1t47 - Revision history

OCA at 08:35, 14 February 2024

OCA — Wed, 14 Feb 2024 08:35:50 GMT

←Older revision		Revision as of 08:35, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='1t47' size='340' side='right'caption='[[1t47]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1t47' size='340' side='right'caption='[[1t47]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1t47]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"streptomyces_avermitilis"_burg_et_al._1979 "streptomyces~~ avermitilis~~" burg et al. 1979~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T47 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1T47 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1t47]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_avermitilis Streptomyces avermitilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T47 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1T47 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>~~, ~~<scene name='pdbligand=NTD:2-{HYDROXY~~[2~~-NITRO-4-(TRIFLUOROMETHYL)PHENYL]METHYLENE}CYCLOHEXANE-1,3-DIONE'>NTD</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='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>HPD, SAV5149 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~33903~~ "~~Streptomyces avermitilis~~" ~~Burg et al. 1979])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=NTD:2-{HYDROXY[2-NITRO-4-(TRIFLUOROMETHYL)PHENYL]METHYLENE}CYCLOHEXANE-1,3-DIONE'>NTD</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[http~~:~~//en.wikipedia.org/wiki/4~~-~~hydroxyphenylpyruvate_dioxygenase~~ 4-~~hydroxyphenylpyruvate dioxygenase~~], ~~with EC number [http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=1.13.11.27 1.13.11.27]~~ </~~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=1t47 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t47 OCA], [https://pdbe.org/1t47 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1t47 RCSB], [https://www.ebi.ac.uk/pdbsum/1t47 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1t47 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=1t47 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t47 OCA], [~~http~~://pdbe.org/1t47 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1t47 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1t47 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1t47 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/HPPD_STRAW HPPD_STRAW]
	== 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=1t47 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=1t47 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Di- and triketone inhibitors of (4-hydroxyphenyl)pyruvate dioxygenase (HPPD) are both effective herbicides and therapeutics. The inhibitory activity is used to halt the production of lipophilic redox cofactors in plants and also in humans to prevent accumulation of toxic metabolic byproducts that arise from specific inborn defects of tyrosine catabolism. The three-dimensional structure of the Fe(II) form of HPPD from Streptomyces avermitilis in complex with the inhibitor 2-[2-nitro-4-(triflouromethyl)benzoyl]-1,3-cyclohexanedione (NTBC) has been determined at a resolution of 2.5 A. NTBC coordinates to the active site metal ion, located at the bottom of a wide solvent-accessible cavity in the C-terminal domain of the protein. The iron is liganded in a predominantly five-coordinate, distorted square-pyramidal arrangement in which Glu349, His187, and His270 are protein-derived ligands and two other ligands are from the 5' and 7' oxygens of NTBC. There is a low-occupancy water molecule in the sixth coordination site in one of the protomers. The distance to His270 is unusually long at 2.5 A, and its orientation is somewhat distorted from ideal ligand geometry to within 2.8 A of the inhibitor nitro group. In contrast to the tetrameric quartenary structure observed for HPPD from other bacterial sources, the asymmetric unit is composed of two weakly associated protomers with a buried surface area of 1266 A(2) and a total of 12 hydrogen-bonding and no electrostatic interactions. The overall tertiary structure is similar to that of HPPD from Pseudomonas fluorescens (Serre et al., (1999) Structure 7, 977-988), although the position of the C-terminal alpha-helix is dramatically shifted. This C-terminal alpha-helix provides Phe364, which in combination with Phe336 sandwiches the phenyl ring of the bound NTBC; no other significant hydrogen-bonding or charge-pairing interactions are observed. Moreover, the structure reveals that, with the exception of Val189, NTBC makes contacts to only fully conserved amino acids. The combination of bidentate metal-ion coordination and pi-stacked aromatic rings is suggestive of a binding mode for the substrate and/or a transition state, which may be the origin of the exceedingly high affinity these inhibitors have for HPPD.
-
-	Structure of the ferrous form of (4-hydroxyphenyl)pyruvate dioxygenase from Streptomyces avermitilis in complex with the therapeutic herbicide, NTBC.,Brownlee JM, Johnson-Winters K, Harrison DH, Moran GR Biochemistry. 2004 Jun 1;43(21):6370-7. PMID:15157070<ref>PMID:15157070</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1t47" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
-	*[[Crystal structure of protein from Staphylococcus aureus\|Crystal structure of protein from Staphylococcus aureus]]
	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]		*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Streptomyces avermitilis burg et al. 1979]]
-	[[Category: 4-hydroxyphenylpyruvate dioxygenase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Brownlee, J]]	+	[[Category: Streptomyces avermitilis]]
-	[[Category: Harrison~~, D H.T~~]]	+	[[Category: Brownlee J]]
-	[[Category: Johnson-Winters, K]]	+	[[Category: Harrison DHT]]
-	[[Category: Moran~~, G R]]~~	+	[[Category: Johnson-Winters K]]
-	~~[[Category: Dioxygenase]]~~	+	[[Category: Moran GR]]
-	~~[[Category: Iron]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Triketone inhibitor~~]]	+

