6tn3 - Revision history

OCA at 13:05, 24 January 2024

OCA — Wed, 24 Jan 2024 13:05:27 GMT

←Older revision		Revision as of 13:05, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6tn3' size='340' side='right'caption='[[6tn3]], [[Resolution\|resolution]] 2.28Å' scene=''>		<StructureSection load='6tn3' size='340' side='right'caption='[[6tn3]], [[Resolution\|resolution]] 2.28Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6tn3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Aspfu Aspfu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TN3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TN3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6tn3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_fumigatus_Af293 Aspergillus fumigatus Af293]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TN3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TN3 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GN1:2-(ACETYLAMINO)~~-2~~-DEOXY-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE'>GN1</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.282Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>AFUA_7G02180 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~330879 ASPFU])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GN1:2-(ACETYLAMINO)-2-DEOXY-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE'>GN1</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>[https://en.wikipedia.org/wiki/UDP-N-acetylglucosamine_diphosphorylase UDP-N-acetylglucosamine diphosphorylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.23 2.7.7.23] </~~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=6tn3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tn3 OCA], [https://pdbe.org/6tn3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6tn3 RCSB], [https://www.ebi.ac.uk/pdbsum/6tn3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6tn3 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=6tn3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tn3 OCA], [https://pdbe.org/6tn3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6tn3 RCSB], [https://www.ebi.ac.uk/pdbsum/6tn3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6tn3 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q4WAR0_ASPFU Q4WAR0_ASPFU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Aspfu~~]]	+	[[Category: Aspergillus fumigatus Af293]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: UDP-N-acetylglucosamine diphosphorylase]]~~	+	[[Category: Guerrero RH]]
-	[[Category: Guerrero~~, R H~~]]	+	[[Category: Raimi OG]]
-	[[Category: Raimi~~, O G]]~~	+
-	~~[[Category: Anti-fungal]]~~	+
-	~~[[Category: Aspergillus fumigatus]]~~	+
-	~~[[Category: Pyrophosphorylase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 08:54, 29 September 2021

OCA — Wed, 29 Sep 2021 08:54:34 GMT

←Older revision		Revision as of 08:54, 29 September 2021
Line 3:		Line 3:
	<StructureSection load='6tn3' size='340' side='right'caption='[[6tn3]], [[Resolution\|resolution]] 2.28Å' scene=''>		<StructureSection load='6tn3' size='340' side='right'caption='[[6tn3]], [[Resolution\|resolution]] 2.28Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6tn3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TN3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6TN3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6tn3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspfu Aspfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TN3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TN3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GN1:2-(ACETYLAMINO)-2-DEOXY-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE'>GN1</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GN1:2-(ACETYLAMINO)-2-DEOXY-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE'>GN1</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/UDP-N-acetylglucosamine_diphosphorylase UDP-N-acetylglucosamine diphosphorylase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.23 2.7.7.23] </span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AFUA_7G02180 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=330879 ASPFU])</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=6tn3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tn3 OCA], [~~http~~://pdbe.org/6tn3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6tn3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6tn3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6tn3 ProSAT]</span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/UDP-N-acetylglucosamine_diphosphorylase UDP-N-acetylglucosamine diphosphorylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.23 2.7.7.23] </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=6tn3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tn3 OCA], [https://pdbe.org/6tn3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6tn3 RCSB], [https://www.ebi.ac.uk/pdbsum/6tn3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6tn3 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	UDP-N-acetylglucosamine pyrophosphorylase (UAP1) catalyses the last step in eukaryotic biosynthesis of uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc), converting UTP and GlcNAc-1P to the sugar nucleotide. Gene disruption studies have shown that this gene is essential in eukaryotes and a possible antifungal target, yet no inhibitors of fungal UAP1 have so far been reported. Here we describe the crystal structures of substrate/product complexes of UAP1 from Aspergillus fumigatus that together provide snapshots of catalysis. A structure with UDP-GlcNAc, pyrophosphate and Mg(2+) provides the first Michaelis complex trapped for this class of enzyme, revealing the structural basis of the previously reported Mg(2+) dependence and direct observation of pyrophosphorolysis. We also show that a highly conserved lysine mimics the role of a second metal observed in structures of bacterial orthologues. A mechanism-inspired UTP alpha,beta-methylenebisphosphonate analogue (meUTP) was designed and synthesized and was shown to be a micromolar inhibitor of the enzyme. The mechanistic insights and inhibitor described here will facilitate future studies towards the discovery of small molecule inhibitors of this currently unexploited potential antifungal drug target.
		+
		+	A mechanism-inspired UDP-N-acetylglucosamine pyrophosphorylase inhibitor.,Raimi OG, Hurtado-Guerrero R, Borodkin V, Ferenbach A, Urbaniak MD, Ferguson MAJ, van Aalten DMF RSC Chem Biol. 2020 Mar 24;1(1):13-25. doi: 10.1039/c9cb00017h. eCollection 2020 , Apr 16. PMID:34458745<ref>PMID:34458745</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6tn3" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aspfu]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: UDP-N-acetylglucosamine diphosphorylase]]		[[Category: UDP-N-acetylglucosamine diphosphorylase]]

