5ze6 - Revision history

OCA at 08:52, 22 November 2023

2023-11-22T08:52:15Z

←Older revision		Revision as of 08:52, 22 November 2023
Line 1:		Line 1:

	==CRYSTAL STRUCTURE OF OCTAPRENYL PYROPHOSPHATE SYNTHASE FROM ESCHERICHIA COLI WITH BPH-981==		==CRYSTAL STRUCTURE OF OCTAPRENYL PYROPHOSPHATE SYNTHASE FROM ESCHERICHIA COLI WITH BPH-981==
-	<StructureSection load='5ze6' size='340' side='right' caption='[[5ze6]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='5ze6' size='340' side='right'caption='[[5ze6]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ze6]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZE6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZE6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ze6]] 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=5ZE6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZE6 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>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.5Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks'>[http~~:~~//en.wikipedia.org/wiki/All~~-~~trans~~-~~octaprenyl~~-~~diphosphate_synthase All-trans-octaprenyl-diphosphate synthase]~~, ~~with EC number [http~~:~~//www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.90 2.5.1.90]~~ </~~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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=5ze6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ze6 OCA], [~~http~~://pdbe.org/5ze6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ze6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ze6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ze6 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=5ze6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ze6 OCA], [https://pdbe.org/5ze6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ze6 RCSB], [https://www.ebi.ac.uk/pdbsum/5ze6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ze6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ISPB_ECOLI ISPB_ECOLI]] Supplies octaprenyl diphosphate, the precursor for the side chain of the isoprenoid quinones ubiquinone and menaquinone.<ref>PMID:8037730</ref>	+	[https://www.uniprot.org/uniprot/ISPB_ECOLI ISPB_ECOLI] Supplies octaprenyl diphosphate, the precursor for the side chain of the isoprenoid quinones ubiquinone and menaquinone.<ref>PMID:8037730</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 5ze6" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~All~~-~~trans-octaprenyl-diphosphate synthase~~]]	+	[[Category: Escherichia coli K-12]]
-	[[Category: Chen~~, C C~~]]	+	[[Category: Large Structures]]
-	[[Category: Guo~~, R T~~]]	+	[[Category: Chen CC]]
-	[[Category: Han, X]]	+	[[Category: Guo RT]]
-	[[Category: Ko~~, T P~~]]	+	[[Category: Han X]]
-	[[Category: Liu~~, W D~~]]	+	[[Category: Ko TP]]
-	[[Category: Zheng~~, Y Y]]~~	+	[[Category: Liu WD]]
-	~~[[Category: Prenyltransferase]]~~	+	[[Category: Zheng YY]]
-	~~[[Category: Product chain length]]~~	+
-	~~[[Category: Site-directed mutagenesis]]~~	+
-	~~[[Category: Transferase-inhibitor complex~~]]	+

OCA at 15:12, 27 February 2019

2019-02-27T15:12:33Z

←Older revision		Revision as of 15:12, 27 February 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ze6 ~~is ON HOLD until Feb 26 2020~~	+	==CRYSTAL STRUCTURE OF OCTAPRENYL PYROPHOSPHATE SYNTHASE FROM ESCHERICHIA COLI WITH BPH-981==
-		+	<StructureSection load='5ze6' size='340' side='right' caption='[[5ze6]], [[Resolution\|resolution]] 2.50Å' scene=''>
-	~~Authors~~: ~~Han~~, X., ~~Liu, W~~.D., ~~Zheng, Y~~.Y., Ko, T.P., ~~Chen, C~~.C., ~~Guo, R~~.T.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ze6]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZE6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZE6 FirstGlance]. <br>
-	~~Description: CRYSTAL STRUCTURE OF OCTAPRENYL PYROPHOSPHATE SYNTHASE FROM ESCHERICHIA COLI 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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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/All-trans-octaprenyl-diphosphate_synthase All-trans-octaprenyl-diphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.90 2.5.1.90] </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=5ze6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ze6 OCA], [http://pdbe.org/5ze6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ze6 RCSB], [http://www.ebi.ac.uk/pdbsum/5ze6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ze6 ProSAT]</span></td></tr>
-	[[Category: Chen, C.C]]	+	</table>
-	~~[[Category: Ko, T.P~~]]	+	== Function ==
-	[[Category: Guo, R.T]]	+	[[http://www.uniprot.org/uniprot/ISPB_ECOLI ISPB_ECOLI]] Supplies octaprenyl diphosphate, the precursor for the side chain of the isoprenoid quinones ubiquinone and menaquinone.<ref>PMID:8037730</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: All-trans-octaprenyl-diphosphate synthase]]
		+	[[Category: Chen, C C]]
		+	[[Category: Guo, R T]]
	[[Category: Han, X]]		[[Category: Han, X]]
-	[[Category: Zheng, Y.Y]]	+	[[Category: Ko, T P]]
		+	[[Category: Liu, W D]]
		+	[[Category: Zheng, Y Y]]
		+	[[Category: Prenyltransferase]]
		+	[[Category: Product chain length]]
		+	[[Category: Site-directed mutagenesis]]
		+	[[Category: Transferase-inhibitor complex]]

OCA at 04:01, 18 April 2018

2018-04-18T04:01:54Z

←Older revision		Revision as of 04:01, 18 April 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ze6 is ON HOLD	+	The entry 5ze6 is ON HOLD until Feb 26 2020

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

-	Description: CRYSTAL STRUCTURE OF OCTAPRENYL PYROPHOSPHATE SYNTHASE FROM ESCHERICHIA COLI WITH BPH-~~629~~	+	Description: CRYSTAL STRUCTURE OF OCTAPRENYL PYROPHOSPHATE SYNTHASE FROM ESCHERICHIA COLI WITH BPH-981
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Liu, W.D]]
	[[Category: Chen, C.C]]		[[Category: Chen, C.C]]
	[[Category: Ko, T.P]]		[[Category: Ko, T.P]]
-	[[Category: Liu, W.D]]
	[[Category: Guo, R.T]]		[[Category: Guo, R.T]]
	[[Category: Han, X]]		[[Category: Han, X]]
	[[Category: Zheng, Y.Y]]		[[Category: Zheng, Y.Y]]

OCA: Protected "5ze6" [edit=sysop:move=sysop]

2018-03-08T03:37:45Z

Protected "5ze6" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:37, 8 March 2018

OCA: New page: '''Unreleased structure''' The entry 5ze6 is ON HOLD Authors: Han, X., Liu, W.D., Zheng, Y.Y., Ko, T.P., Chen, C.C., Guo, R.T. Description: CRYSTAL STRUCTURE OF OCTAPRENYL PYROPHOSPHAT...

2018-03-08T03:37:44Z

New page: '''Unreleased structure''' The entry 5ze6 is ON HOLD Authors: Han, X., Liu, W.D., Zheng, Y.Y., Ko, T.P., Chen, C.C., Guo, R.T. Description: CRYSTAL STRUCTURE OF OCTAPRENYL PYROPHOSPHAT...

New page

'''Unreleased structure'''

The entry 5ze6 is ON HOLD

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

Description: CRYSTAL STRUCTURE OF OCTAPRENYL PYROPHOSPHATE SYNTHASE FROM ESCHERICHIA COLI WITH BPH-629
[[Category: Unreleased Structures]]
[[Category: Chen, C.C]]
[[Category: Ko, T.P]]
[[Category: Liu, W.D]]
[[Category: Guo, R.T]]
[[Category: Han, X]]
[[Category: Zheng, Y.Y]]