5zhe - Revision history

OCA at 08:55, 22 November 2023

OCA — Wed, 22 Nov 2023 08:55:06 GMT

←Older revision		Revision as of 08:55, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='5zhe' size='340' side='right'caption='[[5zhe]], [[Resolution\|resolution]] 2.18Å' scene=''>		<StructureSection load='5zhe' size='340' side='right'caption='[[5zhe]], [[Resolution\|resolution]] 2.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zhe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZHE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZHE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zhe]] is a 2 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=5ZHE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZHE FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=HJX:~~2~~-hydroxy-6-(tetradecyloxy)benzoic+acid'>HJX</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]] 2.18Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks'>[http~~:~~//en.wikipedia.org/wiki/Ditrans,polycis~~-~~undecaprenyl~~-~~diphosphate_synthase_((2E,6E)~~-~~farnesyl-_diphosphate_specific) Ditrans,polycis-undecaprenyl-diphosphate synthase~~ (~~(2E,6E~~)~~-farnesyl- diphosphate specific)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.31 2.5.1.31]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HJX:2-hydroxy-6-(tetradecyloxy)benzoic+acid'>HJX</scene></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=5zhe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zhe OCA], [~~http~~://pdbe.org/5zhe PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zhe RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zhe PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zhe 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=5zhe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zhe OCA], [https://pdbe.org/5zhe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zhe RCSB], [https://www.ebi.ac.uk/pdbsum/5zhe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zhe ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/UPPS_ECOLI UPPS_ECOLI]] Generates ditrans,octacis-undecaprenyl pyrophosphate (UPP) from isopentenyl pyrophosphate (IPP) and farnesyl diphosphate (FPP). UPP is the precursor of glycosyl carrier lipid in the biosynthesis of bacterial cell wall polysaccharide components such as peptidoglycan and lipopolysaccharide.<ref>PMID:12756244</ref>	+	[https://www.uniprot.org/uniprot/UPPS_ECOLI UPPS_ECOLI] Generates ditrans,octacis-undecaprenyl pyrophosphate (UPP) from isopentenyl pyrophosphate (IPP) and farnesyl diphosphate (FPP). UPP is the precursor of glycosyl carrier lipid in the biosynthesis of bacterial cell wall polysaccharide components such as peptidoglycan and lipopolysaccharide.<ref>PMID:12756244</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We report that alkyl-substituted bisphosphonates have activity against Bacillus anthracis Sterne (0.40 mug/mL), Mycobacterium smegmatis (1.4 mug/mL), Bacillus subtilis (1.0 mug/mL), and Staphylococcus aureus (13 mug/mL). In many cases, there is no effect of serum binding, as well as low activity against a human embryonic kidney cell line. Targeting of isoprenoid biosynthesis is involved with 74 having IC(50) values of approximately 100 nM against heptaprenyl diphosphate synthase and 200 nM against farnesyl diphosphate synthase. B. subtilis growth inhibition was rescued by addition of farnesyl diphosphate, menaquinone-4 (MK-4), or undecaprenyl phosphate (UP), and the combination of MK-4 and UP resulted in a 25x increase in ED(50), indicating targeting of both quinone and cell wall biosynthesis. Clostridioides difficile was inhibited by 74, and since this organism does not synthesize quinones, cell wall biosynthesis is the likely target. We also solved three X-ray structures of inhibitors bound to octaprenyl diphosphate and/or undecaprenyl diphosphate synthases.
		+
		+	Discovery of Lipophilic Bisphosphonates That Target Bacterial Cell Wall and Quinone Biosynthesis.,Malwal SR, Chen L, Hicks H, Qu F, Liu W, Shillo A, Law WX, Zhang J, Chandnani N, Han X, Zheng Y, Chen CC, Guo RT, AbdelKhalek A, Seleem MN, Oldfield E J Med Chem. 2019 Mar 14;62(5):2564-2581. doi: 10.1021/acs.jmedchem.8b01878. Epub , 2019 Feb 21. PMID:30730737<ref>PMID:30730737</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5zhe" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Undecaprenyl pyrophosphate synthase\|Undecaprenyl pyrophosphate synthase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chen~~, C C~~]]	+	[[Category: Chen CC]]
-	[[Category: Gao, J]]	+	[[Category: Gao J]]
-	[[Category: Guo~~, R T~~]]	+	[[Category: Guo RT]]
-	[[Category: Ko~~, T P~~]]	+	[[Category: Ko TP]]
-	[[Category: Liu~~, W D~~]]	+	[[Category: Liu WD]]
-	[[Category: Zheng~~, Y Y]]~~	+	[[Category: Zheng YY]]
-	~~[[Category: Acidocalcisomal pyrophosphatase]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Substrate binding]]~~	+
-	~~[[Category: Transferase-inhibitor complex~~]]	+

