1k0j - Revision history

OCA at 07:43, 7 February 2024

OCA — Wed, 07 Feb 2024 07:43:24 GMT

←Older revision		Revision as of 07:43, 7 February 2024
Line 3:		Line 3:
	<StructureSection load='1k0j' size='340' side='right'caption='[[1k0j]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1k0j' size='340' side='right'caption='[[1k0j]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1k0j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K0J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K0J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1k0j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K0J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K0J FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FAD:FLAVIN~~-~~ADENINE+DINUCLEOTIDE'>FAD</scene>~~, ~~<scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</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]] 2.2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1iuw\|1iuw]], [[1k0i\|1k0i]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/4-hydroxybenzoate_3-monooxygenase 4-hydroxybenzoate 3-monooxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.2 1.14.13.2]~~ </~~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=1k0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k0j OCA], [https://pdbe.org/1k0j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k0j RCSB], [https://www.ebi.ac.uk/pdbsum/1k0j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k0j 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=1k0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k0j OCA], [https://pdbe.org/1k0j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k0j RCSB], [https://www.ebi.ac.uk/pdbsum/1k0j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k0j ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PHHY_PSEAE PHHY_PSEAE]
	== 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=1k0j 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=1k0j ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	para-Hydroxybenzoate hydroxylase catalyzes a two-step reaction that demands precise control of solvent access to the catalytic site. The first step of the reaction, reduction of flavin by NADPH, requires access to solvent. The second step, oxygenation of reduced flavin to a flavin C4a-hydroperoxide that transfers the hydroxyl group to the substrate, requires that solvent be excluded to prevent breakdown of the hydroperoxide to oxidized flavin and hydrogen peroxide. These conflicting requirements are met by the coordination of multiple movements involving the protein, the two cofactors, and the substrate. Here, using the R220Q mutant form of para-hydroxybenzoate hydroxylase, we show that in the absence of substrate, the large beta alpha beta domain (residues 1-180) and the smaller sheet domain (residues 180-270) separate slightly, and the flavin swings out to a more exposed position to open an aqueous channel from the solvent to the protein interior. Substrate entry occurs by first binding at a surface site and then sliding into the protein interior. In our study of this mutant, the structure of the complex with pyridine nucleotide was obtained. This cofactor binds in an extended conformation at the enzyme surface in a groove that crosses the binding site of FAD. We postulate that for stereospecific reduction, the flavin swings to an out position and NADPH assumes a folded conformation that brings its nicotinamide moiety into close contact with the isoalloxazine moiety of the flavin. This work clearly shows how complex dynamics can play a central role in catalysis by enzymes.
-
-	Protein and ligand dynamics in 4-hydroxybenzoate hydroxylase.,Wang J, Ortiz-Maldonado M, Entsch B, Massey V, Ballou D, Gatti DL Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):608-13. PMID:11805318<ref>PMID:11805318</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1k0j" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Hydroxylases 3D structures\|Hydroxylases 3D structures]]		*[[Hydroxylases 3D structures\|Hydroxylases 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: 4-hydroxybenzoate 3-monooxygenase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ballou, D]]	+	[[Category: Pseudomonas aeruginosa]]
-	[[Category: Entsch, B]]	+	[[Category: Ballou D]]
-	[[Category: Gatti~~, D L~~]]	+	[[Category: Entsch B]]
-	[[Category: Ortiz-Maldonado, M]]	+	[[Category: Gatti DL]]
-	[[Category: Wang, J]]	+	[[Category: Ortiz-Maldonado M]]
-	~~[[Category: Fad]]~~	+	[[Category: Wang J]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Nadph]]~~	+
-	~~[[Category: Phbh~~]]	+

