1eir - Revision history

OCA at 07:03, 7 February 2024

OCA — Wed, 07 Feb 2024 07:03:23 GMT

←Older revision		Revision as of 07:03, 7 February 2024
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	<StructureSection load='1eir' size='340' side='right'caption='[[1eir]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1eir' size='340' side='right'caption='[[1eir]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1eir]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Pses1 Pses1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EIR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EIR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1eir]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_sp._KKS102 Pseudomonas sp. KKS102]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EIR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EIR FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=BPY:BIPHENYL~~-2~~,3-DIOL'>BPY</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</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]] 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;~~'>~~[[1dhy\|1dhy]], [[1eil\|1eil]], [[1eim\|1eim]], [[1eiq\|1eiq]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BPY:BIPHENYL-2,3-DIOL'>BPY</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Biphenyl-2,3-diol_1,2-dioxygenase Biphenyl-2,3-diol 1,2-dioxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.39 1.13.11.39]~~ </~~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=1eir FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eir OCA], [https://pdbe.org/1eir PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1eir RCSB], [https://www.ebi.ac.uk/pdbsum/1eir PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1eir 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=1eir FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eir OCA], [https://pdbe.org/1eir PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1eir RCSB], [https://www.ebi.ac.uk/pdbsum/1eir PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1eir ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/BPHC_PSES1 BPHC_PSES1]
	== 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=1eir 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=1eir ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	BphC derived from Pseudomonas sp. strain KKS102, an extradiol type catecholic dioxygenase, is a non-heam iron-containing enzyme, playing an important role in the degradation of biphenyl/PCB (Poly Chlorinated Biphenyls) in the microbe. Although we had earlier solved the crystal structure of KKS102 BphC, it was the inactive form with Fe(III) in the active site. In order to determine the active form structure, BphC was re-activated by anaerobic incubation with Fe(II) and ascorbate, and crystallized anaerobically. The crystal structures of activated BphC and its substrate complex (E x S complex) were determined at 2.0 A resolution under cryogenic condition. In addition, crystal structures of unactivated BphC in substrate free and complex forms were also re-determined. Comparison of activated and unactivated E x S complexes reveals that the orientation of the bound substrate in the active site is significantly different between the two. The structural comparison of the substrate free and complex forms of activated BphC show certain small conformational shifts around the active site upon substrate binding. As a result of the conformational shifts, His194, which has been suggested as the catalytic base, takes part in a weak hydrogen bond with hydroxyl group of the substrate.
-
-	Crystal structures of substrate free and complex forms of reactivated BphC, an extradiol type ring-cleavage dioxygenase.,Uragami Y, Senda T, Sugimoto K, Sato N, Nagarajan V, Masai E, Fukuda M, Mitsu Y J Inorg Biochem. 2001 Feb;83(4):269-79. PMID:11293547<ref>PMID:11293547</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1eir" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]		*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pses1~~]]	+	[[Category: Pseudomonas sp. KKS102]]
-	[[Category: Senda, T]]	+	[[Category: Senda T]]
-	~~[[Category: Four repetitions of beta-alpha-beta-beta-beta motif]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 09:37, 21 July 2021

OCA — Wed, 21 Jul 2021 09:37:59 GMT

←Older revision		Revision as of 09:37, 21 July 2021
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	<StructureSection load='1eir' size='340' side='right'caption='[[1eir]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1eir' size='340' side='right'caption='[[1eir]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1eir]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Pses1 Pses1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EIR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1EIR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1eir]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pses1 Pses1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EIR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EIR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BPY:BIPHENYL-2,3-DIOL'>BPY</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BPY:BIPHENYL-2,3-DIOL'>BPY</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dhy\|1dhy]], [[1eil\|1eil]], [[1eim\|1eim]], [[1eiq\|1eiq]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dhy\|1dhy]], [[1eil\|1eil]], [[1eim\|1eim]], [[1eiq\|1eiq]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Biphenyl-2,3-diol_1,2-dioxygenase Biphenyl-2,3-diol 1,2-dioxygenase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.39 1.13.11.39] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Biphenyl-2,3-diol_1,2-dioxygenase Biphenyl-2,3-diol 1,2-dioxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.39 1.13.11.39] </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=1eir FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eir OCA], [~~http~~://pdbe.org/1eir PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1eir RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1eir PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1eir 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=1eir FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eir OCA], [https://pdbe.org/1eir PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1eir RCSB], [https://www.ebi.ac.uk/pdbsum/1eir PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1eir ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 11:15, 16 October 2019

