1u1v - Revision history

OCA at 08:46, 1 May 2024

OCA — Wed, 01 May 2024 08:46:09 GMT

←Older revision		Revision as of 08:46, 1 May 2024
Line 3:		Line 3:
	<StructureSection load='1u1v' size='340' side='right'caption='[[1u1v]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1u1v' size='340' side='right'caption='[[1u1v]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1u1v]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus~~ fluorescens ~~liquefaciens" flugge 1886~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U1V OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1U1V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1u1v]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U1V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U1V FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.7Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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;'>[[1bwz\|1bwz]]~~, ~~[[1sdj\|1sdj]], [[1s7j\|1s7j]], [[1u1w\|1u1w]], [[1u1x\|1u1x]]~~<~~/div></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=1u1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u1v OCA], [https://pdbe.org/1u1v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1u1v RCSB], [https://www.ebi.ac.uk/pdbsum/1u1v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1u1v ProSAT]</span></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">phzF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])~~</td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1u1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u1v OCA], [~~http~~://pdbe.org/1u1v PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1u1v RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1u1v PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1u1v ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PHZF_PSEFL PHZF_PSEFL]] Isomerase that catalyzes the condensation of two molecules of trans-2,3-dihydro-3-hydroxyanthranilic acid (DHHA) into the phenazine ring system. The final product is not yet known.<ref>PMID:19053436</ref> <ref>PMID:15545603</ref>	+	[https://www.uniprot.org/uniprot/PHZF_PSEFL PHZF_PSEFL] Isomerase that catalyzes the condensation of two molecules of trans-2,3-dihydro-3-hydroxyanthranilic acid (DHHA) into the phenazine ring system. The final product is not yet known.<ref>PMID:19053436</ref> <ref>PMID:15545603</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1u1v ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1u1v ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Phenazines produced by Pseudomonas and Streptomyces spp. are heterocyclic nitrogen-containing metabolites with antibiotic, antitumor, and antiparasitic activity. The antibiotic properties of pyocyanin, produced by Pseudomonas aeruginosa, were recognized in the 1890s, although this blue phenazine is now known to be a virulence factor in human disease. Despite their biological significance, the biosynthesis of phenazines is not fully understood. Here we present structural and functional studies of PhzF, an enzyme essential for phenazine synthesis in Pseudomonas spp. PhzF shares topology with diaminopimelate epimerase DapF but lacks the same catalytic residues. The structure of PhzF in complex with its substrate, trans-2,3-dihydro-3-hydroxyanthranilic acid, suggests that it is an isomerase using the conserved glutamate E45 to abstract a proton from C3 of the substrate. The proton is returned to C1 of the substrate after rearrangement of the double-bond system, yielding an enol that converts to the corresponding ketone. PhzF is a dimer that may be bifunctional, providing a shielded cavity for ketone dimerization via double Schiff-base formation to produce the phenazine scaffold. Our proposed mechanism is supported by mass and NMR spectroscopy. The results are discussed in the context of related structures and protein sequences of unknown biochemical function.
-
-	Structure and function of the phenazine biosynthetic protein PhzF from Pseudomonas fluorescens.,Blankenfeldt W, Kuzin AP, Skarina T, Korniyenko Y, Tong L, Bayer P, Janning P, Thomashow LS, Mavrodi DV Proc Natl Acad Sci U S A. 2004 Nov 23;101(47):16431-6. Epub 2004 Nov 15. PMID:15545603<ref>PMID:15545603</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1u1v" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus fluorescens liquefaciens flugge 1886]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bayer, P]]	+	[[Category: Pseudomonas fluorescens]]
-	[[Category: Blankenfeldt, W]]	+	[[Category: Bayer P]]
-	[[Category: Janning, P]]	+	[[Category: Blankenfeldt W]]
-	[[Category: Korniyenko, Y]]	+	[[Category: Janning P]]
-	[[Category: Kuzin~~, A P~~]]	+	[[Category: Korniyenko Y]]
-	[[Category: Mavrodi~~, D V~~]]	+	[[Category: Kuzin AP]]
-	[[Category: Skarina, T]]	+	[[Category: Mavrodi DV]]
-	[[Category: Thomashow~~, L S~~]]	+	[[Category: Skarina T]]
-	[[Category: Tong, L]]	+	[[Category: Thomashow LS]]
-	~~[[Category: Acid/base catalysis]]~~	+	[[Category: Tong L]]
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Open form]]~~	+
-	~~[[Category: Phenazine biosynthesis~~]]	+

