3wyj - Revision history

OCA at 13:34, 8 November 2023

OCA — Wed, 08 Nov 2023 13:34:01 GMT

←Older revision		Revision as of 13:34, 8 November 2023
Line 1:		Line 1:

	==Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-789==		==Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-789==
-	<StructureSection load='3wyj' size='340' side='right'caption='[[3wyj]]' scene=''>	+	<StructureSection load='3wyj' size='340' side='right'caption='[[3wyj]], [[Resolution\|resolution]] 2.10Å' 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=3WYJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WYJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wyj]] 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=3WYJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WYJ 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=3wyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wyj OCA], [https://pdbe.org/3wyj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wyj RCSB], [https://www.ebi.ac.uk/pdbsum/3wyj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wyj ProSAT]</span></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]] 2.1Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=H78:[1-OXIDANYL-2-[3-[3-[[3-[[3-[3-(2-OXIDANYL-2,2-DIPHOSPHONO-ETHYL)PHENYL]PHENYL]SULFAMOYL]PHENYL]SULFONYLAMINO]PHENYL]PHENYL]-1-PHOSPHONO-ETHYL]PHOSPHONIC+ACID'>H78</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=3wyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wyj OCA], [https://pdbe.org/3wyj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wyj RCSB], [https://www.ebi.ac.uk/pdbsum/3wyj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wyj ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[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 the results of an investigation of the activity of a series of amidine and bisamidine compounds against Staphylococcus aureus and Escherichia coli. The most active compounds bound to an AT-rich DNA dodecamer (CGCGAATTCGCG)2 and using DSC were found to increase the melting transition by up to 24 degrees C. Several compounds also inhibited undecaprenyl diphosphate synthase (UPPS) with IC50 values of 100-500 nM, and we found good correlations (R2 = 0.89, S. aureus; R2 = 0.79, E. coli) between experimental and predicted cell growth inhibition by using DNA DeltaTm and UPPS IC50 experimental results together with one computed descriptor. We also solved the structures of three bisamidines binding to DNA as well as three UPPS structures. Overall, the results are of general interest in the context of the development of resistance-resistant antibiotics that involve multitargeting.
		+
		+	Antibacterial Drug Leads: DNA and Enzyme Multitargeting.,Zhu W, Wang Y, Li K, Gao J, Huang CH, Chen CC, Ko TP, Zhang Y, Guo RT, Oldfield E J Med Chem. 2015 Jan 22. PMID:25574764<ref>PMID:25574764</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 3wyj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Undecaprenyl pyrophosphate synthase\|Undecaprenyl pyrophosphate synthase]]		*[[Undecaprenyl pyrophosphate synthase\|Undecaprenyl pyrophosphate synthase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Gao J]]		[[Category: Gao J]]

OCA at 10:38, 31 August 2022

OCA — Wed, 31 Aug 2022 10:38:19 GMT

←Older revision		Revision as of 10:38, 31 August 2022
Line 1:		Line 1:

	==Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-789==		==Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-789==
-	<StructureSection load='3wyj' size='340' side='right'caption='[[3wyj]]~~, [[Resolution\|resolution]] 2.10Å~~' scene=''>	+	<StructureSection load='3wyj' size='340' side='right'caption='[[3wyj]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[3wyj]] is a 2 chain structure.~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WYJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WYJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WYJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WYJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=H78:[1-OXIDANYL-2-[3-[3-[[3-[[3-[3-(2-OXIDANYL-2,2-DIPHOSPHONO-ETHYL)PHENYL]PHENYL]SULFAMOYL]PHENYL]SULFONYLAMINO]PHENYL]PHENYL]-1-PHOSPHONO-ETHYL]PHOSPHONIC+ACID'>H78</scene></td></tr>	+	</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=3wyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wyj OCA], [https://pdbe.org/3wyj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wyj RCSB], [https://www.ebi.ac.uk/pdbsum/3wyj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wyj ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3wyi\|3wyi]]</div></td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://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 [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.31 2.5.1.31] </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=3wyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wyj OCA], [https://pdbe.org/3wyj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wyj RCSB], [https://www.ebi.ac.uk/pdbsum/3wyj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wyj ProSAT]</span></td></tr>	+
	</table>		</table>
-	== Function ==
-	[[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 the results of an investigation of the activity of a series of amidine and bisamidine compounds against Staphylococcus aureus and Escherichia coli. The most active compounds bound to an AT-rich DNA dodecamer (CGCGAATTCGCG)2 and using DSC were found to increase the melting transition by up to 24 degrees C. Several compounds also inhibited undecaprenyl diphosphate synthase (UPPS) with IC50 values of 100-500 nM, and we found good correlations (R2 = 0.89, S. aureus; R2 = 0.79, E. coli) between experimental and predicted cell growth inhibition by using DNA DeltaTm and UPPS IC50 experimental results together with one computed descriptor. We also solved the structures of three bisamidines binding to DNA as well as three UPPS structures. Overall, the results are of general interest in the context of the development of resistance-resistant antibiotics that involve multitargeting.
-
-	Antibacterial Drug Leads: DNA and Enzyme Multitargeting.,Zhu W, Wang Y, Li K, Gao J, Huang CH, Chen CC, Ko TP, Zhang Y, Guo RT, Oldfield E J Med Chem. 2015 Jan 22. PMID:25574764<ref>PMID:25574764</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3wyj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Undecaprenyl pyrophosphate synthase\|Undecaprenyl pyrophosphate synthase]]		*[[Undecaprenyl pyrophosphate synthase\|Undecaprenyl pyrophosphate synthase]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gao, J]]	+	[[Category: Gao J]]
-	[[Category: Guo~~, R T~~]]	+	[[Category: Guo RT]]
-	[[Category: Huang~~, C H~~]]	+	[[Category: Huang CH]]
-	[[Category: Ko~~, T P~~]]	+	[[Category: Ko TP]]
-	[[Category: Oldfield, E]]	+	[[Category: Oldfield E]]
-	~~[[Category: Transferase~~]]	+

OCA at 05:00, 25 August 2022

OCA — Thu, 25 Aug 2022 05:00:16 GMT

←Older revision		Revision as of 05:00, 25 August 2022
Line 3:		Line 3:
	<StructureSection load='3wyj' size='340' side='right'caption='[[3wyj]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3wyj' size='340' side='right'caption='[[3wyj]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3wyj]] is a 2 chain structure ~~with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WYJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WYJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wyj]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WYJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WYJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=H78:[1-OXIDANYL-2-[3-[3-[[3-[[3-[3-(2-OXIDANYL-2,2-DIPHOSPHONO-ETHYL)PHENYL]PHENYL]SULFAMOYL]PHENYL]SULFONYLAMINO]PHENYL]PHENYL]-1-PHOSPHONO-ETHYL]PHOSPHONIC+ACID'>H78</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=H78:[1-OXIDANYL-2-[3-[3-[[3-[[3-[3-(2-OXIDANYL-2,2-DIPHOSPHONO-ETHYL)PHENYL]PHENYL]SULFAMOYL]PHENYL]SULFONYLAMINO]PHENYL]PHENYL]-1-PHOSPHONO-ETHYL]PHOSPHONIC+ACID'>H78</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3wyi\|3wyi]]</div></td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3wyi\|3wyi]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b0174, ispU, JW0169, rth, uppS, yaeS ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://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 [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.31 2.5.1.31] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://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 [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.31 2.5.1.31] </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=3wyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wyj OCA], [https://pdbe.org/3wyj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wyj RCSB], [https://www.ebi.ac.uk/pdbsum/3wyj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wyj 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=3wyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wyj OCA], [https://pdbe.org/3wyj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wyj RCSB], [https://www.ebi.ac.uk/pdbsum/3wyj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wyj ProSAT]</span></td></tr>
Line 28:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Ecoli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Gao, J]]		[[Category: Gao, J]]

OCA at 05:35, 10 August 2022

OCA — Wed, 10 Aug 2022 05:35:46 GMT

←Older revision		Revision as of 05:35, 10 August 2022
Line 1:		Line 1:

	==Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-789==		==Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-789==
-	<StructureSection load='3wyj' size='340' side='right' caption='[[3wyj]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='3wyj' size='340' side='right'caption='[[3wyj]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3wyj]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WYJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3WYJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wyj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WYJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WYJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=H78:[1-OXIDANYL-2-[3-[3-[[3-[[3-[3-(2-OXIDANYL-2,2-DIPHOSPHONO-ETHYL)PHENYL]PHENYL]SULFAMOYL]PHENYL]SULFONYLAMINO]PHENYL]PHENYL]-1-PHOSPHONO-ETHYL]PHOSPHONIC+ACID'>H78</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=H78:[1-OXIDANYL-2-[3-[3-[[3-[[3-[3-(2-OXIDANYL-2,2-DIPHOSPHONO-ETHYL)PHENYL]PHENYL]SULFAMOYL]PHENYL]SULFONYLAMINO]PHENYL]PHENYL]-1-PHOSPHONO-ETHYL]PHOSPHONIC+ACID'>H78</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wyi\|3wyi]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3wyi\|3wyi]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b0174, ispU, JW0169, rth, uppS, yaeS ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b0174, ispU, JW0169, rth, uppS, yaeS ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://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 [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.31 2.5.1.31] </span></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=3wyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wyj OCA], [~~http~~://pdbe.org/3wyj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3wyj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3wyj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3wyj 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=3wyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wyj OCA], [https://pdbe.org/3wyj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wyj RCSB], [https://www.ebi.ac.uk/pdbsum/3wyj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wyj 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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 29:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Ecoli]]		[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Gao, J]]		[[Category: Gao, J]]
	[[Category: Guo, R T]]		[[Category: Guo, R T]]

OCA at 09:37, 21 February 2019

OCA — Thu, 21 Feb 2019 09:37:09 GMT

←Older revision		Revision as of 09:37, 21 February 2019
Line 3:		Line 3:
	<StructureSection load='3wyj' size='340' side='right' caption='[[3wyj]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3wyj' size='340' side='right' caption='[[3wyj]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3wyj]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WYJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WYJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wyj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WYJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WYJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=H78:[1-OXIDANYL-2-[3-[3-[[3-[[3-[3-(2-OXIDANYL-2,2-DIPHOSPHONO-ETHYL)PHENYL]PHENYL]SULFAMOYL]PHENYL]SULFONYLAMINO]PHENYL]PHENYL]-1-PHOSPHONO-ETHYL]PHOSPHONIC+ACID'>H78</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=H78:[1-OXIDANYL-2-[3-[3-[[3-[[3-[3-(2-OXIDANYL-2,2-DIPHOSPHONO-ETHYL)PHENYL]PHENYL]SULFAMOYL]PHENYL]SULFONYLAMINO]PHENYL]PHENYL]-1-PHOSPHONO-ETHYL]PHOSPHONIC+ACID'>H78</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wyi\|3wyi]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wyi\|3wyi]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b0174, ispU, JW0169, rth, uppS, yaeS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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='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='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=3wyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wyj OCA], [http://pdbe.org/3wyj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wyj RCSB], [http://www.ebi.ac.uk/pdbsum/3wyj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wyj ProSAT]</span></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=3wyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wyj OCA], [http://pdbe.org/3wyj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wyj RCSB], [http://www.ebi.ac.uk/pdbsum/3wyj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wyj ProSAT]</span></td></tr>
Line 20:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 3wyj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3wyj" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Undecaprenyl pyrophosphate synthase\|Undecaprenyl pyrophosphate synthase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecoli]]
	[[Category: Gao, J]]		[[Category: Gao, J]]
	[[Category: Guo, R T]]		[[Category: Guo, R T]]

OCA at 16:34, 11 August 2016

OCA — Thu, 11 Aug 2016 16:34:53 GMT

←Older revision		Revision as of 16:34, 11 August 2016
Line 1:		Line 1:
		+
	==Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-789==		==Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-789==
	<StructureSection load='3wyj' size='340' side='right' caption='[[3wyj]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3wyj' size='340' side='right' caption='[[3wyj]], [[Resolution\|resolution]] 2.10Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wyi\|3wyi]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wyi\|3wyi]]</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='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='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=3wyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wyj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wyj RCSB], [http://www.ebi.ac.uk/pdbsum/3wyj PDBsum]</span></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=3wyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wyj OCA], [http://pdbe.org/3wyj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wyj RCSB], [http://www.ebi.ac.uk/pdbsum/3wyj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wyj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3wyj" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:42, 7 February 2015