OCA at 11:52, 13 March 2019

OCA — Wed, 13 Mar 2019 11:52:16 GMT

←Older revision		Revision as of 11:52, 13 March 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5zhe is ~~ON HOLD until Mar 13 2020~~	+	==STRUCTURE OF E. COLI UNDECAPRENYL DIPHOSPHATE SYNTHASE IN COMPLEX WITH BPH-981==
-		+	<StructureSection load='5zhe' size='340' side='right'caption='[[5zhe]], [[Resolution\|resolution]] 2.18Å' scene=''>
-	~~Authors~~: ~~Gao, J~~., ~~Liu~~, ~~W.D.~~, ~~Zheng~~, Y.Y.~~, Ko, T~~.P.~~, Chen, C~~.C.~~, Guo, R~~.T.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5zhe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZHE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZHE FirstGlance]. <br>
-	~~Description~~: ~~STRUCTURE OF E~~. ~~COLI UNDECAPRENYL DIPHOSPHATE SYNTHASE IN COMPLEX WITH BPH~~-~~981~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HJX:2-hydroxy-6-(tetradecyloxy)benzoic+acid'>HJX</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/Ditrans,polycis-undecaprenyl-diphosphate_synthase_((2E,6E)-farnesyl-_diphosphate_specific) Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl- diphosphate specific)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.31 2.5.1.31] </span></td></tr>
-	[[~~Category~~: ~~Liu~~, W.D]]	+	<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=5zhe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zhe OCA], [http://pdbe.org/5zhe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zhe RCSB], [http://www.ebi.ac.uk/pdbsum/5zhe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zhe ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Chen, C~~.C]]	+	</table>
-	[[Category: ~~Ko, T.P~~]]	+	== Function ==
-	[[Category: ~~Guo~~, ~~R.T~~]]	+	[[http://www.uniprot.org/uniprot/UPPS_ECOLI UPPS_ECOLI]] Generates ditrans,octacis-undecaprenyl pyrophosphate (UPP) from isopentenyl pyrophosphate (IPP) and farnesyl diphosphate (FPP). UPP is the precursor of glycosyl carrier lipid in the biosynthesis of bacterial cell wall polysaccharide components such as peptidoglycan and lipopolysaccharide.<ref>PMID:12756244</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Chen, C C]]
	[[Category: Gao, J]]		[[Category: Gao, J]]
-	[[Category: Zheng, Y.Y]]	+	[[Category: Guo, R T]]
		+	[[Category: Ko, T P]]
		+	[[Category: Liu, W D]]
		+	[[Category: Zheng, Y Y]]
		+	[[Category: Acidocalcisomal pyrophosphatase]]
		+	[[Category: Metal-binding]]
		+	[[Category: Substrate binding]]
		+	[[Category: Transferase-inhibitor complex]]

OCA at 03:49, 30 May 2018

OCA — Wed, 30 May 2018 03:49:11 GMT

←Older revision		Revision as of 03:49, 30 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5zhe is ON HOLD	+	The entry 5zhe is ON HOLD until Mar 13 2020

	Authors: Gao, J., Liu, W.D., Zheng, Y.Y., Ko, T.P., Chen, C.C., Guo, R.T.		Authors: Gao, J., Liu, W.D., Zheng, Y.Y., Ko, T.P., Chen, C.C., Guo, R.T.

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

OCA — Wed, 21 Mar 2018 06:00:09 GMT

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

←Older revision

Revision as of 06:00, 21 March 2018

OCA: New page: '''Unreleased structure''' The entry 5zhe is ON HOLD Authors: Gao, J., Liu, W.D., Zheng, Y.Y., Ko, T.P., Chen, C.C., Guo, R.T. Description: STRUCTURE OF E. COLI UNDECAPRENYL DIPHOSPHAT...

OCA — Wed, 21 Mar 2018 06:00:08 GMT

New page: '''Unreleased structure''' The entry 5zhe is ON HOLD Authors: Gao, J., Liu, W.D., Zheng, Y.Y., Ko, T.P., Chen, C.C., Guo, R.T. Description: STRUCTURE OF E. COLI UNDECAPRENYL DIPHOSPHAT...

New page

'''Unreleased structure'''

The entry 5zhe is ON HOLD

Authors: Gao, J., Liu, W.D., Zheng, Y.Y., Ko, T.P., Chen, C.C., Guo, R.T.

Description: STRUCTURE OF E. COLI UNDECAPRENYL DIPHOSPHATE SYNTHASE IN COMPLEX WITH BPH-981
[[Category: Unreleased Structures]]
[[Category: Liu, W.D]]
[[Category: Chen, C.C]]
[[Category: Ko, T.P]]
[[Category: Guo, R.T]]
[[Category: Gao, J]]
[[Category: Zheng, Y.Y]]