OCA at 07:18, 30 December 2020

OCA — Wed, 30 Dec 2020 07:18:54 GMT

←Older revision		Revision as of 07:18, 30 December 2020
Line 1:		Line 1:

	==Structure and function of phenazine-biosynthesis protein PhzF from Pseudomonas fluorescens 2-79==		==Structure and function of phenazine-biosynthesis protein PhzF from Pseudomonas fluorescens 2-79==
-	<StructureSection load='1u1v' size='340' side='right' caption='[[1u1v]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='1u1v' size='340' side='right'caption='[[1u1v]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1u1v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus fluorescens liquefaciens" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U1V OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1U1V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1u1v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus fluorescens liquefaciens" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U1V OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1U1V FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bwz\|1bwz]], [[1sdj\|1sdj]], [[1s7j\|1s7j]], [[1u1w\|1u1w]], [[1u1x\|1u1x]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1bwz\|1bwz]], [[1sdj\|1sdj]], [[1s7j\|1s7j]], [[1u1w\|1u1w]], [[1u1x\|1u1x]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">phzF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">phzF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</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=1u1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u1v OCA], [http://pdbe.org/1u1v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u1v RCSB], [http://www.ebi.ac.uk/pdbsum/1u1v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1u1v ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1u1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u1v OCA], [http://pdbe.org/1u1v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u1v RCSB], [http://www.ebi.ac.uk/pdbsum/1u1v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1u1v ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 36:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus fluorescens liquefaciens flugge 1886]]		[[Category: Bacillus fluorescens liquefaciens flugge 1886]]
		+	[[Category: Large Structures]]
	[[Category: Bayer, P]]		[[Category: Bayer, P]]
	[[Category: Blankenfeldt, W]]		[[Category: Blankenfeldt, W]]

OCA at 08:56, 21 March 2018

OCA — Wed, 21 Mar 2018 08:56:47 GMT

←Older revision		Revision as of 08:56, 21 March 2018
Line 1:		Line 1:
		+
	==Structure and function of phenazine-biosynthesis protein PhzF from Pseudomonas fluorescens 2-79==		==Structure and function of phenazine-biosynthesis protein PhzF from Pseudomonas fluorescens 2-79==
	<StructureSection load='1u1v' size='340' side='right' caption='[[1u1v]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1u1v' size='340' side='right' caption='[[1u1v]], [[Resolution\|resolution]] 1.70Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bwz\|1bwz]], [[1sdj\|1sdj]], [[1s7j\|1s7j]], [[1u1w\|1u1w]], [[1u1x\|1u1x]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bwz\|1bwz]], [[1sdj\|1sdj]], [[1s7j\|1s7j]], [[1u1w\|1u1w]], [[1u1x\|1u1x]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">phzF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">phzF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</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=1u1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u1v OCA], [http://pdbe.org/1u1v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u1v RCSB], [http://www.ebi.ac.uk/pdbsum/1u1v 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=1u1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u1v OCA], [http://pdbe.org/1u1v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u1v RCSB], [http://www.ebi.ac.uk/pdbsum/1u1v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1u1v ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/u1/1u1v_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/u1/1u1v_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 12:03, 8 February 2016

OCA — Mon, 08 Feb 2016 12:03:36 GMT

←Older revision		Revision as of 12:03, 8 February 2016
Line 19:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1u1v ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 11:23, 10 September 2015

OCA — Thu, 10 Sep 2015 11:23:38 GMT

←Older revision		Revision as of 11:23, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1u1v' size='340' side='right' caption='[[1u1v]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1u1v' size='340' side='right' caption='[[1u1v]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1u1v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pseudomonas_fluorescens Pseudomonas~~ fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U1V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U1V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1u1v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus fluorescens liquefaciens" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U1V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U1V FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bwz\|1bwz]], [[1sdj\|1sdj]], [[1s7j\|1s7j]], [[1u1w\|1u1w]], [[1u1x\|1u1x]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bwz\|1bwz]], [[1sdj\|1sdj]], [[1s7j\|1s7j]], [[1u1w\|1u1w]], [[1u1x\|1u1x]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">phzF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 ~~Pseudomonas~~ fluorescens])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">phzF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</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=1u1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u1v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1u1v RCSB], [http://www.ebi.ac.uk/pdbsum/1u1v 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=1u1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u1v OCA], [http://pdbe.org/1u1v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u1v RCSB], [http://www.ebi.ac.uk/pdbsum/1u1v PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 29:
	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 1u1v" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pseudomonas~~ fluorescens]]	+	[[Category: Bacillus fluorescens liquefaciens flugge 1886]]
	[[Category: Bayer, P]]		[[Category: Bayer, P]]
	[[Category: Blankenfeldt, W]]		[[Category: Blankenfeldt, W]]

