5chr - Revision history

OCA at 12:20, 6 March 2024

2024-03-06T12:20:32Z

←Older revision		Revision as of 12:20, 6 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5chr]] 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=5CHR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CHR FirstGlance]. <br>		<table><tr><td colspan='2'>[[5chr]] 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=5CHR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CHR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4NC:4-NITROCATECHOL'>4NC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</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]] 1.98Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4NC:4-NITROCATECHOL'>4NC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=5chr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5chr OCA], [https://pdbe.org/5chr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5chr RCSB], [https://www.ebi.ac.uk/pdbsum/5chr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5chr 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=5chr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5chr OCA], [https://pdbe.org/5chr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5chr RCSB], [https://www.ebi.ac.uk/pdbsum/5chr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5chr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/Q9NAV7_9ANNE Q9NAV7_9ANNE]		[https://www.uniprot.org/uniprot/Q9NAV7_9ANNE Q9NAV7_9ANNE]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The marine hemoglobin dehaloperoxidase (DHP) from Amphitrite ornata was found to catalyze the H2O2-dependent oxidation of nitrophenols, an unprecedented nonmicrobial degradation pathway for nitrophenols by a hemoglobin. Using 4-nitrophenol (4-NP) as a representative substrate, the major monooxygenated product was 4-nitrocatechol (4-NC). Isotope labeling studies confirmed that the O atom incorporated was derived exclusively from H2O2, indicative of a peroxygenase mechanism for 4-NP oxidation. Accordingly, X-ray crystal structures of 4-NP (1.87 A) and 4-NC (1.98 A) bound to DHP revealed a binding site in close proximity to the heme cofactor. Peroxygenase activity could be initiated from either the ferric or oxyferrous states with equivalent substrate conversion and product distribution. The 4-NC product was itself a peroxidase substrate for DHP, leading to the secondary products 5-nitrobenzene-triol and hydroxy-5-nitro-1,2-benzoquinone. DHP was able to react with 2,4-dinitrophenol (2,4-DNP) but was unreactive against 2,4,6-trinitrophenol (2,4,6-TNP). pH dependence studies demonstrated increased reactivity at lower pH for both 4-NP and 2,4-DNP, suggestive of a pH effect that precludes the reaction with 2,4,6-TNP at or near physiological conditions. Stopped-flow UV-visible spectroscopic studies strongly implicate a role for Compound I in the mechanism of 4-NP oxidation. The results demonstrate that there may be a much larger number of nonmicrobial enzymes that are underrepresented when it comes to understanding the degradation of persistent organic pollutants such as nitrophenols in the environment.
-
-	Nonmicrobial Nitrophenol Degradation via Peroxygenase Activity of Dehaloperoxidase-Hemoglobin from Amphitrite ornata.,McCombs NL, D'Antonio J, Barrios DA, Carey LM, Ghiladi RA Biochemistry. 2016 May 3;55(17):2465-78. doi: 10.1021/acs.biochem.6b00143. Epub, 2016 Apr 22. PMID:27070125<ref>PMID:27070125</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5chr" 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>

OCA at 12:06, 14 June 2023

2023-06-14T12:06:52Z

←Older revision		Revision as of 12:06, 14 June 2023
Line 3:		Line 3:
	<StructureSection load='5chr' size='340' side='right'caption='[[5chr]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='5chr' size='340' side='right'caption='[[5chr]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5chr]] 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=5CHR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5CHR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5chr]] 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=5CHR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CHR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4NC:4-NITROCATECHOL'>4NC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</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=4NC:4-NITROCATECHOL'>4NC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</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">[[5chq\|5chq]]~~</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=5chr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5chr OCA], [https://pdbe.org/5chr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5chr RCSB], [https://www.ebi.ac.uk/pdbsum/5chr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5chr ProSAT]</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=5chr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5chr OCA], [~~http~~://pdbe.org/5chr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5chr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5chr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5chr ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9NAV7_9ANNE Q9NAV7_9ANNE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 27:
	[[Category: Amphitrite ornata]]		[[Category: Amphitrite ornata]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Carey, L]]	+	[[Category: Carey L]]
-	[[Category: Ghiladi, R]]	+	[[Category: Ghiladi R]]
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Substrate~~]]	+

OCA at 07:27, 27 November 2019

2019-11-27T07:27:42Z

←Older revision		Revision as of 07:27, 27 November 2019
Line 1:		Line 1:

	==Dehaloperoxidase B in complex with substrate p-nitrocatechol==		==Dehaloperoxidase B in complex with substrate p-nitrocatechol==
-	<StructureSection load='5chr' size='340' side='right' caption='[[5chr]], [[Resolution\|resolution]] 1.98Å' scene=''>	+	<StructureSection load='5chr' size='340' side='right'caption='[[5chr]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5chr]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CHR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CHR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5chr]] 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=5CHR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CHR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4NC:4-NITROCATECHOL'>4NC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</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=4NC:4-NITROCATECHOL'>4NC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</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">[[5chq\|5chq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5chq\|5chq]]</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=5chr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5chr OCA], [http://pdbe.org/5chr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5chr RCSB], [http://www.ebi.ac.uk/pdbsum/5chr 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=5chr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5chr OCA], [http://pdbe.org/5chr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5chr RCSB], [http://www.ebi.ac.uk/pdbsum/5chr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5chr ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 5chr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5chr" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dehaloperoxidase 3D structures\|Dehaloperoxidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Amphitrite ornata]]
		+	[[Category: Large Structures]]
	[[Category: Carey, L]]		[[Category: Carey, L]]
	[[Category: Ghiladi, R]]		[[Category: Ghiladi, R]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Substrate]]		[[Category: Substrate]]