OCA at 11:41, 24 December 2020

OCA — Thu, 24 Dec 2020 11:41:47 GMT

←Older revision		Revision as of 11:41, 24 December 2020
Line 1:		Line 1:

	==Structure of fe2-HPPD bound to NTBC==		==Structure of fe2-HPPD bound to NTBC==
-	<StructureSection load='1t47' size='340' side='right' caption='[[1t47]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='1t47' size='340' side='right'caption='[[1t47]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1t47]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"streptomyces_avermitilis"_burg_et_al._1979 "streptomyces avermitilis" burg et al. 1979]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T47 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1T47 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1t47]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"streptomyces_avermitilis"_burg_et_al._1979 "streptomyces avermitilis" burg et al. 1979]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T47 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1T47 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=NTD:2-{HYDROXY[2-NITRO-4-(TRIFLUOROMETHYL)PHENYL]METHYLENE}CYCLOHEXANE-1,3-DIONE'>NTD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=NTD:2-{HYDROXY[2-NITRO-4-(TRIFLUOROMETHYL)PHENYL]METHYLENE}CYCLOHEXANE-1,3-DIONE'>NTD</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HPD, SAV5149 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33903 "Streptomyces avermitilis" Burg et al. 1979])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HPD, SAV5149 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33903 "Streptomyces avermitilis" Burg et al. 1979])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxyphenylpyruvate_dioxygenase 4-hydroxyphenylpyruvate dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.27 1.13.11.27] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxyphenylpyruvate_dioxygenase 4-hydroxyphenylpyruvate dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.27 1.13.11.27] </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=1t47 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t47 OCA], [http://pdbe.org/1t47 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t47 RCSB], [http://www.ebi.ac.uk/pdbsum/1t47 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1t47 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=1t47 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t47 OCA], [http://pdbe.org/1t47 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t47 RCSB], [http://www.ebi.ac.uk/pdbsum/1t47 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1t47 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 31:		Line 31:
	==See Also==		==See Also==
	*[[Crystal structure of protein from Staphylococcus aureus\|Crystal structure of protein from Staphylococcus aureus]]		*[[Crystal structure of protein from Staphylococcus aureus\|Crystal structure of protein from Staphylococcus aureus]]
-	*[[Dioxygenase\|Dioxygenase]]	+	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 38:		Line 38:
	[[Category: Streptomyces avermitilis burg et al. 1979]]		[[Category: Streptomyces avermitilis burg et al. 1979]]
	[[Category: 4-hydroxyphenylpyruvate dioxygenase]]		[[Category: 4-hydroxyphenylpyruvate dioxygenase]]
		+	[[Category: Large Structures]]
	[[Category: Brownlee, J]]		[[Category: Brownlee, J]]
	[[Category: Harrison, D H.T]]		[[Category: Harrison, D H.T]]