OCA at 23:10, 24 December 2014

OCA — Wed, 24 Dec 2014 23:10:25 GMT

←Older revision		Revision as of 23:10, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1u1v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U1V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U1V FirstGlance]. <br>		<table><tr><td colspan='2'>[[1u1v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U1V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U1V FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bwz\|1bwz]], [[1sdj\|1sdj]], [[1s7j\|1s7j]], [[1u1w\|1u1w]], [[1u1x\|1u1x]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bwz\|1bwz]], [[1sdj\|1sdj]], [[1s7j\|1s7j]], [[1u1w\|1u1w]], [[1u1x\|1u1x]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">phzF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 Pseudomonas fluorescens])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">phzF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 Pseudomonas fluorescens])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1u1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u1v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1u1v RCSB], [http://www.ebi.ac.uk/pdbsum/1u1v 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=1u1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u1v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1u1v RCSB], [http://www.ebi.ac.uk/pdbsum/1u1v PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PHZF_PSEFL PHZF_PSEFL]] Isomerase that catalyzes the condensation of two molecules of trans-2,3-dihydro-3-hydroxyanthranilic acid (DHHA) into the phenazine ring system. The final product is not yet known.<ref>PMID:19053436</ref> <ref>PMID:15545603</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Pseudomonas fluorescens]]		[[Category: Pseudomonas fluorescens]]
-	[[Category: Bayer, P.]]	+	[[Category: Bayer, P]]
-	[[Category: Blankenfeldt, W.]]	+	[[Category: Blankenfeldt, W]]
-	[[Category: Janning, P.]]	+	[[Category: Janning, P]]
-	[[Category: Korniyenko, Y.]]	+	[[Category: Korniyenko, Y]]
-	[[Category: Kuzin, A P.]]	+	[[Category: Kuzin, A P]]
-	[[Category: Mavrodi, D V.]]	+	[[Category: Mavrodi, D V]]
-	[[Category: Skarina, T.]]	+	[[Category: Skarina, T]]
-	[[Category: Thomashow, L S.]]	+	[[Category: Thomashow, L S]]
-	[[Category: Tong, L.]]	+	[[Category: Tong, L]]
	[[Category: Acid/base catalysis]]		[[Category: Acid/base catalysis]]
	[[Category: Isomerase]]		[[Category: Isomerase]]

OCA at 19:13, 29 September 2014

OCA — Mon, 29 Sep 2014 19:13:47 GMT

←Older revision		Revision as of 19:13, 29 September 2014
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-	[[~~Image:~~1u1v.~~png~~\|~~left~~\|200px]]	+	==Structure and function of phenazine-biosynthesis protein PhzF from Pseudomonas fluorescens 2-79==
		+	<StructureSection load='1u1v' size='340' side='right' caption='[[1u1v]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1u1v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U1V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U1V FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bwz\|1bwz]], [[1sdj\|1sdj]], [[1s7j\|1s7j]], [[1u1w\|1u1w]], [[1u1x\|1u1x]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">phzF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 Pseudomonas fluorescens])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1u1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u1v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1u1v RCSB], [http://www.ebi.ac.uk/pdbsum/1u1v PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/u1/1u1v_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Phenazines produced by Pseudomonas and Streptomyces spp. are heterocyclic nitrogen-containing metabolites with antibiotic, antitumor, and antiparasitic activity. The antibiotic properties of pyocyanin, produced by Pseudomonas aeruginosa, were recognized in the 1890s, although this blue phenazine is now known to be a virulence factor in human disease. Despite their biological significance, the biosynthesis of phenazines is not fully understood. Here we present structural and functional studies of PhzF, an enzyme essential for phenazine synthesis in Pseudomonas spp. PhzF shares topology with diaminopimelate epimerase DapF but lacks the same catalytic residues. The structure of PhzF in complex with its substrate, trans-2,3-dihydro-3-hydroxyanthranilic acid, suggests that it is an isomerase using the conserved glutamate E45 to abstract a proton from C3 of the substrate. The proton is returned to C1 of the substrate after rearrangement of the double-bond system, yielding an enol that converts to the corresponding ketone. PhzF is a dimer that may be bifunctional, providing a shielded cavity for ketone dimerization via double Schiff-base formation to produce the phenazine scaffold. Our proposed mechanism is supported by mass and NMR spectroscopy. The results are discussed in the context of related structures and protein sequences of unknown biochemical function.

