5dnd - Revision history

OCA at 21:51, 28 June 2023

2023-06-28T21:51:19Z

←Older revision		Revision as of 21:51, 28 June 2023
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	==Crystal structure of the Asn-bound guinea pig L-asparaginase 1 catalytic domain active site mutant T116A==		==Crystal structure of the Asn-bound guinea pig L-asparaginase 1 catalytic domain active site mutant T116A==
-	<StructureSection load='5dnd' size='340' side='right' caption='[[5dnd]], [[Resolution\|resolution]] 2.29Å' scene=''>	+	<StructureSection load='5dnd' size='340' side='right'caption='[[5dnd]], [[Resolution\|resolution]] 2.29Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dnd]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Cavpo Cavpo~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DND OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5DND FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dnd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Cavia_porcellus Cavia porcellus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DND OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DND FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=ASN:ASPARAGINE'>ASN</scene~~>, ~~<scene name='pdbligand=EDO:1,~~2~~-ETHANEDIOL'>EDO</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]] 2.29Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[4r8k\|4r8k]], [[4r8l\|4r8l]], [[5dnc\|5dnc]], [[5dne\|5dne]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASN:ASPARAGINE'>ASN</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">ASPG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10141 CAVPO])~~</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=5dnd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dnd OCA], [https://pdbe.org/5dnd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dnd RCSB], [https://www.ebi.ac.uk/pdbsum/5dnd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dnd 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=5dnd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dnd OCA], [~~http~~://pdbe.org/5dnd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5dnd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5dnd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5dnd ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/H0W0T5_CAVPO H0W0T5_CAVPO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5dnd" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5dnd" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Asparaginase 3D structures\|Asparaginase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Cavpo~~]]	+	[[Category: Cavia porcellus]]
-	[[Category: ~~Lavie, A~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Schalk,~~ A M]]	+	[[Category: Lavie A]]
-	[[Category: ~~Asparaginase]]~~	+	[[Category: Schalk AM]]
-	~~[[Category: Hydrolase~~]]	+

OCA at 09:12, 1 November 2017

2017-11-01T09:12:51Z

←Older revision		Revision as of 09:12, 1 November 2017
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	<StructureSection load='5dnd' size='340' side='right' caption='[[5dnd]], [[Resolution\|resolution]] 2.29Å' scene=''>		<StructureSection load='5dnd' size='340' side='right' caption='[[5dnd]], [[Resolution\|resolution]] 2.29Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dnd]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DND OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DND FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dnd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Cavpo Cavpo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DND OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DND FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ASN:ASPARAGINE'>ASN</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ASN:ASPARAGINE'>ASN</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4r8k\|4r8k]], [[4r8l\|4r8l]], [[5dnc\|5dnc]], [[5dne\|5dne]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4r8k\|4r8k]], [[4r8l\|4r8l]], [[5dnc\|5dnc]], [[5dne\|5dne]]</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=5dnd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dnd OCA], [http://pdbe.org/5dnd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dnd RCSB], [http://www.ebi.ac.uk/pdbsum/5dnd PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ASPG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10141 CAVPO])</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=5dnd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dnd OCA], [http://pdbe.org/5dnd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dnd RCSB], [http://www.ebi.ac.uk/pdbsum/5dnd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dnd ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Cavpo]]
	[[Category: Lavie, A]]		[[Category: Lavie, A]]
	[[Category: Schalk, A M]]		[[Category: Schalk, A M]]
	[[Category: Asparaginase]]		[[Category: Asparaginase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 18:21, 10 May 2016

2016-05-10T18:21:39Z

←Older revision		Revision as of 18:21, 10 May 2016
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		+
	==Crystal structure of the Asn-bound guinea pig L-asparaginase 1 catalytic domain active site mutant T116A==		==Crystal structure of the Asn-bound guinea pig L-asparaginase 1 catalytic domain active site mutant T116A==
	<StructureSection load='5dnd' size='340' side='right' caption='[[5dnd]], [[Resolution\|resolution]] 2.29Å' scene=''>		<StructureSection load='5dnd' size='340' side='right' caption='[[5dnd]], [[Resolution\|resolution]] 2.29Å' scene=''>

