5zlf - Revision history

OCA at 08:59, 22 November 2023

OCA — Wed, 22 Nov 2023 08:59:33 GMT

←Older revision		Revision as of 08:59, 22 November 2023
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	<StructureSection load='5zlf' size='340' side='right'caption='[[5zlf]], [[Resolution\|resolution]] 2.84Å' scene=''>		<StructureSection load='5zlf' size='340' side='right'caption='[[5zlf]], [[Resolution\|resolution]] 2.84Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zlf]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZLF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZLF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zlf]] 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=5ZLF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZLF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B29:[2-(3-DIBENZOFURAN-4-YL-PHENYL)-1-HYDROXY-1-PHOSPHONO-ETHYL]-PHOSPHONIC+ACID'>B29</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]] 2.845Å</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=B29:[2-(3-DIBENZOFURAN-4-YL-PHENYL)-1-HYDROXY-1-PHOSPHONO-ETHYL]-PHOSPHONIC+ACID'>B29</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=5zlf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zlf OCA], [~~http~~://pdbe.org/5zlf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zlf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zlf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zlf 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=5zlf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zlf OCA], [https://pdbe.org/5zlf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zlf RCSB], [https://www.ebi.ac.uk/pdbsum/5zlf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zlf 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 5zlf" 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: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chen~~, C C~~]]	+	[[Category: Chen CC]]
-	[[Category: Guo~~, R T~~]]	+	[[Category: Guo RT]]
-	[[Category: Han, X]]	+	[[Category: Han X]]
-	[[Category: Ko~~, T P~~]]	+	[[Category: Ko TP]]
-	[[Category: Liu~~, W D~~]]	+	[[Category: Liu WD]]
-	[[Category: Zheng~~, Y Y]]~~	+	[[Category: Zheng YY]]
-	~~[[Category: Prenyltransferase]]~~	+
-	~~[[Category: Product chain length]]~~	+
-	~~[[Category: Site-directed mutagenesis]]~~	+
-	~~[[Category: Transferase-inhibitor complex~~]]	+

OCA at 06:31, 27 March 2019

OCA — Wed, 27 Mar 2019 06:31:09 GMT

←Older revision		Revision as of 06:31, 27 March 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 5zlf ~~is ON HOLD until Mar 27 2020~~	+	==CRYSTAL STRUCTURE OF OCTAPRENYL PYROPHOSPHATE SYNTHASE FROM ESCHERICHIA COLI WITH ligand BPH-629==
-		+	<StructureSection load='5zlf' size='340' side='right'caption='[[5zlf]], [[Resolution\|resolution]] 2.84Å' 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'>[[5zlf]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZLF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZLF FirstGlance]. <br>
-	~~Description: CRYSTAL STRUCTURE OF OCTAPRENYL PYROPHOSPHATE SYNTHASE FROM ESCHERICHIA COLI WITH ligand BPH-629~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B29:[2-(3-DIBENZOFURAN-4-YL-PHENYL)-1-HYDROXY-1-PHOSPHONO-ETHYL]-PHOSPHONIC+ACID'>B29</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=5zlf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zlf OCA], [http://pdbe.org/5zlf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zlf RCSB], [http://www.ebi.ac.uk/pdbsum/5zlf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zlf 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: Large Structures]]
		+	[[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 03:50, 30 May 2018

OCA — Wed, 30 May 2018 03:50:03 GMT

←Older revision		Revision as of 03:50, 30 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5zlf is ON HOLD	+	The entry 5zlf is ON HOLD until Mar 27 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.

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

OCA — Wed, 04 Apr 2018 04:34:10 GMT

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

←Older revision

Revision as of 04:34, 4 April 2018

OCA: New page: '''Unreleased structure''' The entry 5zlf 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...

OCA — Wed, 04 Apr 2018 04:34:09 GMT

New page: '''Unreleased structure''' The entry 5zlf 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 5zlf 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 ligand BPH-629
[[Category: Unreleased Structures]]
[[Category: Liu, W.D]]
[[Category: Chen, C.C]]
[[Category: Ko, T.P]]
[[Category: Guo, R.T]]
[[Category: Han, X]]
[[Category: Zheng, Y.Y]]