2qfk - Revision history

OCA at 09:16, 21 February 2024

OCA — Wed, 21 Feb 2024 09:16:03 GMT

←Older revision		Revision as of 09:16, 21 February 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2qfk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QFK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QFK FirstGlance]. <br>		<table><tr><td colspan='2'>[[2qfk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QFK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QFK FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>~~, ~~<scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.62Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[2qfn\|2qfn]]~~</~~div~~><~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">dhpA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= Amphitrite ornata])~~</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=2qfk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qfk OCA], [https://pdbe.org/2qfk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qfk RCSB], [https://www.ebi.ac.uk/pdbsum/2qfk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qfk 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=2qfk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qfk OCA], [https://pdbe.org/2qfk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qfk RCSB], [https://www.ebi.ac.uk/pdbsum/2qfk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qfk ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9NAV8_9ANNE Q9NAV8_9ANNE]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 20:
	</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=2qfk 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=2qfk ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The dehaloperoxidase (DHP) from the terebellid polychaete Amphitrite ornata is an enzyme that converts para-halogenated phenols to the corresponding quinones in the presence of hydrogen peroxide. Its enzymatic activity is similar to that of heme peroxidases such as horseradish peroxidase, yet it has the structural characteristics of the globin family of proteins, the main functions of which are oxygen transport and storage. In order to investigate the dual function of this hemoglobin peroxidase, the enzyme was expressed in Escherichia coli as a recombinant protein in its wild-type form and as a mutant protein in which Cys73 was replaced by a serine residue (C73S). Both the wild-type and mutant proteins were crystallized and their structures were determined at 100 K to a resolution of 1.62 A. The structure of the wild-type protein demonstrated that it was in the metaquo form, with the heme iron in the ferric oxidation state and the bound water lying 2.2 A from the heme iron. The structure of the C73S mutant protein was shown to contain a ferrous heme iron with a bound oxygen molecule. The bent bonding geometry of the Fe-O(1)-O(2) adduct results in a hydrogen bond of length 2.8 A between the second O atom, O(2), of molecular oxygen and N(2) of the distal histidine residue (His55) in both subunits contained within the asymmetric unit. This hydrogen-bonding interaction between His55 and the bound diatomic oxygen molecule provides new insight into the catalytic activation of H(2)O(2), which is essential for peroxidase activity.
-
-	X-ray crystal structural analysis of the binding site in the ferric and oxyferrous forms of the recombinant heme dehaloperoxidase cloned from Amphitrite ornata.,de Serrano V, Chen Z, Davis MF, Franzen S Acta Crystallogr D Biol Crystallogr. 2007 Oct;63(Pt 10):1094-101. Epub, 2007 Sep 19. PMID:17881827<ref>PMID:17881827</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2qfk" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Dehaloperoxidase 3D structures\|Dehaloperoxidase 3D structures]]		*[[Dehaloperoxidase 3D structures\|Dehaloperoxidase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Amphitrite ornata]]		[[Category: Amphitrite ornata]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chen, Z]]	+	[[Category: Chen Z]]
-	[[Category: Davis~~, M F~~]]	+	[[Category: Davis MF]]
-	[[Category: Franzen, S]]	+	[[Category: Franzen S]]
-	[[Category: Serrano~~, V S.de]]~~	+	[[Category: De Serrano VS]]
-	~~[[Category: Crystal structure of dehaloperoxidase]]~~	+
-	~~[[Category: Dhp]]~~	+
-	~~[[Category: Globin]]~~	+
-	~~[[Category: Heme protein]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 08:18, 25 June 2021

OCA — Fri, 25 Jun 2021 08:18:34 GMT

←Older revision		Revision as of 08:18, 25 June 2021
Line 1:		Line 1:

	==X-ray Crystal Structure Analysis of the Binding Site in the Ferric and Oxyferrous Forms of the Recombinant Heme Dehaloperoxidase Cloned from Amphitrite ornata==		==X-ray Crystal Structure Analysis of the Binding Site in the Ferric and Oxyferrous Forms of the Recombinant Heme Dehaloperoxidase Cloned from Amphitrite ornata==
-	<StructureSection load='2qfk' size='340' side='right' caption='[[2qfk]], [[Resolution\|resolution]] 1.62Å' scene=''>	+	<StructureSection load='2qfk' size='340' side='right'caption='[[2qfk]], [[Resolution\|resolution]] 1.62Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2qfk]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QFK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2QFK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2qfk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QFK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QFK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</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">[[2qfn\|2qfn]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2qfn\|2qfn]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dhpA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= Amphitrite ornata])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dhpA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= Amphitrite ornata])</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=2qfk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qfk OCA], [~~http~~://pdbe.org/2qfk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2qfk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2qfk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2qfk 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=2qfk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qfk OCA], [https://pdbe.org/2qfk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qfk RCSB], [https://www.ebi.ac.uk/pdbsum/2qfk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qfk 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/qf/2qfk_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qf/2qfk_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 2qfk" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2qfk" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dehaloperoxidase 3D structures\|Dehaloperoxidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 33:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Amphitrite ornata]]		[[Category: Amphitrite ornata]]
		+	[[Category: Large Structures]]
	[[Category: Chen, Z]]		[[Category: Chen, Z]]
	[[Category: Davis, M F]]		[[Category: Davis, M F]]

