6p1y - Revision history

OCA at 07:21, 11 October 2023

OCA — Wed, 11 Oct 2023 07:21:46 GMT

←Older revision		Revision as of 07:21, 11 October 2023
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	<StructureSection load='6p1y' size='340' side='right'caption='[[6p1y]], [[Resolution\|resolution]] 2.33Å' scene=''>		<StructureSection load='6p1y' size='340' side='right'caption='[[6p1y]], [[Resolution\|resolution]] 2.33Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6p1y]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P1Y OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6P1Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6p1y]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P1Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6P1Y FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=NH4:AMMONIUM+ION'>NH4</scene~~>, ~~<scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</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]] 2.33Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~PYR~~:~~PYRUVIC~~+~~ACID~~'>~~PYR~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Aspartate_1-decarboxylase Aspartate 1-decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.11 4.1.1.11]~~ </~~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=6p1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p1y OCA], [https://pdbe.org/6p1y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6p1y RCSB], [https://www.ebi.ac.uk/pdbsum/6p1y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6p1y 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=6p1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p1y OCA], [~~http~~://pdbe.org/6p1y PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6p1y RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6p1y PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6p1y ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PAND_MYCTU PAND_MYCTU]] Catalyzes the pyruvoyl-dependent decarboxylation of aspartate to produce beta-alanine (By similarity).	+	[https://www.uniprot.org/uniprot/PAND_MYCTU PAND_MYCTU] Catalyzes the pyruvoyl-dependent decarboxylation of aspartate to produce beta-alanine (By similarity).
	<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 6p1y" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6p1y" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aspartate decarboxylase 3D structures\|Aspartate decarboxylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Aspartate 1-decarboxylase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Li, X~~]]	+	[[Category: Mycobacterium tuberculosis H37Rv]]
-	[[Category: ~~Sacchettini, J C~~]]	+	[[Category: Li X]]
-	[[Category: ~~Sun, Q~~]]	+	[[Category: Sacchettini JC]]
-	[[Category: ~~Structural genomic]]~~	+	[[Category: Sun Q]]
-	~~[[Category: Drug-resistance]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Mutant]]~~	+
-	~~[[Category: Poa]]~~	+
-	~~[[Category: Tbsgc~~]]	+

OCA at 08:02, 5 February 2020

OCA — Wed, 05 Feb 2020 08:02:49 GMT

←Older revision		Revision as of 08:02, 5 February 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6p1y is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of Mtb aspartate decarboxylase mutant M117I==
		+	<StructureSection load='6p1y' size='340' side='right'caption='[[6p1y]], [[Resolution\|resolution]] 2.33Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6p1y]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P1Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P1Y FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aspartate_1-decarboxylase Aspartate 1-decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.11 4.1.1.11] </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=6p1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p1y OCA], [http://pdbe.org/6p1y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p1y RCSB], [http://www.ebi.ac.uk/pdbsum/6p1y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p1y ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PAND_MYCTU PAND_MYCTU]] Catalyzes the pyruvoyl-dependent decarboxylation of aspartate to produce beta-alanine (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Pyrazinamide has been a mainstay in the multidrug regimens used to treat tuberculosis. It is active against the persistent, non-replicating mycobacteria responsible for the protracted therapy required to cure tuberculosis. Pyrazinamide is a pro-drug that is converted into pyrazinoic acid (POA) by pyrazinamidase, however, the exact target of the drug has been difficult to determine. Here we show the enzyme PanD binds POA in its active site in a manner consistent with competitive inhibition. The active site is not directly accessible to the inhibitor, suggesting the protein must undergo a conformational change to bind the inhibitor. This is consistent with the slow binding kinetics we determined for POA. Drug-resistant mutations cluster near loops that lay on top of the active site. These resistant mutants show reduced affinity and residence time of POA consistent with a model where resistance occurs by destabilizing the closed conformation of the active site.

-	~~Authors~~:	+	The molecular basis of pyrazinamide activity on Mycobacterium tuberculosis PanD.,Sun Q, Li X, Perez LM, Shi W, Zhang Y, Sacchettini JC Nat Commun. 2020 Jan 17;11(1):339. doi: 10.1038/s41467-019-14238-3. PMID:31953389<ref>PMID:31953389</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6p1y" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Aspartate 1-decarboxylase]]
		+	[[Category: Large Structures]]
		+	[[Category: Li, X]]
		+	[[Category: Sacchettini, J C]]
		+	[[Category: Sun, Q]]
		+	[[Category: Structural genomic]]
		+	[[Category: Drug-resistance]]
		+	[[Category: Lyase]]
		+	[[Category: Mutant]]
		+	[[Category: Poa]]
		+	[[Category: Tbsgc]]

OCA at 13:43, 28 August 2019

OCA — Wed, 28 Aug 2019 13:43:24 GMT

←Older revision		Revision as of 13:43, 28 August 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6p1y is ON HOLD	+	The entry 6p1y is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6p1y" [edit=sysop:move=sysop]

OCA — Wed, 29 May 2019 04:36:23 GMT

Protected "6p1y" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:36, 29 May 2019

OCA: New page: '''Unreleased structure''' The entry 6p1y is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 29 May 2019 04:36:22 GMT

New page: '''Unreleased structure''' The entry 6p1y is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6p1y is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]