OCA at 07:26, 14 March 2018

OCA — Wed, 14 Mar 2018 07:26:49 GMT

←Older revision		Revision as of 07:26, 14 March 2018
Line 1:		Line 1:
		+
	==Structure of fe2-HPPD bound to NTBC==		==Structure of fe2-HPPD bound to NTBC==
	<StructureSection load='1t47' size='340' side='right' caption='[[1t47]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1t47' size='340' side='right' caption='[[1t47]], [[Resolution\|resolution]] 2.50Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HPD, SAV5149 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33903 "Streptomyces avermitilis" Burg et al. 1979])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HPD, SAV5149 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33903 "Streptomyces avermitilis" Burg et al. 1979])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxyphenylpyruvate_dioxygenase 4-hydroxyphenylpyruvate dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.27 1.13.11.27] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxyphenylpyruvate_dioxygenase 4-hydroxyphenylpyruvate dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.27 1.13.11.27] </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=1t47 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t47 OCA], [http://pdbe.org/1t47 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t47 RCSB], [http://www.ebi.ac.uk/pdbsum/1t47 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=1t47 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t47 OCA], [http://pdbe.org/1t47 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t47 RCSB], [http://www.ebi.ac.uk/pdbsum/1t47 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1t47 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/t4/1t47_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/t4/1t47_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 16:17, 9 February 2016

OCA — Tue, 09 Feb 2016 16:17:01 GMT

←Older revision		Revision as of 16:17, 9 February 2016
Line 16:		Line 16:
	<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=1t47 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:56, 10 September 2015

OCA — Thu, 10 Sep 2015 23:56:48 GMT

←Older revision		Revision as of 23:56, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1t47' size='340' side='right' caption='[[1t47]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1t47' size='340' side='right' caption='[[1t47]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1t47]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Streptomyces_avermitilis Streptomyces~~ avermitilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T47 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T47 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1t47]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"streptomyces_avermitilis"_burg_et_al._1979 "streptomyces avermitilis" burg et al. 1979]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T47 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T47 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=NTD:2-{HYDROXY[2-NITRO-4-(TRIFLUOROMETHYL)PHENYL]METHYLENE}CYCLOHEXANE-1,3-DIONE'>NTD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=NTD:2-{HYDROXY[2-NITRO-4-(TRIFLUOROMETHYL)PHENYL]METHYLENE}CYCLOHEXANE-1,3-DIONE'>NTD</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HPD, SAV5149 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33903 Streptomyces avermitilis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HPD, SAV5149 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33903 "Streptomyces avermitilis" Burg et al. 1979])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxyphenylpyruvate_dioxygenase 4-hydroxyphenylpyruvate dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.27 1.13.11.27] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxyphenylpyruvate_dioxygenase 4-hydroxyphenylpyruvate dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.27 1.13.11.27] </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=1t47 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t47 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t47 RCSB], [http://www.ebi.ac.uk/pdbsum/1t47 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=1t47 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t47 OCA], [http://pdbe.org/1t47 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t47 RCSB], [http://www.ebi.ac.uk/pdbsum/1t47 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 26:
	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 1t47" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Streptomyces avermitilis burg et al. 1979]]
	[[Category: 4-hydroxyphenylpyruvate dioxygenase]]		[[Category: 4-hydroxyphenylpyruvate dioxygenase]]
-	[[Category: Streptomyces avermitilis]]
	[[Category: Brownlee, J]]		[[Category: Brownlee, J]]
	[[Category: Harrison, D H.T]]		[[Category: Harrison, D H.T]]