OCA at 09:46, 18 October 2017

OCA — Wed, 18 Oct 2017 09:46:09 GMT

←Older revision		Revision as of 09:46, 18 October 2017
Line 1:		Line 1:
		+
	==X-ray Crystal Structure Analysis of the Binding Site in the Ferric and Oxyferrous Forms of the Recombinant Heme Dehaloperoxidase Cloned from Amphitrite ornata==		==X-ray Crystal Structure Analysis of the Binding Site in the Ferric and Oxyferrous Forms of the Recombinant Heme Dehaloperoxidase Cloned from Amphitrite ornata==
	<StructureSection load='2qfk' size='340' side='right' caption='[[2qfk]], [[Resolution\|resolution]] 1.62Å' scene=''>		<StructureSection load='2qfk' size='340' side='right' caption='[[2qfk]], [[Resolution\|resolution]] 1.62Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</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">[[2qfn\|2qfn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qfn\|2qfn]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dhpA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~129555~~ Amphitrite ornata])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dhpA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= Amphitrite ornata])</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=2qfk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qfk OCA], [http://pdbe.org/2qfk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qfk RCSB], [http://www.ebi.ac.uk/pdbsum/2qfk 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=2qfk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qfk OCA], [http://pdbe.org/2qfk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qfk RCSB], [http://www.ebi.ac.uk/pdbsum/2qfk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2qfk ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 27:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 2qfk" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2qfk" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Dehaloperoxidase\|Dehaloperoxidase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 22:09, 7 February 2016

OCA — Sun, 07 Feb 2016 22:09:51 GMT

←Older revision		Revision as of 22:09, 7 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=2qfk ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 05:22, 10 September 2015

OCA — Thu, 10 Sep 2015 05:22:51 GMT

←Older revision		Revision as of 05:22, 10 September 2015
Line 6:		Line 6:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qfn\|2qfn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qfn\|2qfn]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dhpA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=129555 Amphitrite ornata])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dhpA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=129555 Amphitrite ornata])</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=2qfk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qfk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qfk RCSB], [http://www.ebi.ac.uk/pdbsum/2qfk 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=2qfk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qfk OCA], [http://pdbe.org/2qfk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qfk RCSB], [http://www.ebi.ac.uk/pdbsum/2qfk 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 2qfk" style="background-color:#fffaf0;"></div>

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

OCA at 16:14, 19 January 2015

OCA — Mon, 19 Jan 2015 16:14:15 GMT

←Older revision		Revision as of 16:14, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2qfk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QFK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QFK FirstGlance]. <br>		<table><tr><td colspan='2'>[[2qfk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QFK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QFK FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qfn\|2qfn]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qfn\|2qfn]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dhpA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=129555 Amphitrite ornata])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dhpA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=129555 Amphitrite ornata])</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=2qfk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qfk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qfk RCSB], [http://www.ebi.ac.uk/pdbsum/2qfk 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=2qfk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qfk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qfk RCSB], [http://www.ebi.ac.uk/pdbsum/2qfk 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: Amphitrite ornata]]		[[Category: Amphitrite ornata]]
-	[[Category: Chen, Z.]]	+	[[Category: Chen, Z]]
-	[[Category: Davis, M F.]]	+	[[Category: Davis, M F]]
-	[[Category: Franzen, S.]]	+	[[Category: Franzen, S]]
-	[[Category: Serrano, V S.de.]]	+	[[Category: Serrano, V S.de]]
	[[Category: Crystal structure of dehaloperoxidase]]		[[Category: Crystal structure of dehaloperoxidase]]
	[[Category: Dhp]]		[[Category: Dhp]]

