3hpv - Revision history

OCA at 15:52, 1 November 2023

2023-11-01T15:52:35Z

←Older revision		Revision as of 15:52, 1 November 2023
Line 3:		Line 3:
	<StructureSection load='3hpv' size='340' side='right'caption='[[3hpv]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3hpv' size='340' side='right'caption='[[3hpv]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3hpv]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"pseudomonas_alkylphenolia"_veeranagouda_et_al._2009 "pseudomonas alkylphenolia" veeranagouda et al. 2009~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HPV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HPV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3hpv]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_alkylphenolica Pseudomonas alkylphenolica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HPV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HPV 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>~~</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]] 2.3Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>Pseudomonas sp. KL28 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~237609~~ "~~Pseudomonas alkylphenolia~~" ~~Veeranagouda et al. 2009])</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></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Catechol_2,3-dioxygenase Catechol 2,3-dioxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.2 1.13.11.2]~~ </~~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=3hpv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hpv OCA], [https://pdbe.org/3hpv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hpv RCSB], [https://www.ebi.ac.uk/pdbsum/3hpv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hpv 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=3hpv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hpv OCA], [https://pdbe.org/3hpv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hpv RCSB], [https://www.ebi.ac.uk/pdbsum/3hpv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hpv ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q7WYF5_9PSED Q7WYF5_9PSED]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Pseudomonas alkylphenolia veeranagouda et al. 2009]]
-	[[Category: Catechol 2,3-dioxygenase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Cho, J H~~]]	+	[[Category: Pseudomonas alkylphenolica]]
-	[[Category: ~~Rhee, S~~]]	+	[[Category: Cho J-H]]
-	[[Category: ~~Aromatic hydrocarbons catabolism]]~~	+	[[Category: Rhee S]]
-	~~[[Category: Dioxygenase]]~~	+
-	~~[[Category: Iron]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Repeated motif~~]]	+

OCA at 11:54, 30 March 2022

2022-03-30T11:54:17Z

←Older revision		Revision as of 11:54, 30 March 2022
Line 1:		Line 1:

	==Crystal Structure Analysis of the 2,3-dioxygenase LapB from Pseudomonas sp. KL28==		==Crystal Structure Analysis of the 2,3-dioxygenase LapB from Pseudomonas sp. KL28==
-	<StructureSection load='3hpv' size='340' side='right' caption='[[3hpv]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='3hpv' size='340' side='right'caption='[[3hpv]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3hpv]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"pseudomonas_alkylphenolia"_veeranagouda_et_al._2009 "pseudomonas alkylphenolia" veeranagouda et al. 2009]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HPV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3HPV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3hpv]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"pseudomonas_alkylphenolia"_veeranagouda_et_al._2009 "pseudomonas alkylphenolia" veeranagouda et al. 2009]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HPV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HPV 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></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></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pseudomonas sp. KL28 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=237609 "Pseudomonas alkylphenolia" Veeranagouda et al. 2009])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pseudomonas sp. KL28 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=237609 "Pseudomonas alkylphenolia" Veeranagouda et al. 2009])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Catechol_2,3-dioxygenase Catechol 2,3-dioxygenase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.2 1.13.11.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Catechol_2,3-dioxygenase Catechol 2,3-dioxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.2 1.13.11.2] </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=3hpv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hpv OCA], [~~http~~://pdbe.org/3hpv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3hpv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3hpv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3hpv 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=3hpv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hpv OCA], [https://pdbe.org/3hpv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hpv RCSB], [https://www.ebi.ac.uk/pdbsum/3hpv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hpv ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hp/3hpv_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hp/3hpv_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 28:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 3hpv" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3hpv" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 37:
	[[Category: Pseudomonas alkylphenolia veeranagouda et al. 2009]]		[[Category: Pseudomonas alkylphenolia veeranagouda et al. 2009]]
	[[Category: Catechol 2,3-dioxygenase]]		[[Category: Catechol 2,3-dioxygenase]]
		+	[[Category: Large Structures]]
	[[Category: Cho, J H]]		[[Category: Cho, J H]]
	[[Category: Rhee, S]]		[[Category: Rhee, S]]