OCA — Sat, 07 Feb 2015 15:42:57 GMT

←Older revision		Revision as of 15:42, 7 February 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-789==
		+	<StructureSection load='3wyj' size='340' side='right' caption='[[3wyj]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3wyj]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WYJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WYJ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=H78:[1-OXIDANYL-2-[3-[3-[[3-[[3-[3-(2-OXIDANYL-2,2-DIPHOSPHONO-ETHYL)PHENYL]PHENYL]SULFAMOYL]PHENYL]SULFONYLAMINO]PHENYL]PHENYL]-1-PHOSPHONO-ETHYL]PHOSPHONIC+ACID'>H78</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wyi\|3wyi]]</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='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=3wyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wyj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wyj RCSB], [http://www.ebi.ac.uk/pdbsum/3wyj PDBsum]</span></td></tr>
		+	</table>
		+	== 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>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We report the results of an investigation of the activity of a series of amidine and bisamidine compounds against Staphylococcus aureus and Escherichia coli. The most active compounds bound to an AT-rich DNA dodecamer (CGCGAATTCGCG)2 and using DSC were found to increase the melting transition by up to 24 degrees C. Several compounds also inhibited undecaprenyl diphosphate synthase (UPPS) with IC50 values of 100-500 nM, and we found good correlations (R2 = 0.89, S. aureus; R2 = 0.79, E. coli) between experimental and predicted cell growth inhibition by using DNA DeltaTm and UPPS IC50 experimental results together with one computed descriptor. We also solved the structures of three bisamidines binding to DNA as well as three UPPS structures. Overall, the results are of general interest in the context of the development of resistance-resistant antibiotics that involve multitargeting.

-	~~The entry 3wyj is ON HOLD until Paper Publication~~	+	Antibacterial Drug Leads: DNA and Enzyme Multitargeting.,Zhu W, Wang Y, Li K, Gao J, Huang CH, Chen CC, Ko TP, Zhang Y, Guo RT, Oldfield E J Med Chem. 2015 Jan 22. PMID:25574764<ref>PMID:25574764</ref>

-	~~Authors: Gao~~, J.~~, Ko, T~~.~~P., Huang, C.H., Oldfield, E~~., Guo, R.T.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-789~~	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Gao, J]]
		+	[[Category: Guo, R T]]
		+	[[Category: Huang, C H]]
		+	[[Category: Ko, T P]]
	[[Category: Oldfield, E]]		[[Category: Oldfield, E]]
-	[[Category: ~~Ko, T.P]]~~	+	[[Category: Transferase]]
-	~~[[Category: Huang, C.H]]~~	+
-	~~[[Category: Guo, R.T]]~~	+
-	~~[[Category: Gao, J~~]]	+

OCA at 13:06, 24 December 2014

OCA — Wed, 24 Dec 2014 13:06:17 GMT

←Older revision		Revision as of 13:06, 24 December 2014
Line 6:		Line 6:

	Description: Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-789		Description: Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-789
		+	[[Category: Unreleased Structures]]
		+	[[Category: Oldfield, E]]
		+	[[Category: Ko, T.P]]
		+	[[Category: Huang, C.H]]
		+	[[Category: Guo, R.T]]
		+	[[Category: Gao, J]]

OCA at 09:41, 29 October 2014

OCA — Wed, 29 Oct 2014 09:41:58 GMT

←Older revision		Revision as of 09:41, 29 October 2014
Line 3:		Line 3:
	The entry 3wyj is ON HOLD until Paper Publication		The entry 3wyj is ON HOLD until Paper Publication

-	Authors: ~~Guo~~, R.T., Huang, C.H., ~~Gao~~, J., Ko, T.~~P., Oldfield, E~~.	+	Authors: Gao, J., Ko, T.P., Huang, C.H., Oldfield, E., Guo, R.T.

	Description: Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-789		Description: Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-789

OCA at 09:02, 20 October 2014

OCA — Mon, 20 Oct 2014 09:02:19 GMT

←Older revision		Revision as of 09:02, 20 October 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3wyj is ON HOLD	+	The entry 3wyj is ON HOLD until Paper Publication

	Authors: Guo, R.T., Huang, C.H., Gao, J., Ko, T.P., Oldfield, E.		Authors: Guo, R.T., Huang, C.H., Gao, J., Ko, T.P., Oldfield, E.

	Description: Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-789		Description: Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-789