OCA — Wed, 16 Oct 2019 11:15:47 GMT

←Older revision		Revision as of 11:15, 16 October 2019
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	==2,3-DIHYDROXYBIPHENYL-1,2-DIOXYGENASE==		==2,3-DIHYDROXYBIPHENYL-1,2-DIOXYGENASE==
-	<StructureSection load='1eir' size='340' side='right' caption='[[1eir]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='1eir' size='340' side='right'caption='[[1eir]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1eir]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pses1 Pses1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EIR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EIR FirstGlance]. <br>		<table><tr><td colspan='2'>[[1eir]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pses1 Pses1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EIR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EIR FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 1eir" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1eir" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 33:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]		[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]
		+	[[Category: Large Structures]]
	[[Category: Pses1]]		[[Category: Pses1]]
	[[Category: Senda, T]]		[[Category: Senda, T]]
	[[Category: Four repetitions of beta-alpha-beta-beta-beta motif]]		[[Category: Four repetitions of beta-alpha-beta-beta-beta motif]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 07:19, 20 December 2017

OCA — Wed, 20 Dec 2017 07:19:52 GMT

←Older revision		Revision as of 07:19, 20 December 2017
Line 1:		Line 1:
		+
	==2,3-DIHYDROXYBIPHENYL-1,2-DIOXYGENASE==		==2,3-DIHYDROXYBIPHENYL-1,2-DIOXYGENASE==
	<StructureSection load='1eir' size='340' side='right' caption='[[1eir]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1eir' size='340' side='right' caption='[[1eir]], [[Resolution\|resolution]] 2.00Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dhy\|1dhy]], [[1eil\|1eil]], [[1eim\|1eim]], [[1eiq\|1eiq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dhy\|1dhy]], [[1eil\|1eil]], [[1eim\|1eim]], [[1eiq\|1eiq]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biphenyl-2,3-diol_1,2-dioxygenase Biphenyl-2,3-diol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.39 1.13.11.39] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biphenyl-2,3-diol_1,2-dioxygenase Biphenyl-2,3-diol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.39 1.13.11.39] </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=1eir FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eir OCA], [http://pdbe.org/1eir PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1eir RCSB], [http://www.ebi.ac.uk/pdbsum/1eir 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=1eir FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eir OCA], [http://pdbe.org/1eir PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1eir RCSB], [http://www.ebi.ac.uk/pdbsum/1eir PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1eir ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ei/1eir_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ei/1eir_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 1eir" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1eir" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Dioxygenase\|Dioxygenase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 01:03, 9 February 2016

OCA — Tue, 09 Feb 2016 01:03:53 GMT

←Older revision		Revision as of 01:03, 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=1eir ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 17:05, 10 September 2015

OCA — Thu, 10 Sep 2015 17:05:46 GMT

←Older revision		Revision as of 17:05, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1eir' size='340' side='right' caption='[[1eir]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1eir' size='340' side='right' caption='[[1eir]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1eir]] is a 1 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=1EIR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EIR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1eir]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pses1 Pses1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EIR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EIR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BPY:BIPHENYL-2,3-DIOL'>BPY</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BPY:BIPHENYL-2,3-DIOL'>BPY</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dhy\|1dhy]], [[1eil\|1eil]], [[1eim\|1eim]], [[1eiq\|1eiq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dhy\|1dhy]], [[1eil\|1eil]], [[1eim\|1eim]], [[1eiq\|1eiq]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biphenyl-2,3-diol_1,2-dioxygenase Biphenyl-2,3-diol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.39 1.13.11.39] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biphenyl-2,3-diol_1,2-dioxygenase Biphenyl-2,3-diol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.39 1.13.11.39] </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=1eir FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eir OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1eir RCSB], [http://www.ebi.ac.uk/pdbsum/1eir 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=1eir FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eir OCA], [http://pdbe.org/1eir PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1eir RCSB], [http://www.ebi.ac.uk/pdbsum/1eir PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	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 1eir" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]		[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]
-	[[Category: ~~Pseudomonas sp~~]]	+	[[Category: Pses1]]
	[[Category: Senda, T]]		[[Category: Senda, T]]
	[[Category: Four repetitions of beta-alpha-beta-beta-beta motif]]		[[Category: Four repetitions of beta-alpha-beta-beta-beta motif]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 19:29, 22 December 2014

OCA — Mon, 22 Dec 2014 19:29:38 GMT

←Older revision		Revision as of 19:29, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1eir]] is a 1 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=1EIR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EIR FirstGlance]. <br>		<table><tr><td colspan='2'>[[1eir]] is a 1 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=1EIR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EIR FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BPY:BIPHENYL-2,3-DIOL'>BPY</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BPY:BIPHENYL-2,3-DIOL'>BPY</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dhy\|1dhy]], [[1eil\|1eil]], [[1eim\|1eim]], [[1eiq\|1eiq]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dhy\|1dhy]], [[1eil\|1eil]], [[1eim\|1eim]], [[1eiq\|1eiq]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biphenyl-2,3-diol_1,2-dioxygenase Biphenyl-2,3-diol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.39 1.13.11.39] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biphenyl-2,3-diol_1,2-dioxygenase Biphenyl-2,3-diol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.39 1.13.11.39] </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=1eir FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eir OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1eir RCSB], [http://www.ebi.ac.uk/pdbsum/1eir 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=1eir FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eir OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1eir RCSB], [http://www.ebi.ac.uk/pdbsum/1eir 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 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]		[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]
-	[[Category: Pseudomonas sp.]]	+	[[Category: Pseudomonas sp]]
-	[[Category: Senda, T.]]	+	[[Category: Senda, T]]
	[[Category: Four repetitions of beta-alpha-beta-beta-beta motif]]		[[Category: Four repetitions of beta-alpha-beta-beta-beta motif]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 11:29, 24 September 2014