OCA at 07:44, 1 November 2017

2017-11-01T07:44:02Z

←Older revision		Revision as of 07:44, 1 November 2017
Line 1:		Line 1:
		+
	==Crystal Structure Analysis of the 2,3-dioxygenase LapB from Pseudomonas sp. KL28==		==Crystal Structure Analysis of the 2,3-dioxygenase LapB from Pseudomonas sp. KL28==
	<StructureSection load='3hpv' size='340' side='right' caption='[[3hpv]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3hpv' size='340' side='right' caption='[[3hpv]], [[Resolution\|resolution]] 2.30Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pseudomonas sp. KL28 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=237609 "Pseudomonas alkylphenolia" Veeranagouda et al. 2009])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pseudomonas sp. KL28 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=237609 "Pseudomonas alkylphenolia" Veeranagouda et al. 2009])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catechol_2,3-dioxygenase Catechol 2,3-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.2 1.13.11.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catechol_2,3-dioxygenase Catechol 2,3-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.2 1.13.11.2] </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=3hpv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hpv OCA], [http://pdbe.org/3hpv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hpv RCSB], [http://www.ebi.ac.uk/pdbsum/3hpv 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=3hpv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hpv OCA], [http://pdbe.org/3hpv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hpv RCSB], [http://www.ebi.ac.uk/pdbsum/3hpv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3hpv ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 27:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 3hpv" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3hpv" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Dioxygenase\|Dioxygenase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 01:31, 10 February 2016

2016-02-10T01:31:03Z

←Older revision		Revision as of 01:31, 10 February 2016
Line 6:		Line 6:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pseudomonas sp. KL28 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=237609 "Pseudomonas alkylphenolia" Veeranagouda et al. 2009])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pseudomonas sp. KL28 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=237609 "Pseudomonas alkylphenolia" Veeranagouda et al. 2009])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catechol_2,3-dioxygenase Catechol 2,3-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.2 1.13.11.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catechol_2,3-dioxygenase Catechol 2,3-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.2 1.13.11.2] </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=3hpv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hpv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hpv RCSB], [http://www.ebi.ac.uk/pdbsum/3hpv 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=3hpv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hpv OCA], [http://pdbe.org/3hpv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hpv RCSB], [http://www.ebi.ac.uk/pdbsum/3hpv PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	<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=3hpv ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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 3hpv" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 18:17, 21 December 2014

2014-12-21T18:17:20Z

←Older revision		Revision as of 18:17, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3hpv\| PDB=3hpv \| SCENE= }}~~	+	==Crystal Structure Analysis of the 2,3-dioxygenase LapB from Pseudomonas sp. KL28==
-	===Crystal Structure Analysis of the 2,3-dioxygenase LapB from Pseudomonas sp. KL28===	+	<StructureSection load='3hpv' size='340' side='right' caption='[[3hpv]], [[Resolution\|resolution]] 2.30Å' scene=''>
-	~~{{ABSTRACT_PUBMED_19828456}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3hpv]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"pseudomonas_alkylphenolia"_veeranagouda_et_al._2009 "pseudomonas alkylphenolia" veeranagouda et al. 2009]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HPV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HPV 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></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pseudomonas sp. KL28 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=237609 "Pseudomonas alkylphenolia" Veeranagouda et al. 2009])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catechol_2,3-dioxygenase Catechol 2,3-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.2 1.13.11.2] </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=3hpv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hpv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hpv RCSB], [http://www.ebi.ac.uk/pdbsum/3hpv 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/hp/3hpv_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 ==
		+	LapB is a non-heme Fe(II)-dependent 2,3-dioxygenase that catalyzes the second step of a long-chain alkylphenol (lap) degradation pathway in Pseudomonas sp. KL28 and belongs to the superfamily of type I extradiol dioxygenases. In this study, the crystal structures of substrate-free LapB and its complexes with a substrate or product were determined, along with a functional analysis of the active site residues. Structural features of the homotetramer are similar to those of other type I extradiol dioxygenases. In particular, the active site is located in the C-domain of each monomer, with a 2-His-1-carboxylate motif as the first coordination shell to iron ion. A comparison of three different structures in the catalytic cycle indicated catalysis-related local conformational changes in the active site. Specifically, the active site loop containing His-248 exhibits positional changes upon binding of the substrate and establishes a hydrogen-bonding network with Tyr-257, which is near the hydroxyl group of the substrate. Kinetic analysis of the mutant enzymes H248A, H248N, and Y257F showed that these three mutant enzymes are inactive, suggesting that this hydrogen-bonding network plays a crucial role in catalysis by deprotonating the incoming substrate and leaving it in a monoanionic state. Additional functional analysis of His-201, by using H201A and H201N mutants, near the dioxygen-binding site also supports its role as base and acid catalyst in the late stage of catalysis. We also noticed a disordered-to-ordered structural transition in the C-terminal region, resulting in the opening or closing of the active site. These results provide detailed insights into the structural and functional features of an extradiol dioxygenase that can accommodate a wide range of alkylcatechols.