-	~~{{STRUCTURE_1u1v\| PDB=1u1v \| SCENE= }}~~	+	Structure and function of the phenazine biosynthetic protein PhzF from Pseudomonas fluorescens.,Blankenfeldt W, Kuzin AP, Skarina T, Korniyenko Y, Tong L, Bayer P, Janning P, Thomashow LS, Mavrodi DV Proc Natl Acad Sci U S A. 2004 Nov 23;101(47):16431-6. Epub 2004 Nov 15. PMID:15545603<ref>PMID:15545603</ref>

-	~~===Structure and function~~ of ~~phenazine-biosynthesis protein PhzF from Pseudomonas fluorescens 2-79===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15545603}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1u1v]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1U1V OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015545603<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Pseudomonas fluorescens]]		[[Category: Pseudomonas fluorescens]]
	[[Category: Bayer, P.]]		[[Category: Bayer, P.]]

OCA: Protected "1u1v" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 12:09:12 GMT

Protected "1u1v" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:09, 5 January 2013

OCA at 12:09, 5 January 2013

OCA — Sat, 05 Jan 2013 12:09:10 GMT

←Older revision		Revision as of 12:09, 5 January 2013
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-	{{Seed}}
	[[Image:1u1v.png\|left\|200px]]		[[Image:1u1v.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1u1v", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1u1v\| PDB=1u1v \| SCENE= }}		{{STRUCTURE_1u1v\| PDB=1u1v \| SCENE= }}

	===Structure and function of phenazine-biosynthesis protein PhzF from Pseudomonas fluorescens 2-79===		===Structure and function of phenazine-biosynthesis protein PhzF from Pseudomonas fluorescens 2-79===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15545603}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15545603 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_15545603}}		{{ABSTRACT_PUBMED_15545603}}

	==About this Structure==		==About this Structure==
-	~~1U1V~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U1V OCA].	+	[[1u1v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U1V OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15545603~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015545603</ref><references group="xtra"/>
	[[Category: Pseudomonas fluorescens]]		[[Category: Pseudomonas fluorescens]]
	[[Category: Bayer, P.]]		[[Category: Bayer, P.]]
Line 36:		Line 24:
	[[Category: Acid/base catalysis]]		[[Category: Acid/base catalysis]]
	[[Category: Isomerase]]		[[Category: Isomerase]]
		+	[[Category: Lyase]]
	[[Category: Open form]]		[[Category: Open form]]
	[[Category: Phenazine biosynthesis]]		[[Category: Phenazine biosynthesis]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 21:51:13 2009''

OCA at 19:51, 16 February 2009

OCA — Mon, 16 Feb 2009 19:51:16 GMT

←Older revision		Revision as of 19:51, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1U1V is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U1V OCA].	+	1U1V is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U1V OCA].

	==Reference==		==Reference==
-	Structure and function of the phenazine biosynthetic protein PhzF from Pseudomonas fluorescens., Blankenfeldt W, Kuzin AP, Skarina T, Korniyenko Y, Tong L, Bayer P, Janning P, Thomashow LS, Mavrodi DV, Proc Natl Acad Sci U S A. 2004 Nov 23;101(47):16431-6. Epub 2004 Nov 15. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/15545603 15545603]~~	+	<ref group="xtra">PMID:15545603</ref><references group="xtra"/>
	[[Category: Pseudomonas fluorescens]]		[[Category: Pseudomonas fluorescens]]
-	[[Category: Single protein]]
	[[Category: Bayer, P.]]		[[Category: Bayer, P.]]
	[[Category: Blankenfeldt, W.]]		[[Category: Blankenfeldt, W.]]
Line 40:		Line 39:
	[[Category: Phenazine biosynthesis]]		[[Category: Phenazine biosynthesis]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon ~~Jul 28 02~~:48:~~26 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 21:51:13 2009''