OCA at 08:23, 29 September 2014

OCA — Mon, 29 Sep 2014 08:23:45 GMT

←Older revision		Revision as of 08:23, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2qfk.~~png~~\|~~left~~\|200px]]	+	==X-ray Crystal Structure Analysis of the Binding Site in the Ferric and Oxyferrous Forms of the Recombinant Heme Dehaloperoxidase Cloned from Amphitrite ornata==
		+	<StructureSection load='2qfk' size='340' side='right' caption='[[2qfk]], [[Resolution\|resolution]] 1.62Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2qfk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QFK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QFK FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qfn\|2qfn]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dhpA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=129555 Amphitrite ornata])</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=2qfk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qfk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qfk RCSB], [http://www.ebi.ac.uk/pdbsum/2qfk 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/qf/2qfk_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 ==
		+	The dehaloperoxidase (DHP) from the terebellid polychaete Amphitrite ornata is an enzyme that converts para-halogenated phenols to the corresponding quinones in the presence of hydrogen peroxide. Its enzymatic activity is similar to that of heme peroxidases such as horseradish peroxidase, yet it has the structural characteristics of the globin family of proteins, the main functions of which are oxygen transport and storage. In order to investigate the dual function of this hemoglobin peroxidase, the enzyme was expressed in Escherichia coli as a recombinant protein in its wild-type form and as a mutant protein in which Cys73 was replaced by a serine residue (C73S). Both the wild-type and mutant proteins were crystallized and their structures were determined at 100 K to a resolution of 1.62 A. The structure of the wild-type protein demonstrated that it was in the metaquo form, with the heme iron in the ferric oxidation state and the bound water lying 2.2 A from the heme iron. The structure of the C73S mutant protein was shown to contain a ferrous heme iron with a bound oxygen molecule. The bent bonding geometry of the Fe-O(1)-O(2) adduct results in a hydrogen bond of length 2.8 A between the second O atom, O(2), of molecular oxygen and N(2) of the distal histidine residue (His55) in both subunits contained within the asymmetric unit. This hydrogen-bonding interaction between His55 and the bound diatomic oxygen molecule provides new insight into the catalytic activation of H(2)O(2), which is essential for peroxidase activity.

-	~~{{STRUCTURE_2qfk\| PDB=2qfk \| SCENE= }}~~	+	X-ray crystal structural analysis of the binding site in the ferric and oxyferrous forms of the recombinant heme dehaloperoxidase cloned from Amphitrite ornata.,de Serrano V, Chen Z, Davis MF, Franzen S Acta Crystallogr D Biol Crystallogr. 2007 Oct;63(Pt 10):1094-101. Epub, 2007 Sep 19. PMID:17881827<ref>PMID:17881827</ref>

-	~~===X-ray Crystal Structure Analysis~~ of the ~~Binding Site in the Ferric and Oxyferrous Forms of the Recombinant Heme Dehaloperoxidase Cloned from Amphitrite ornata===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17881827}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2qfk]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Amphitrite_ornata Amphitrite ornata]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2QFK OCA].~~	+

	==See Also==		==See Also==
	*[[Dehaloperoxidase\|Dehaloperoxidase]]		*[[Dehaloperoxidase\|Dehaloperoxidase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:017881827<~~/~~ref~~><~~ref group="xtra">PMID:019187035</ref><references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Amphitrite ornata]]		[[Category: Amphitrite ornata]]
	[[Category: Chen, Z.]]		[[Category: Chen, Z.]]

OCA at 08:00, 20 October 2012

OCA — Sat, 20 Oct 2012 08:00:00 GMT

←Older revision		Revision as of 08:00, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2qfk]] is a 2 chain structure ~~of [[Dehaloperoxidase]]~~ with sequence from [http://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QFK OCA].	+	[[2qfk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QFK OCA].

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

OCA: Protected "2qfk" [edit=sysop:move=sysop]

OCA — Wed, 25 Jul 2012 18:07:42 GMT

Protected "2qfk" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:07, 25 July 2012

OCA at 18:07, 25 July 2012

OCA — Wed, 25 Jul 2012 18:07:41 GMT

←Older revision		Revision as of 18:07, 25 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2qfk.png\|left\|200px]]		[[Image:2qfk.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2qfk", 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_2qfk\| PDB=2qfk \| SCENE= }}		{{STRUCTURE_2qfk\| PDB=2qfk \| SCENE= }}

	===X-ray Crystal Structure Analysis of the Binding Site in the Ferric and Oxyferrous Forms of the Recombinant Heme Dehaloperoxidase Cloned from Amphitrite ornata===		===X-ray Crystal Structure Analysis of the Binding Site in the Ferric and Oxyferrous Forms of the Recombinant Heme Dehaloperoxidase Cloned from Amphitrite ornata===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17881827}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17881827 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17881827}}		{{ABSTRACT_PUBMED_17881827}}

	==About this Structure==		==About this Structure==
-	~~2QFK~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QFK OCA].	+	[[2qfk]] is a 2 chain structure of [[Dehaloperoxidase]] with sequence from [http://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QFK OCA].
		+
		+	==See Also==
		+	*[[Dehaloperoxidase\|Dehaloperoxidase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17881827~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017881827</ref><ref group="xtra">PMID:019187035</ref><references group="xtra"/>
	[[Category: Amphitrite ornata]]		[[Category: Amphitrite ornata]]
	[[Category: Chen, Z.]]		[[Category: Chen, Z.]]
Line 34:		Line 25:
	[[Category: Heme protein]]		[[Category: Heme protein]]
	[[Category: Transport protein]]		[[Category: Transport protein]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 16:49:39 2009''