OCA at 06:47, 11 August 2021

OCA — Wed, 11 Aug 2021 06:47:35 GMT

←Older revision		Revision as of 06:47, 11 August 2021
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	<StructureSection load='1k0j' size='340' side='right'caption='[[1k0j]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1k0j' size='340' side='right'caption='[[1k0j]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1k0j]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K0J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1K0J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1k0j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K0J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K0J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</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=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</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">[[1iuw\|1iuw]], [[1k0i\|1k0i]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1iuw\|1iuw]], [[1k0i\|1k0i]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/4-hydroxybenzoate_3-monooxygenase 4-hydroxybenzoate 3-monooxygenase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.2 1.14.13.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/4-hydroxybenzoate_3-monooxygenase 4-hydroxybenzoate 3-monooxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.2 1.14.13.2] </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=1k0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k0j OCA], [~~http~~://pdbe.org/1k0j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1k0j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1k0j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1k0j 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=1k0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k0j OCA], [https://pdbe.org/1k0j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k0j RCSB], [https://www.ebi.ac.uk/pdbsum/1k0j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k0j ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 09:27, 6 November 2019

OCA — Wed, 06 Nov 2019 09:27:46 GMT

←Older revision		Revision as of 09:27, 6 November 2019
Line 1:		Line 1:

	==Pseudomonas aeruginosa phbh R220Q in complex with NADPH and free of p-OHB==		==Pseudomonas aeruginosa phbh R220Q in complex with NADPH and free of p-OHB==
-	<StructureSection load='1k0j' size='340' side='right' caption='[[1k0j]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='1k0j' size='340' side='right'caption='[[1k0j]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1k0j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K0J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K0J FirstGlance]. <br>		<table><tr><td colspan='2'>[[1k0j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K0J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K0J FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 1k0j" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1k0j" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Hydroxylases 3D structures\|Hydroxylases 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: 4-hydroxybenzoate 3-monooxygenase]]		[[Category: 4-hydroxybenzoate 3-monooxygenase]]
		+	[[Category: Large Structures]]
	[[Category: Ballou, D]]		[[Category: Ballou, D]]
	[[Category: Entsch, B]]		[[Category: Entsch, B]]

OCA at 09:02, 17 January 2018

OCA — Wed, 17 Jan 2018 09:02:44 GMT

←Older revision		Revision as of 09:02, 17 January 2018
Line 1:		Line 1:
		+
	==Pseudomonas aeruginosa phbh R220Q in complex with NADPH and free of p-OHB==		==Pseudomonas aeruginosa phbh R220Q in complex with NADPH and free of p-OHB==
	<StructureSection load='1k0j' size='340' side='right' caption='[[1k0j]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1k0j' size='340' side='right' caption='[[1k0j]], [[Resolution\|resolution]] 2.20Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iuw\|1iuw]], [[1k0i\|1k0i]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iuw\|1iuw]], [[1k0i\|1k0i]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxybenzoate_3-monooxygenase 4-hydroxybenzoate 3-monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.2 1.14.13.2] </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-hydroxybenzoate_3-monooxygenase 4-hydroxybenzoate 3-monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.2 1.14.13.2] </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=1k0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k0j OCA], [http://pdbe.org/1k0j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1k0j RCSB], [http://www.ebi.ac.uk/pdbsum/1k0j 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=1k0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k0j OCA], [http://pdbe.org/1k0j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1k0j RCSB], [http://www.ebi.ac.uk/pdbsum/1k0j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1k0j 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/k0/1k0j_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k0/1k0j_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>
Line 27:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1k0j" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1k0j" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Hydroxylase\|Hydroxylase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 22:28, 9 February 2016

OCA — Tue, 09 Feb 2016 22:28:13 GMT

←Older revision		Revision as of 22:28, 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=1k0j ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 29:

	==See Also==		==See Also==
-	*[[~~P-hydroxybenzoate hydroxylase~~\|~~P-hydroxybenzoate hydroxylase~~]]	+	*[[Hydroxylase\|Hydroxylase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 02:39, 11 September 2015

