6v23 - Revision history

OCA at 08:02, 11 October 2023

OCA — Wed, 11 Oct 2023 08:02:22 GMT

←Older revision		Revision as of 08:02, 11 October 2023
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	<StructureSection load='6v23' size='340' side='right'caption='[[6v23]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='6v23' size='340' side='right'caption='[[6v23]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6v23]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V23 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6V23 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6v23]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V23 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6V23 FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>ansB, b2957, JW2924 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=83333 ECOLI])</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]] 1.75Å</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'>[https://proteopedia.org/fgij/fg.htm?mol=6v23 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v23 OCA], [https://pdbe.org/6v23 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6v23 RCSB], [https://www.ebi.ac.uk/pdbsum/6v23 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6v23 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=6v23 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v23 OCA], [~~http~~://pdbe.org/6v23 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6v23 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6v23 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6v23 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/ASPG2_ECOLI ASPG2_ECOLI]
	<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: Escherichia coli K-12]]
-	~~[[Category: Ecoli~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Lubkowski, J]]	+	[[Category: Lubkowski J]]
-	[[Category: Wlodawer, A]]	+	[[Category: Wlodawer A]]
-	~~[[Category: Anti-cancer drug]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: L-asparagine hydrolase~~]]	+

OCA at 07:34, 27 May 2020

OCA — Wed, 27 May 2020 07:34:40 GMT

←Older revision		Revision as of 07:34, 27 May 2020
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	==Ligand-free L-aspraginase II from E. coli (EcAII)==		==Ligand-free L-aspraginase II from E. coli (EcAII)==
-	<StructureSection load='6v23' size='340' side='right'caption='[[6v23]]' scene=''>	+	<StructureSection load='6v23' size='340' side='right'caption='[[6v23]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V23 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6V23 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6v23]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V23 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6V23 FirstGlance]. <br>
-	</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=6v23 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v23 OCA], [http://pdbe.org/6v23 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6v23 RCSB], [http://www.ebi.ac.uk/pdbsum/6v23 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6v23 ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ansB, b2957, JW2924 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=6v23 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v23 OCA], [http://pdbe.org/6v23 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6v23 RCSB], [http://www.ebi.ac.uk/pdbsum/6v23 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6v23 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Two bacterial type II l-asparaginases, from Escherichia coli and Dickeya chrysanthemi, have played a critical role for more than 40 years as therapeutic agents against juvenile leukemias and lymphomas. Despite a long history of successful pharmacological applications and the apparent simplicity of the catalytic reaction, controversies still exist regarding major steps of the mechanism. In this report, we provide a detailed description of the reaction catalyzed by E. coli type II l-asparaginase (EcAII). Our model was developed on the basis of new structural and biochemical experiments combined with previously published data. The proposed mechanism is supported by quantum chemistry calculations based on density functional theory. We provide strong evidence that EcAII catalyzes the reaction according to the double-displacement (ping-pong) mechanism, with formation of a covalent intermediate. Several steps of catalysis by EcAII are unique when compared to reactions catalyzed by other known hydrolytic enzymes. Here, the reaction is initiated by a weak nucleophile, threonine, without direct assistance of a general base, although a distant general base is identified. Furthermore, tetrahedral intermediates formed during the catalytic process are stabilized by a never previously described motif. Although the scheme of the catalytic mechanism was developed only on the basis of data obtained from EcAII and its variants, this novel mechanism of enzymatic hydrolysis could potentially apply to most (and possibly all) l-asparaginases.
		+
		+	Mechanism of Catalysis by l-Asparaginase.,Lubkowski J, Vanegas J, Chan WK, Lorenzi PL, Weinstein JN, Sukharev S, Fushman D, Rempe S, Anishkin A, Wlodawer A Biochemistry. 2020 May 11. doi: 10.1021/acs.biochem.0c00116. PMID:32364696<ref>PMID:32364696</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6v23" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Asparaginase]]
		+	[[Category: Ecoli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Lubkowski J]]	+	[[Category: Lubkowski, J]]
-	[[Category: Wlodawer A]]	+	[[Category: Wlodawer, A]]
		+	[[Category: Anti-cancer drug]]
		+	[[Category: Hydrolase]]
		+	[[Category: L-asparagine hydrolase]]

OCA at 05:48, 20 May 2020

OCA — Wed, 20 May 2020 05:48:58 GMT

←Older revision		Revision as of 05:48, 20 May 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6v23 ~~is ON HOLD~~	+	==Ligand-free L-aspraginase II from E. coli (EcAII)==
-		+	<StructureSection load='6v23' size='340' side='right'caption='[[6v23]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V23 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6V23 FirstGlance]. <br>
-	~~Description~~:	+	</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=6v23 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v23 OCA], [http://pdbe.org/6v23 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6v23 RCSB], [http://www.ebi.ac.uk/pdbsum/6v23 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6v23 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Lubkowski J]]
		+	[[Category: Wlodawer A]]

OCA: Protected "6v23" [edit=sysop:move=sysop]

OCA — Wed, 04 Dec 2019 06:34:53 GMT

Protected "6v23" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:34, 4 December 2019

OCA: New page: '''Unreleased structure''' The entry 6v23 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 04 Dec 2019 06:34:51 GMT

New page: '''Unreleased structure''' The entry 6v23 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6v23 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]