OCA at 06:38, 6 January 2015

OCA — Tue, 06 Jan 2015 06:38:41 GMT

←Older revision		Revision as of 06:38, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1t47]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_avermitilis Streptomyces avermitilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T47 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T47 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1t47]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_avermitilis Streptomyces avermitilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T47 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T47 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=NTD:2-{HYDROXY[2-NITRO-4-(TRIFLUOROMETHYL)PHENYL]METHYLENE}CYCLOHEXANE-1,3-DIONE'>NTD</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=NTD:2-{HYDROXY[2-NITRO-4-(TRIFLUOROMETHYL)PHENYL]METHYLENE}CYCLOHEXANE-1,3-DIONE'>NTD</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HPD, SAV5149 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33903 Streptomyces avermitilis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HPD, SAV5149 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33903 Streptomyces avermitilis])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxyphenylpyruvate_dioxygenase 4-hydroxyphenylpyruvate dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.27 1.13.11.27] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxyphenylpyruvate_dioxygenase 4-hydroxyphenylpyruvate dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.27 1.13.11.27] </span></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=1t47 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t47 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t47 RCSB], [http://www.ebi.ac.uk/pdbsum/1t47 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=1t47 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t47 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t47 RCSB], [http://www.ebi.ac.uk/pdbsum/1t47 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	[[Category: 4-hydroxyphenylpyruvate dioxygenase]]		[[Category: 4-hydroxyphenylpyruvate dioxygenase]]
	[[Category: Streptomyces avermitilis]]		[[Category: Streptomyces avermitilis]]
-	[[Category: Brownlee, J.]]	+	[[Category: Brownlee, J]]
-	[[Category: Harrison, D H.T.]]	+	[[Category: Harrison, D H.T]]
-	[[Category: Johnson-Winters, K.]]	+	[[Category: Johnson-Winters, K]]
-	[[Category: Moran, G R.]]	+	[[Category: Moran, G R]]
	[[Category: Dioxygenase]]		[[Category: Dioxygenase]]
	[[Category: Iron]]		[[Category: Iron]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Triketone inhibitor]]		[[Category: Triketone inhibitor]]

OCA at 19:22, 29 September 2014

OCA — Mon, 29 Sep 2014 19:22:25 GMT

←Older revision		Revision as of 19:22, 29 September 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1t47\| PDB=1t47 \| SCENE= }}~~	+	==Structure of fe2-HPPD bound to NTBC==
-	===Structure of fe2-HPPD bound to NTBC===	+	<StructureSection load='1t47' size='340' side='right' caption='[[1t47]], [[Resolution\|resolution]] 2.50Å' scene=''>
-	{~~{ABSTRACT_PUBMED_15157070}~~}	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1t47]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_avermitilis Streptomyces avermitilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T47 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T47 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=NTD:2-{HYDROXY[2-NITRO-4-(TRIFLUOROMETHYL)PHENYL]METHYLENE}CYCLOHEXANE-1,3-DIONE'>NTD</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HPD, SAV5149 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33903 Streptomyces avermitilis])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxyphenylpyruvate_dioxygenase 4-hydroxyphenylpyruvate dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.27 1.13.11.27] </span></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=1t47 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t47 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t47 RCSB], [http://www.ebi.ac.uk/pdbsum/1t47 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/t4/1t47_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 ==
		+	Di- and triketone inhibitors of (4-hydroxyphenyl)pyruvate dioxygenase (HPPD) are both effective herbicides and therapeutics. The inhibitory activity is used to halt the production of lipophilic redox cofactors in plants and also in humans to prevent accumulation of toxic metabolic byproducts that arise from specific inborn defects of tyrosine catabolism. The three-dimensional structure of the Fe(II) form of HPPD from Streptomyces avermitilis in complex with the inhibitor 2-[2-nitro-4-(triflouromethyl)benzoyl]-1,3-cyclohexanedione (NTBC) has been determined at a resolution of 2.5 A. NTBC coordinates to the active site metal ion, located at the bottom of a wide solvent-accessible cavity in the C-terminal domain of the protein. The iron is liganded in a predominantly five-coordinate, distorted square-pyramidal arrangement in which Glu349, His187, and His270 are protein-derived ligands and two other ligands are from the 5' and 7' oxygens of NTBC. There is a low-occupancy water molecule in the sixth coordination site in one of the protomers. The distance to His270 is unusually long at 2.5 A, and its orientation is somewhat distorted from ideal ligand geometry to within 2.8 A of the inhibitor nitro group. In contrast to the tetrameric quartenary structure observed for HPPD from other bacterial sources, the asymmetric unit is composed of two weakly associated protomers with a buried surface area of 1266 A(2) and a total of 12 hydrogen-bonding and no electrostatic interactions. The overall tertiary structure is similar to that of HPPD from Pseudomonas fluorescens (Serre et al., (1999) Structure 7, 977-988), although the position of the C-terminal alpha-helix is dramatically shifted. This C-terminal alpha-helix provides Phe364, which in combination with Phe336 sandwiches the phenyl ring of the bound NTBC; no other significant hydrogen-bonding or charge-pairing interactions are observed. Moreover, the structure reveals that, with the exception of Val189, NTBC makes contacts to only fully conserved amino acids. The combination of bidentate metal-ion coordination and pi-stacked aromatic rings is suggestive of a binding mode for the substrate and/or a transition state, which may be the origin of the exceedingly high affinity these inhibitors have for HPPD.

