7rud - Revision history

OCA at 16:39, 18 October 2023

OCA — Wed, 18 Oct 2023 16:39:02 GMT

←Older revision		Revision as of 16:39, 18 October 2023
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	<StructureSection load='7rud' size='340' side='right'caption='[[7rud]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='7rud' size='340' side='right'caption='[[7rud]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7rud]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RUD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RUD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7rud]] is a 4 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=7RUD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RUD FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=7QE:(2Z)~~-3,~~3,3-trifluoro-~~2~~-(hydroxyimino)propanoic+acid'>7QE</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]] 2.8Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks'>[https~~:~~//en.wikipedia.org/wiki/3~~-~~deoxy-7-phosphoheptulonate_synthase~~ 3-~~deoxy~~-7-~~phosphoheptulonate synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.54 2.5.1.54]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7QE:(2Z)-3,3,3-trifluoro-2-(hydroxyimino)propanoic+acid'>7QE</scene></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=7rud FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rud OCA], [https://pdbe.org/7rud PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rud RCSB], [https://www.ebi.ac.uk/pdbsum/7rud PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rud 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=7rud FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rud OCA], [https://pdbe.org/7rud PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rud RCSB], [https://www.ebi.ac.uk/pdbsum/7rud PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rud ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/AROG_ECOLI AROG_ECOLI]] Stereospecific condensation of phosphoenolpyruvate (PEP) and D-erythrose-4-phosphate (E4P) giving rise to 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP).	+	[https://www.uniprot.org/uniprot/AROG_ECOLI AROG_ECOLI] Stereospecific condensation of phosphoenolpyruvate (PEP) and D-erythrose-4-phosphate (E4P) giving rise to 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP).
	<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 7rud" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7rud" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DAHP synthase 3D structures\|DAHP synthase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: 3-~~deoxy-7-phosphoheptulonate synthase~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Berti~~, P J~~]]	+	[[Category: Berti PJ]]
-	[[Category: Brown, C]]	+	[[Category: Brown C]]
-	[[Category: Grainger, R]]	+	[[Category: Grainger R]]
-	[[Category: Heimhalt, M]]	+	[[Category: Heimhalt M]]
-	[[Category: Junop~~, M S~~]]	+	[[Category: Junop MS]]
-	[[Category: Mukherjee, P]]	+	[[Category: Mukherjee P]]
-	[[Category: Szabla, R]]	+	[[Category: Szabla R]]
-	[[Category: Turner, R]]	+	[[Category: Turner R]]
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Dahp synthase]]~~	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Transferase-transferase inhibitor complex~~]]	+