-	~~==About this Structure==~~	+	Crystal structure and functional analysis of the extradiol dioxygenase LapB from a long-chain alkylphenol degradation pathway in Pseudomonas.,Cho JH, Jung DK, Lee K, Rhee S J Biol Chem. 2009 Dec 4;284(49):34321-30. Epub 2009 Oct 14. PMID:19828456<ref>PMID:19828456</ref>
-	~~[[3hpv]] is~~ a 4 chain ~~structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/"pseudomonas_alkylphenolia"_veeranagouda_et_al._2009 "pseudomonas alkylphenolia" veeranagouda et al~~. 2009]. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=3HPV OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[Dioxygenase\|Dioxygenase]]		*[[Dioxygenase\|Dioxygenase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:019828456</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Pseudomonas alkylphenolia veeranagouda et al. 2009]]		[[Category: Pseudomonas alkylphenolia veeranagouda et al. 2009]]
	[[Category: Catechol 2,3-dioxygenase]]		[[Category: Catechol 2,3-dioxygenase]]
-	[[Category: Cho, J H.]]	+	[[Category: Cho, J H]]
-	[[Category: Rhee, S.]]	+	[[Category: Rhee, S]]
	[[Category: Aromatic hydrocarbons catabolism]]		[[Category: Aromatic hydrocarbons catabolism]]
	[[Category: Dioxygenase]]		[[Category: Dioxygenase]]

OCA at 06:29, 22 January 2014

2014-01-22T06:29:14Z

←Older revision		Revision as of 06:29, 22 January 2014
Line 1:		Line 1:
-	[[Image:3hpv.png\|left\|200px]]
-
	{{STRUCTURE_3hpv\| PDB=3hpv \| SCENE= }}		{{STRUCTURE_3hpv\| PDB=3hpv \| SCENE= }}
-
	===Crystal Structure Analysis of the 2,3-dioxygenase LapB from Pseudomonas sp. KL28===		===Crystal Structure Analysis of the 2,3-dioxygenase LapB from Pseudomonas sp. KL28===
		+	{{ABSTRACT_PUBMED_19828456}}

-	~~{{ABSTRACT_PUBMED_019828456}}~~	+	==About this Structure==
		+	[[3hpv]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"pseudomonas_alkylphenolia"_veeranagouda_et_al._2009 "pseudomonas alkylphenolia" veeranagouda et al. 2009]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HPV OCA].

-	==~~About this Structure~~==	+	==See Also==
-	[[~~3hpv~~]] ~~is a 4 chain structure with sequence from [http~~://~~en.wikipedia.org~~/~~wiki/Pseudomonas_sp. Pseudomonas sp.]. Full crystallographic information is available from~~ [~~http~~:~~//oca~~.~~weizmann.ac.il/oca-bin/ocashort?id=3HPV OCA~~].	+	*[[Dioxygenase\|Dioxygenase]]
		+
		+	==Reference==
		+	<ref group="xtra">PMID:019828456</ref><references group="xtra"/><references/>
		+	[[Category: Pseudomonas alkylphenolia veeranagouda et al. 2009]]
	[[Category: Catechol 2,3-dioxygenase]]		[[Category: Catechol 2,3-dioxygenase]]
-	[[Category: Pseudomonas sp.]]
	[[Category: Cho, J H.]]		[[Category: Cho, J H.]]
	[[Category: Rhee, S.]]		[[Category: Rhee, S.]]