OCA at 08:53, 20 January 2016

2016-01-20T08:53:32Z

←Older revision		Revision as of 08:53, 20 January 2016
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	<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=5dnd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dnd OCA], [http://pdbe.org/5dnd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dnd RCSB], [http://www.ebi.ac.uk/pdbsum/5dnd 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=5dnd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dnd OCA], [http://pdbe.org/5dnd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dnd RCSB], [http://www.ebi.ac.uk/pdbsum/5dnd PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacterial L-asparaginases play an important role in the treatment of certain types of blood cancers. We are exploring the guinea pig L-asparaginase (gpASNase1) as a potential replacement for the immunogenic bacterial enzymes. The exact mechanism used by L-asparaginases to catalyze the hydrolysis of asparagine into aspartic acid and ammonia has been recently put into question. Earlier experimental data suggested that the reaction proceeds via a covalent intermediate using a ping-pong mechanism while recent computational work advocates the direct displacement of the amine by an activated water. To shed light on this controversy, we generated gpASNase1 mutants of conserved active site residues (T19A, T116A, T19A-T116A, K188M, Y308F) suspected to play a role in hydrolysis. Using x-ray crystallography, we determined the crystal structures of the T19A, T116A, and K188M mutants soaked in asparagine. We also characterized their steady-state kinetic properties and analyzed the conversion of asparagine to aspartate using NMR. Our structures reveal bound asparagine in the active site that has unambiguously not formed a covalent intermediate. Kinetic and NMR assays detect significant residual activity for all of the mutants. Furthermore, no burst of ammonia production was observed that would indicate covalent intermediate formation and the presence of a ping-pong mechanism. Hence, despite using a variety of techniques, we were unable to obtain experimental evidence that would support the formation of a covalent intermediate. Consequently, our observations support a direct displacement rather than a ping-pong mechanism for L-asparaginases.
		+
		+	Experimental Data in Support of a Direct Displacement Mechanism for Type I/II L-Asparaginases.,Schalk AM, Antanasijevic A, Caffrey M, Lavie A J Biol Chem. 2016 Jan 5. pii: jbc.M115.699884. PMID:26733195<ref>PMID:26733195</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5dnd" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 20:32, 13 January 2016

2016-01-13T20:32:04Z

←Older revision		Revision as of 20:32, 13 January 2016
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	==Crystal structure of the Asn-bound guinea pig L-asparaginase 1 catalytic domain active site mutant T116A==
-		+	<StructureSection load='5dnd' size='340' side='right' caption='[[5dnd]], [[Resolution\|resolution]] 2.29Å' scene=''>
-	~~The entry 5dnd is ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5dnd]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DND OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DND FirstGlance]. <br>
-	~~Authors: Schalk, A.M., Lavie, A.~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ASN:ASPARAGINE'>ASN</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4r8k\|4r8k]], [[4r8l\|4r8l]], [[5dnc\|5dnc]], [[5dne\|5dne]]</td></tr>
-	~~Description:~~ Crystal structure of the Asn-bound guinea pig L-asparaginase 1 catalytic domain active site mutant T116A	+	<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=5dnd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dnd OCA], [http://pdbe.org/5dnd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dnd RCSB], [http://www.ebi.ac.uk/pdbsum/5dnd PDBsum]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Schalk~~, A.M]]	+	__TOC__
		+	</StructureSection>
	[[Category: Lavie, A]]		[[Category: Lavie, A]]
		+	[[Category: Schalk, A M]]
		+	[[Category: Asparaginase]]
		+	[[Category: Hydrolase]]

OCA at 02:30, 16 October 2015

2015-10-16T02:30:38Z

←Older revision		Revision as of 02:30, 16 October 2015
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Schalk, A.M., Lavie, A.		Authors: Schalk, A.M., Lavie, A.

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

2015-09-30T13:13:08Z

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

←Older revision

Revision as of 13:13, 30 September 2015

OCA: New page: '''Unreleased structure''' The entry 5dnd is ON HOLD Authors: Schalk, A.M., Lavie, A. Description: Crystal structure of the Asn-bound guinea pig L-asparaginase 1 catalytic domain activ...

2015-09-30T13:13:07Z

New page: '''Unreleased structure''' The entry 5dnd is ON HOLD Authors: Schalk, A.M., Lavie, A. Description: Crystal structure of the Asn-bound guinea pig L-asparaginase 1 catalytic domain activ...

New page

'''Unreleased structure'''

The entry 5dnd is ON HOLD

Authors: Schalk, A.M., Lavie, A.

Description: Crystal structure of the Asn-bound guinea pig L-asparaginase 1 catalytic domain active site mutant T116A
[[Category: Unreleased Structures]]
[[Category: Schalk, A.M]]
[[Category: Lavie, A]]