.org/5k4g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k4g RCSB], [http://www.ebi.ac.uk/pdbsum/5k4g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k4g ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5k4g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k4g OCA], [http://pdbe.org/5k4g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k4g RCSB], [http://www.ebi.ac.uk/pdbsum/5k4g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k4g ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5k4g" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5k4g" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Asparaginase 3D structures\|Asparaginase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Asparaginase]]		[[Category: Asparaginase]]
		+	[[Category: Large Structures]]
		+	[[Category: Vibrio succinogenes]]
	[[Category: Lave, A]]		[[Category: Lave, A]]
	[[Category: Nguyen, H A]]		[[Category: Nguyen, H A]]

OCA at 13:46, 29 March 2017

OCA — Wed, 29 Mar 2017 13:46:23 GMT

←Older revision		Revision as of 13:46, 29 March 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5k4g is ~~ON HOLD until Paper~~ Publication	+	==Wolinella succinogenes L-asparaginase S121 + L-aspartic acid, open conformation==
		+	<StructureSection load='5k4g' size='340' side='right' caption='[[5k4g]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5k4g]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K4G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K4G FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k3o\|5k3o]], [[5k45\|5k45]], [[5k4h\|5k4h]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Asparaginase Asparaginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.1 3.5.1.1] </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=5k4g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k4g OCA], [http://pdbe.org/5k4g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k4g RCSB], [http://www.ebi.ac.uk/pdbsum/5k4g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k4g ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Many side effects of current FDA-approved L-asparaginases have been related to their secondary L-glutaminase activity. The Wolinella succinogenes L-asparaginase (WoA) has been reported to be L-glutaminase free, suggesting it would have fewer side effects. Unexpectedly, the WoA variant with a proline at position 121 (WoA-P121) was found to have L-glutaminase activity in contrast to Uniprot entry P50286 (WoA-S121) that has a serine residue at this position. Towards understanding how this residue impacts the L-glutaminase property, kinetic analysis was coupled with crystal structure determination of these WoA variants. WoA-S121 was confirmed to have much lower L-glutaminase activity than WoA-P121, yet both showed comparable L-asparaginase activity. Structures of the WoA variants in complex with L-aspartic acid versus L-glutamic acid provide insights into their differential substrate selectivity. Structural analysis suggests a mechanism by which residue 121 impacts the conformation of the conserved tyrosine 27, a component of the catalytically-important flexible N-terminal loop. Surprisingly, we could fully model this loop in either its open or closed conformations, revealing the roles of specific residues of an evolutionary conserved motif among this L-asparaginase family. Together, this work showcases critical residues that influence the ability of the flexible N-terminal loop for adopting its active conformation, thereby effecting substrate specificity.

-	~~Authors~~:	+	The differential ability of asparagine and glutamine in promoting the closed/active enzyme conformation rationalizes the Wolinella succinogenes L-asparaginase substrate specificity.,Nguyen HA, Durden DL, Lavie A Sci Rep. 2017 Jan 31;7:41643. doi: 10.1038/srep41643. PMID:28139703<ref>PMID:28139703</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5k4g" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Asparaginase]]
		+	[[Category: Lave, A]]
		+	[[Category: Nguyen, H A]]
		+	[[Category: Hydrolase]]
		+	[[Category: L-aspartic acid]]
		+	[[Category: Open conformation]]
		+	[[Category: S121]]

OCA at 13:07, 10 August 2016

OCA — Wed, 10 Aug 2016 13:07:47 GMT

←Older revision		Revision as of 13:07, 10 August 2016
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5k4g is ON HOLD	+	The entry 5k4g is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5k4g" [edit=sysop:move=sysop]

OCA — Wed, 01 Jun 2016 14:18:52 GMT

Protected "5k4g" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:18, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5k4g is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 01 Jun 2016 14:18:51 GMT

New page: '''Unreleased structure''' The entry 5k4g is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5k4g is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]