OCA: Protected "3hpv" [edit=sysop:move=sysop]

2013-03-06T15:03:39Z

Protected "3hpv" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:03, 6 March 2013

OCA at 15:03, 6 March 2013

2013-03-06T15:03:34Z

←Older revision		Revision as of 15:03, 6 March 2013
Line 1:		Line 1:
-	~~{{Seed}}~~	+	[[Image:3hpv.png\|left\|200px]]
-	[[Image:3hpv.~~jpg~~\|left\|200px]]	+

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3hpv", 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_3hpv\| PDB=3hpv \| SCENE= }}		{{STRUCTURE_3hpv\| PDB=3hpv \| SCENE= }}

	===Crystal Structure Analysis of the 2,3-dioxygenase LapB from Pseudomonas sp. KL28===		===Crystal Structure Analysis of the 2,3-dioxygenase LapB from Pseudomonas sp. KL28===

		+	{{ABSTRACT_PUBMED_019828456}}

	==About this Structure==		==About this Structure==
-	~~3HPV~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Pseudomonas_sp.~~_kl28~~ Pseudomonas sp. ~~kl28~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HPV OCA].	+	[[3hpv]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_sp. Pseudomonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HPV OCA].
	[[Category: Catechol 2,3-dioxygenase]]		[[Category: Catechol 2,3-dioxygenase]]
-	[[Category: Pseudomonas sp. ~~kl28~~]]	+	[[Category: Pseudomonas sp.]]
	[[Category: Cho, J H.]]		[[Category: Cho, J H.]]
	[[Category: Rhee, S.]]		[[Category: Rhee, S.]]
Line 24:		Line 18:
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Repeated motif]]		[[Category: Repeated motif]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 21 10:36:42 2009''

OCA at 08:36, 21 October 2009

2009-10-21T08:36:44Z

←Older revision		Revision as of 08:36, 21 October 2009
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3hpv.jpg\|left\|200px]]

-	The ~~entry 3hpv~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3hpv", 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_3hpv\| PDB=3hpv \| SCENE= }}

-	~~Authors: Cho, J.~~,-~~H., Rhee, S~~.	+	===Crystal Structure Analysis of the 2,3-dioxygenase LapB from Pseudomonas sp. KL28===

-	Description: Crystal Structure Analysis of the 2,3-dioxygenase LapB from Pseudomonas sp. KL28

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jun 17 09~~:47:44 2009''	+	==About this Structure==
		+	3HPV is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Pseudomonas_sp._kl28 Pseudomonas sp. kl28]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HPV OCA].
		+	[[Category: Catechol 2,3-dioxygenase]]
		+	[[Category: Pseudomonas sp. kl28]]
		+	[[Category: Cho, J H.]]
		+	[[Category: Rhee, S.]]
		+	[[Category: Aromatic hydrocarbons catabolism]]
		+	[[Category: Dioxygenase]]
		+	[[Category: Iron]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Repeated motif]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 21 10:36:42 2009''

OCA at 06:47, 17 June 2009

2009-06-17T06:47:44Z

←Older revision		Revision as of 06:47, 17 June 2009
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

-	Authors: Cho, J. -H~~, Jung, D. -K, Lee, K~~., Rhee, S.	+	Authors: Cho, J.,-H., Rhee, S.

	Description: Crystal Structure Analysis of the 2,3-dioxygenase LapB from Pseudomonas sp. KL28		Description: Crystal Structure Analysis of the 2,3-dioxygenase LapB from Pseudomonas sp. KL28

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun ~~10 18~~:01:02 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 17 09:47:44 2009''