OCA at 06:33, 1 December 2021

OCA — Wed, 01 Dec 2021 06:33:05 GMT

←Older revision		Revision as of 06:33, 1 December 2021
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	==DAHP synthase complex with trifluoropyruvate oxime==		==DAHP synthase complex with trifluoropyruvate oxime==
-	<StructureSection load='7rud' size='340' side='right'caption='[[7rud]]' scene=''>	+	<StructureSection load='7rud' size='340' side='right'caption='[[7rud]], [[Resolution\|resolution]] 2.80Å' 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=7RUD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RUD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7rud]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RUD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RUD FirstGlance]. <br>
-	</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=7rud FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rud OCA], [https://pdbe.org/7rud PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rud RCSB], [https://www.ebi.ac.uk/pdbsum/7rud PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rud ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7QE:(2Z)-3,3,3-trifluoro-2-(hydroxyimino)propanoic+acid'>7QE</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/3-deoxy-7-phosphoheptulonate_synthase 3-deoxy-7-phosphoheptulonate synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.54 2.5.1.54] </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=7rud FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rud OCA], [https://pdbe.org/7rud PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rud RCSB], [https://www.ebi.ac.uk/pdbsum/7rud PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rud ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/AROG_ECOLI AROG_ECOLI]] Stereospecific condensation of phosphoenolpyruvate (PEP) and D-erythrose-4-phosphate (E4P) giving rise to 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	3-Deoxy-d-arabinoheptulosonate-7-phosphate (DAHP) synthase catalyzes the first step in the shikimate biosynthetic pathway and is an antimicrobial target. We used an inhibitor-in-pieces approach, based on the previously reported inhibitor DAHP oxime, to screen inhibitor fragments in the presence and absence of glycerol 3-phosphate to occupy the distal end of the active site. This led to DAHP hydrazone, the most potent inhibitor to date, Ki = 10 +/- 1 nM. Three trifluoropyruvate (TFP)-based inhibitor fragments were efficient inhibitors with ligand efficiencies of up to 0.7 kcal mol(-1)/atom compared with 0.2 kcal mol(-1)/atom for a typical good inhibitor. The crystal structures showed the TFP-based inhibitors binding upside down in the active site relative to DAHP oxime, providing new avenues for inhibitor development. The ethyl esters of TFP oxime and TFP semicarbazone prevented E. coli growth in culture with IC50 = 0.21 +/- 0.01 and 0.77 +/- 0.08 mg mL(-1), respectively. Overexpressing DAHP synthase relieved growth inhibition, demonstrating that DAHP synthase was the target. Growth inhibition occurred in media containing aromatic amino acids, suggesting that growth inhibition was due to depletion of some other product(s) of the shikimate pathway, possibly folate.
		+
		+	An Inhibitor-in-Pieces Approach to DAHP Synthase Inhibition: Potent Enzyme and Bacterial Growth Inhibition.,Heimhalt M, Mukherjee P, Grainger RA, Szabla R, Brown C, Turner R, Junop MS, Berti PJ ACS Infect Dis. 2021 Nov 11. doi: 10.1021/acsinfecdis.1c00462. PMID:34761906<ref>PMID:34761906</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7rud" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: 3-deoxy-7-phosphoheptulonate synthase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Berti PJ]]	+	[[Category: Berti, P J]]
-	[[Category: Brown C]]	+	[[Category: Brown, C]]
-	[[Category: Grainger R]]	+	[[Category: Grainger, R]]
-	[[Category: Heimhalt M]]	+	[[Category: Heimhalt, M]]
-	[[Category: Junop MS]]	+	[[Category: Junop, M S]]
-	[[Category: Mukherjee P]]	+	[[Category: Mukherjee, P]]
-	[[Category: Szabla R]]	+	[[Category: Szabla, R]]
-	[[Category: Turner R]]	+	[[Category: Turner, R]]
		+	[[Category: Complex]]
		+	[[Category: Dahp synthase]]
		+	[[Category: Inhibitor]]
		+	[[Category: Lyase]]
		+	[[Category: Transferase-transferase inhibitor complex]]

OCA at 13:39, 17 November 2021

OCA — Wed, 17 Nov 2021 13:39:32 GMT

←Older revision		Revision as of 13:39, 17 November 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7rud is ~~ON HOLD until Paper Publication~~	+	==DAHP synthase complex with trifluoropyruvate oxime==
-		+	<StructureSection load='7rud' size='340' side='right'caption='[[7rud]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RUD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RUD FirstGlance]. <br>
-	~~Description~~:	+	</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=7rud FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rud OCA], [https://pdbe.org/7rud PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rud RCSB], [https://www.ebi.ac.uk/pdbsum/7rud PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rud ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Berti PJ]]
		+	[[Category: Brown C]]
		+	[[Category: Grainger R]]
		+	[[Category: Heimhalt M]]
		+	[[Category: Junop MS]]
		+	[[Category: Mukherjee P]]
		+	[[Category: Szabla R]]
		+	[[Category: Turner R]]

OCA at 05:35, 22 September 2021

OCA — Wed, 22 Sep 2021 05:35:12 GMT

←Older revision		Revision as of 05:35, 22 September 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7rud is ON HOLD	+	The entry 7rud is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7rud" [edit=sysop:move=sysop]

OCA — Wed, 25 Aug 2021 05:18:32 GMT

Protected "7rud" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:18, 25 August 2021

OCA: New page: '''Unreleased structure''' The entry 7rud is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 25 Aug 2021 05:18:31 GMT

New page: '''Unreleased structure''' The entry 7rud is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7rud is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]