OCA — Wed, 24 Sep 2014 11:29:43 GMT

←Older revision		Revision as of 11:29, 24 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1eir.~~png~~\|~~left~~\|200px]]	+	==2,3-DIHYDROXYBIPHENYL-1,2-DIOXYGENASE==
		+	<StructureSection load='1eir' size='340' side='right' caption='[[1eir]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1eir]] is a 1 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=1EIR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EIR FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BPY:BIPHENYL-2,3-DIOL'>BPY</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dhy\|1dhy]], [[1eil\|1eil]], [[1eim\|1eim]], [[1eiq\|1eiq]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biphenyl-2,3-diol_1,2-dioxygenase Biphenyl-2,3-diol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.39 1.13.11.39] </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=1eir FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eir OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1eir RCSB], [http://www.ebi.ac.uk/pdbsum/1eir 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/ei/1eir_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 ==
		+	BphC derived from Pseudomonas sp. strain KKS102, an extradiol type catecholic dioxygenase, is a non-heam iron-containing enzyme, playing an important role in the degradation of biphenyl/PCB (Poly Chlorinated Biphenyls) in the microbe. Although we had earlier solved the crystal structure of KKS102 BphC, it was the inactive form with Fe(III) in the active site. In order to determine the active form structure, BphC was re-activated by anaerobic incubation with Fe(II) and ascorbate, and crystallized anaerobically. The crystal structures of activated BphC and its substrate complex (E x S complex) were determined at 2.0 A resolution under cryogenic condition. In addition, crystal structures of unactivated BphC in substrate free and complex forms were also re-determined. Comparison of activated and unactivated E x S complexes reveals that the orientation of the bound substrate in the active site is significantly different between the two. The structural comparison of the substrate free and complex forms of activated BphC show certain small conformational shifts around the active site upon substrate binding. As a result of the conformational shifts, His194, which has been suggested as the catalytic base, takes part in a weak hydrogen bond with hydroxyl group of the substrate.

-	~~{{STRUCTURE_1eir\| PDB=1eir \| SCENE= }}~~	+	Crystal structures of substrate free and complex forms of reactivated BphC, an extradiol type ring-cleavage dioxygenase.,Uragami Y, Senda T, Sugimoto K, Sato N, Nagarajan V, Masai E, Fukuda M, Mitsu Y J Inorg Biochem. 2001 Feb;83(4):269-79. PMID:11293547<ref>PMID:11293547</ref>

-	~~===2~~,~~3-DIHYDROXYBIPHENYL-1,2-DIOXYGENASE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-		+	==See Also==
-	==~~About this Structure~~==	+	*[[Dioxygenase\|Dioxygenase]]
-	[[~~1eir~~]] is a 1 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=1EIR OCA].	+	== References ==
-		+	<references/>
-	==~~Reference~~==	+	__TOC__
-	<~~ref group="xtra">PMID:011293547<~~/~~ref~~><~~references group="xtra"~~/>	+	</StructureSection>
	[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]		[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]
	[[Category: Pseudomonas sp.]]		[[Category: Pseudomonas sp.]]

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

OCA — Thu, 08 Nov 2012 14:41:23 GMT

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

←Older revision

Revision as of 14:41, 8 November 2012

OCA at 14:41, 8 November 2012

OCA — Thu, 08 Nov 2012 14:41:20 GMT

←Older revision		Revision as of 14:41, 8 November 2012
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-	{{Seed}}
	[[Image:1eir.png\|left\|200px]]		[[Image:1eir.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1eir", 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_1eir\| PDB=1eir \| SCENE= }}		{{STRUCTURE_1eir\| PDB=1eir \| SCENE= }}

	===2,3-DIHYDROXYBIPHENYL-1,2-DIOXYGENASE===		===2,3-DIHYDROXYBIPHENYL-1,2-DIOXYGENASE===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_11293547}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 11293547 is the PubMed ID number.
-	-->
-	{{ABSTRACT_PUBMED_11293547}}

	==About this Structure==		==About this Structure==
-	~~1EIR~~ is a 1 chain structure of 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=1EIR OCA].	+	[[1eir]] is a 1 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=1EIR OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~11293547~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:011293547</ref><references group="xtra"/>
	[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]		[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]
	[[Category: Pseudomonas sp.]]		[[Category: Pseudomonas sp.]]
	[[Category: Senda, T.]]		[[Category: Senda, T.]]
	[[Category: Four repetitions of beta-alpha-beta-beta-beta motif]]		[[Category: Four repetitions of beta-alpha-beta-beta-beta motif]]
-		+	[[Category: Oxidoreductase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 05:12:23 2009''~~	+