OCA at 12:01, 13 May 2016

2016-05-13T12:01:26Z

←Older revision		Revision as of 12:01, 13 May 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5chr is ~~ON HOLD until Paper~~ Publication	+	==Dehaloperoxidase B in complex with substrate p-nitrocatechol==
		+	<StructureSection load='5chr' size='340' side='right' caption='[[5chr]], [[Resolution\|resolution]] 1.98Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5chr]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CHR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CHR FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4NC:4-NITROCATECHOL'>4NC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</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">[[5chq\|5chq]]</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=5chr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5chr OCA], [http://pdbe.org/5chr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5chr RCSB], [http://www.ebi.ac.uk/pdbsum/5chr PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The marine hemoglobin dehaloperoxidase (DHP) from Amphitrite ornata was found to catalyze the H2O2-dependent oxidation of nitrophenols, an unprecedented nonmicrobial degradation pathway for nitrophenols by a hemoglobin. Using 4-nitrophenol (4-NP) as a representative substrate, the major monooxygenated product was 4-nitrocatechol (4-NC). Isotope labeling studies confirmed that the O atom incorporated was derived exclusively from H2O2, indicative of a peroxygenase mechanism for 4-NP oxidation. Accordingly, X-ray crystal structures of 4-NP (1.87 A) and 4-NC (1.98 A) bound to DHP revealed a binding site in close proximity to the heme cofactor. Peroxygenase activity could be initiated from either the ferric or oxyferrous states with equivalent substrate conversion and product distribution. The 4-NC product was itself a peroxidase substrate for DHP, leading to the secondary products 5-nitrobenzene-triol and hydroxy-5-nitro-1,2-benzoquinone. DHP was able to react with 2,4-dinitrophenol (2,4-DNP) but was unreactive against 2,4,6-trinitrophenol (2,4,6-TNP). pH dependence studies demonstrated increased reactivity at lower pH for both 4-NP and 2,4-DNP, suggestive of a pH effect that precludes the reaction with 2,4,6-TNP at or near physiological conditions. Stopped-flow UV-visible spectroscopic studies strongly implicate a role for Compound I in the mechanism of 4-NP oxidation. The results demonstrate that there may be a much larger number of nonmicrobial enzymes that are underrepresented when it comes to understanding the degradation of persistent organic pollutants such as nitrophenols in the environment.

-	~~Authors:~~ Carey, L., ~~Ghiladi, R~~.	+	Nonmicrobial Nitrophenol Degradation via Peroxygenase Activity of Dehaloperoxidase-Hemoglobin from Amphitrite ornata.,McCombs NL, D'Antonio J, Barrios DA, Carey LM, Ghiladi RA Biochemistry. 2016 May 3;55(17):2465-78. doi: 10.1021/acs.biochem.6b00143. Epub, 2016 Apr 22. PMID:27070125<ref>PMID:27070125</ref>

-	~~Description: Dehaloperoxidase B in complex with substrate p-nitrocatechol~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
		+	<div class="pdbe-citations 5chr" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Carey, L]]		[[Category: Carey, L]]
	[[Category: Ghiladi, R]]		[[Category: Ghiladi, R]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Substrate]]

OCA at 10:32, 16 December 2015

2015-12-16T10:32:27Z

←Older revision		Revision as of 10:32, 16 December 2015
Line 7:		Line 7:
	Description: Dehaloperoxidase B in complex with substrate p-nitrocatechol		Description: Dehaloperoxidase B in complex with substrate p-nitrocatechol
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Ghiladi, R]]
	[[Category: Carey, L]]		[[Category: Carey, L]]
		+	[[Category: Ghiladi, R]]

OCA at 10:46, 20 August 2015

2015-08-20T10:46:09Z

←Older revision		Revision as of 10:46, 20 August 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5chr is ON HOLD	+	The entry 5chr is ON HOLD until Paper Publication

	Authors: Carey, L., Ghiladi, R.		Authors: Carey, L., Ghiladi, R.

OCA: Protected "5chr" [edit=sysop:move=sysop]

2015-07-22T13:08:48Z

Protected "5chr" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:08, 22 July 2015

OCA: New page: '''Unreleased structure''' The entry 5chr is ON HOLD Authors: Carey, L., Ghiladi, R. Description: Dehaloperoxidase B in complex with substrate p-nitrocatechol [[Category: Unreleased St...

2015-07-22T13:08:47Z

New page: '''Unreleased structure''' The entry 5chr is ON HOLD Authors: Carey, L., Ghiladi, R. Description: Dehaloperoxidase B in complex with substrate p-nitrocatechol [[Category: Unreleased St...

New page

'''Unreleased structure'''

The entry 5chr is ON HOLD

Authors: Carey, L., Ghiladi, R.

Description: Dehaloperoxidase B in complex with substrate p-nitrocatechol
[[Category: Unreleased Structures]]
[[Category: Ghiladi, R]]
[[Category: Carey, L]]