OCA — Fri, 11 Sep 2015 02:39:04 GMT

←Older revision		Revision as of 02:39, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1k0j' size='340' side='right' caption='[[1k0j]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1k0j' size='340' side='right' caption='[[1k0j]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1k0j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pseudomonas_aeruginosa Pseudomonas aeruginosa~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K0J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K0J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1k0j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K0J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K0J FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</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=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</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">[[1iuw\|1iuw]], [[1k0i\|1k0i]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iuw\|1iuw]], [[1k0i\|1k0i]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxybenzoate_3-monooxygenase 4-hydroxybenzoate 3-monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.2 1.14.13.2] </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-hydroxybenzoate_3-monooxygenase 4-hydroxybenzoate 3-monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.2 1.14.13.2] </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=1k0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k0j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1k0j RCSB], [http://www.ebi.ac.uk/pdbsum/1k0j 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=1k0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k0j OCA], [http://pdbe.org/1k0j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1k0j RCSB], [http://www.ebi.ac.uk/pdbsum/1k0j 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 1k0j" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: 4-hydroxybenzoate 3-monooxygenase]]		[[Category: 4-hydroxybenzoate 3-monooxygenase]]
-	[[Category: Pseudomonas aeruginosa]]
	[[Category: Ballou, D]]		[[Category: Ballou, D]]
	[[Category: Entsch, B]]		[[Category: Entsch, B]]

OCA at 16:49, 5 January 2015

OCA — Mon, 05 Jan 2015 16:49:06 GMT

←Older revision		Revision as of 16:49, 5 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1k0j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K0J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K0J FirstGlance]. <br>		<table><tr><td colspan='2'>[[1k0j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K0J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K0J FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</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=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iuw\|1iuw]], [[1k0i\|1k0i]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iuw\|1iuw]], [[1k0i\|1k0i]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxybenzoate_3-monooxygenase 4-hydroxybenzoate 3-monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.2 1.14.13.2] </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-hydroxybenzoate_3-monooxygenase 4-hydroxybenzoate 3-monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.2 1.14.13.2] </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=1k0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k0j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1k0j RCSB], [http://www.ebi.ac.uk/pdbsum/1k0j 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=1k0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k0j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1k0j RCSB], [http://www.ebi.ac.uk/pdbsum/1k0j 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 35:		Line 35:
	[[Category: 4-hydroxybenzoate 3-monooxygenase]]		[[Category: 4-hydroxybenzoate 3-monooxygenase]]
	[[Category: Pseudomonas aeruginosa]]		[[Category: Pseudomonas aeruginosa]]
-	[[Category: Ballou, D.]]	+	[[Category: Ballou, D]]
-	[[Category: Entsch, B.]]	+	[[Category: Entsch, B]]
-	[[Category: Gatti, D L.]]	+	[[Category: Gatti, D L]]
-	[[Category: Ortiz-Maldonado, M.]]	+	[[Category: Ortiz-Maldonado, M]]
-	[[Category: Wang, J.]]	+	[[Category: Wang, J]]
	[[Category: Fad]]		[[Category: Fad]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Nadph]]		[[Category: Nadph]]
	[[Category: Phbh]]		[[Category: Phbh]]