OCA at 09:21, 1 April 2020

OCA — Wed, 01 Apr 2020 09:21:33 GMT

←Older revision		Revision as of 09:21, 1 April 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6tn3 is ~~ON HOLD~~	+	==Crystal Structure of Aspergillus fumigatus UDP-N-acetylglucosamine pyrophosphorylase in complex with GlcNAc-1P==
-		+	<StructureSection load='6tn3' size='340' side='right'caption='[[6tn3]], [[Resolution\|resolution]] 2.28Å' scene=''>
-	~~Authors~~: ~~Raimi~~, O.G., ~~Guerrero~~, R.H.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6tn3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TN3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6TN3 FirstGlance]. <br>
-	~~Description~~: ~~Crystal Structure of Aspergillus fumigatus~~ UDP-N-acetylglucosamine ~~pyrophosphorylase in complex with GlcNAc-1P~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GN1:2-(ACETYLAMINO)-2-DEOXY-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE'>GN1</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-N-acetylglucosamine_diphosphorylase UDP-N-acetylglucosamine diphosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.23 2.7.7.23] </span></td></tr>
-	[[Category: Raimi, O.G]]	+	<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=6tn3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tn3 OCA], [http://pdbe.org/6tn3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tn3 RCSB], [http://www.ebi.ac.uk/pdbsum/6tn3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tn3 ProSAT]</span></td></tr>
-	[[Category: ~~Guerrero, R.H~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: UDP-N-acetylglucosamine diphosphorylase]]
		+	[[Category: Guerrero, R H]]
		+	[[Category: Raimi, O G]]
		+	[[Category: Anti-fungal]]
		+	[[Category: Aspergillus fumigatus]]
		+	[[Category: Pyrophosphorylase]]
		+	[[Category: Transferase]]

OCA: Protected "6tn3" [edit=sysop:move=sysop]

OCA — Wed, 11 Dec 2019 13:40:51 GMT

Protected "6tn3" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:40, 11 December 2019

OCA: New page: '''Unreleased structure''' The entry 6tn3 is ON HOLD Authors: Raimi, O.G., Guerrero, R.H. Description: Crystal Structure of Aspergillus fumigatus UDP-N-acetylglucosamine pyrophosphoryl...

OCA — Wed, 11 Dec 2019 13:40:49 GMT

New page: '''Unreleased structure''' The entry 6tn3 is ON HOLD Authors: Raimi, O.G., Guerrero, R.H. Description: Crystal Structure of Aspergillus fumigatus UDP-N-acetylglucosamine pyrophosphoryl...

New page

'''Unreleased structure'''

The entry 6tn3 is ON HOLD

Authors: Raimi, O.G., Guerrero, R.H.

Description: Crystal Structure of Aspergillus fumigatus UDP-N-acetylglucosamine pyrophosphorylase in complex with GlcNAc-1P
[[Category: Unreleased Structures]]
[[Category: Raimi, O.G]]
[[Category: Guerrero, R.H]]