-	~~==About this~~ Structure==	+	Structure of the ferrous form of (4-hydroxyphenyl)pyruvate dioxygenase from Streptomyces avermitilis in complex with the therapeutic herbicide, NTBC.,Brownlee JM, Johnson-Winters K, Harrison DH, Moran GR Biochemistry. 2004 Jun 1;43(21):6370-7. PMID:15157070<ref>PMID:15157070</ref>
-	~~[[1t47]] is a 2 chain structure with sequence~~ from ~~[http://en.wikipedia.org/wiki/Streptomyces_avermitilis~~ Streptomyces avermitilis]. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=1T47 OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[Crystal structure of protein from Staphylococcus aureus\|Crystal structure of protein from Staphylococcus aureus]]		*[[Crystal structure of protein from Staphylococcus aureus\|Crystal structure of protein from Staphylococcus aureus]]
-		+	*[[Dioxygenase\|Dioxygenase]]
-	==~~Reference~~==	+	== References ==
-	<~~ref group="xtra">PMID:015157070<~~/~~ref~~><~~references group="xtra"~~/>	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: 4-hydroxyphenylpyruvate dioxygenase]]		[[Category: 4-hydroxyphenylpyruvate dioxygenase]]
	[[Category: Streptomyces avermitilis]]		[[Category: Streptomyces avermitilis]]

OCA at 10:14, 11 March 2013

OCA — Mon, 11 Mar 2013 10:14:48 GMT

←Older revision		Revision as of 10:14, 11 March 2013
Line 1:		Line 1:
-	[[Image:1t47.png\|left\|200px]]
-
	{{STRUCTURE_1t47\| PDB=1t47 \| SCENE= }}		{{STRUCTURE_1t47\| PDB=1t47 \| SCENE= }}
-
	===Structure of fe2-HPPD bound to NTBC===		===Structure of fe2-HPPD bound to NTBC===
-
	{{ABSTRACT_PUBMED_15157070}}		{{ABSTRACT_PUBMED_15157070}}

OCA: Protected "1t47" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 12:23:35 GMT

Protected "1t47" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:23, 5 January 2013

OCA at 12:23, 5 January 2013

OCA — Sat, 05 Jan 2013 12:23:30 GMT

←Older revision		Revision as of 12:23, 5 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1t47.png\|left\|200px]]		[[Image:1t47.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1t47", 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_1t47\| PDB=1t47 \| SCENE= }}		{{STRUCTURE_1t47\| PDB=1t47 \| SCENE= }}

	===Structure of fe2-HPPD bound to NTBC===		===Structure of fe2-HPPD bound to NTBC===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15157070}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15157070 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15157070}}		{{ABSTRACT_PUBMED_15157070}}

	==About this Structure==		==About this Structure==
-	~~1T47~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Streptomyces_avermitilis Streptomyces avermitilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T47 OCA].	+	[[1t47]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_avermitilis Streptomyces avermitilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T47 OCA].
		+
		+	==See Also==
		+	*[[Crystal structure of protein from Staphylococcus aureus\|Crystal structure of protein from Staphylococcus aureus]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15157070~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015157070</ref><references group="xtra"/>
	[[Category: 4-hydroxyphenylpyruvate dioxygenase]]		[[Category: 4-hydroxyphenylpyruvate dioxygenase]]
	[[Category: Streptomyces avermitilis]]		[[Category: Streptomyces avermitilis]]
Line 32:		Line 23:
	[[Category: Dioxygenase]]		[[Category: Dioxygenase]]
	[[Category: Iron]]		[[Category: Iron]]
		+	[[Category: Oxidoreductase]]
	[[Category: Triketone inhibitor]]		[[Category: Triketone inhibitor]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 11:07:08 2009''