OCA at 12:45, 28 September 2014

OCA — Sun, 28 Sep 2014 12:45:25 GMT

←Older revision		Revision as of 12:45, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1k0j.~~png~~\|~~left~~\|200px]]	+	==Pseudomonas aeruginosa phbh R220Q in complex with NADPH and free of p-OHB==
		+	<StructureSection load='1k0j' size='340' side='right' caption='[[1k0j]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1k0j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K0J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K0J FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iuw\|1iuw]], [[1k0i\|1k0i]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxybenzoate_3-monooxygenase 4-hydroxybenzoate 3-monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.2 1.14.13.2] </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=1k0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k0j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1k0j RCSB], [http://www.ebi.ac.uk/pdbsum/1k0j 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/k0/1k0j_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 ==
		+	para-Hydroxybenzoate hydroxylase catalyzes a two-step reaction that demands precise control of solvent access to the catalytic site. The first step of the reaction, reduction of flavin by NADPH, requires access to solvent. The second step, oxygenation of reduced flavin to a flavin C4a-hydroperoxide that transfers the hydroxyl group to the substrate, requires that solvent be excluded to prevent breakdown of the hydroperoxide to oxidized flavin and hydrogen peroxide. These conflicting requirements are met by the coordination of multiple movements involving the protein, the two cofactors, and the substrate. Here, using the R220Q mutant form of para-hydroxybenzoate hydroxylase, we show that in the absence of substrate, the large beta alpha beta domain (residues 1-180) and the smaller sheet domain (residues 180-270) separate slightly, and the flavin swings out to a more exposed position to open an aqueous channel from the solvent to the protein interior. Substrate entry occurs by first binding at a surface site and then sliding into the protein interior. In our study of this mutant, the structure of the complex with pyridine nucleotide was obtained. This cofactor binds in an extended conformation at the enzyme surface in a groove that crosses the binding site of FAD. We postulate that for stereospecific reduction, the flavin swings to an out position and NADPH assumes a folded conformation that brings its nicotinamide moiety into close contact with the isoalloxazine moiety of the flavin. This work clearly shows how complex dynamics can play a central role in catalysis by enzymes.

-	~~{{STRUCTURE_1k0j\| PDB=1k0j \| SCENE= }}~~	+	Protein and ligand dynamics in 4-hydroxybenzoate hydroxylase.,Wang J, Ortiz-Maldonado M, Entsch B, Massey V, Ballou D, Gatti DL Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):608-13. PMID:11805318<ref>PMID:11805318</ref>

-	~~===Pseudomonas aeruginosa phbh R220Q in complex with NADPH and free~~ of ~~p-OHB===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_11805318}}~~	+	==See Also==
-		+	*[[P-hydroxybenzoate hydroxylase\|P-hydroxybenzoate hydroxylase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~1k0j~~]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K0J OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:011805318<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: 4-hydroxybenzoate 3-monooxygenase]]		[[Category: 4-hydroxybenzoate 3-monooxygenase]]
	[[Category: Pseudomonas aeruginosa]]		[[Category: Pseudomonas aeruginosa]]

OCA: Protected "1k0j" [edit=sysop:move=sysop]

OCA — Wed, 05 Dec 2012 11:13:21 GMT

Protected "1k0j" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:13, 5 December 2012

OCA at 11:13, 5 December 2012

OCA — Wed, 05 Dec 2012 11:13:19 GMT

←Older revision		Revision as of 11:13, 5 December 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1k0j.png\|left\|200px]]		[[Image:1k0j.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1k0j", 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_1k0j\| PDB=1k0j \| SCENE= }}		{{STRUCTURE_1k0j\| PDB=1k0j \| SCENE= }}

	===Pseudomonas aeruginosa phbh R220Q in complex with NADPH and free of p-OHB===		===Pseudomonas aeruginosa phbh R220Q in complex with NADPH and free of p-OHB===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_11805318}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 11805318 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_11805318}}		{{ABSTRACT_PUBMED_11805318}}

	==About this Structure==		==About this Structure==
-	~~1K0J~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K0J OCA].	+	[[1k0j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K0J OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~11805318~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:011805318</ref><references group="xtra"/>
	[[Category: 4-hydroxybenzoate 3-monooxygenase]]		[[Category: 4-hydroxybenzoate 3-monooxygenase]]
	[[Category: Pseudomonas aeruginosa]]		[[Category: Pseudomonas aeruginosa]]
Line 32:		Line 20:
	[[Category: Wang, J.]]		[[Category: Wang, J.]]
	[[Category: Fad]]		[[Category: Fad]]
-	[[Category: ~~Mechanism~~]]	+	[[Category: Hydrolase]]
	[[Category: Nadph]]		[[Category: Nadph]]
	[[Category: Phbh]]		[[Category: Phbh]]
-	[[Category: Structure]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 13:14:04 2009''